1. Computational and Systems Biology
  2. Genetics and Genomics

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci

  1. Reza K Hammond
  2. Matthew C Pahl
  3. Chun Su
  4. Diana L Cousminer
  5. Michelle E Leonard
  6. Sumei Lu
  7. Claudia A Doege
  8. Yadav Wagley
  9. Kenyaita M Hodge
  10. Chiara Lasconi
  11. Matthew E Johnson
  12. James A Pippin
  13. Kurt D Hankenson
  14. Rudolph L Leibel
  15. Alessandra Chesi
  16. Andrew D Wells
  17. Struan FA Grant  Is a corresponding author
  1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, United States
  2. Division of Human Genetics, The Children’s Hospital of Philadelphia, United States
  3. Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, United States
  4. Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, United States
  5. Columbia Stem Cell Initiative, Vagelos College of Physicians and Surgeons, Columbia University, United States
  6. Department of Orthopaedic Surgery, University of Michigan Medical School, United States
  7. Division of Molecular Genetics (Pediatrics) and the Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, United States
  8. Department of Pathology, The Children’s Hospital of Philadelphia, United States
  9. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, United States
  10. University of Pennsylvania, United States
  11. The Children’s Hospital of Philadelphia, United States
https://doi.org/10.7554/eLife.62206
Share this article
Cite this article
  1. Reza K Hammond
  2. Matthew C Pahl
  3. Chun Su
  4. Diana L Cousminer
  5. Michelle E Leonard
  6. Sumei Lu
  7. Claudia A Doege
  8. Yadav Wagley
  9. Kenyaita M Hodge
  10. Chiara Lasconi
  11. Matthew E Johnson
  12. James A Pippin
  13. Kurt D Hankenson
  14. Rudolph L Leibel
  15. Alessandra Chesi
  16. Andrew D Wells
  17. Struan FA Grant
(2021)
Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci
eLife 10:e62206.
https://doi.org/10.7554/eLife.62206
  2. Download BibTeX
  3. Download .RIS

Abstract

To uncover novel significant association signals (p<5×10−8), genome-wide association studies (GWAS) requires increasingly larger sample sizes to overcome statistical correction for multiple testing. As an alternative, we aimed to identify associations among suggestive signals (5 × 10−8≤p<5×10−4) in increasingly powered GWAS efforts using chromatin accessibility and direct contact with gene promoters as biological constraints. We conducted retrospective analyses of three GIANT BMI GWAS efforts using ATAC-seq and promoter-focused Capture C data from human adipocytes and embryonic stem cell (ESC)-derived hypothalamic-like neurons. This approach, with its extremely low false-positive rate, identified 15 loci at p<5×10−5 in the 2010 GWAS, of which 13 achieved genome-wide significance by 2018, including at NAV1, MTIF3, and ADCY3. Eighty percent of constrained 2015 loci achieved genome-wide significance in 2018. We observed similar results in waist-to-hip ratio analyses. In conclusion, biological constraints on sub-significant GWAS signals can reveal potentially true-positive loci for further investigation in existing data sets without increasing sample size.

Introduction

Genome-wide association studies (GWAS) have been widely employed to identify genetic variants that are associated with risk for disease and physiologically relevant traits (Tam et al., 2019; Visscher et al., 2017). GWAS was first described in 2005 (Klein et al., 2005) and has since been utilized to study a large range of common and complex traits in humans. As of July 2020, the GWAS Catalog consisted of 4628 publications reporting a total of 189,811 associations that achieved genome-wide significance (p<5×10−8) between genetic variants and human common complex traits. For instance, in 2009, 54 near-independent genome-wide significant (GWS) signals associated with variation in height had been identified in a population of tens of thousands of individuals (Visscher, 2008), while by 2014, that number had jumped to 697 and was estimated to explain more than 20% of the trait’s heritability (Wood et al., 2014). The number of significant GWS signals increased to 3,290 in 2018, accounting for nearly a quarter of the heritability (Yengo et al., 2018). And yet, despite these successes, GWAS has a clear shortcoming in that a large proportion of predicted heritability remains unexplained despite a constantly growing number of implicated loci (Tam et al., 2019). These novel loci are only identifiable using larger sample sizes, which come at a significant cost of both time and money, and each successive independent signal explains less and less of the overall estimated heritability (Zuk et al., 2012).

The additional signals achieving genome-wide significance in successive rounds of GWAS are often those that failed to achieve the commonly utilized p=5×10−8 threshold in initial rounds, a strict bar that can only be met when larger cohort sizes are recruited. Various approaches have been previously utilized to identify sub-threshold signals that go on to achieve genome-wide significance. Sub-threshold signals have been selected for replication in a stage 2 GWAS due to their proximity to putative candidate genes to identify novel loci, as with the identification of the obesity locus NPC1 and replicated subsequently in a large meta-analysis (Meyre et al., 2009; Turcot et al., 2018). Epigenomic maps have also been utilized to implicate biologically relevant sub-threshold variants that were subsequently experimentally validated (Wang et al., 2016). We explored if it would be possible to apply a systematic genome-wide molecular-genetics-based approach to sub-threshold signals to predict single nucleotide polymorphisms (SNPs) that would go on to achieve genome-wide significance in a future round of GWAS. Over the past decade, sequencing technologies such aa RNA-seq (Wang et al., 2009), ATAC-seq (Buenrostro et al., 2013), and high-resolution promoter-focused Capture C Chesi et al., 2019; Hughes et al., 2014; Su et al., 2020 have been developed to facilitate the annotation of genes and their regulatory elements. Such data have been utilized to identify physical variant-to-gene interactions via three-dimensional genomics to implicate effector genes at GWAS loci where both sequence variant and gene reside within regions of open chromatin (Arnold et al., 2015; Çalışkan et al., 2019; Chesi et al., 2019; Cousminer et al., 2020; Javierre et al., 2016; Smemo et al., 2014; Su et al., 2019; Su et al., 2020). By leveraging high-resolution promoter-focused Capture C with ATAC-seq, it is possible to physically connect putatively functional non-coding elements, such as enhancers, harboring disease-relevant SNPs to promoters of specific genes thereby potentially mechanistically implicated in the SNP-associated phenotype. We hypothesized that by applying this variant-to-gene mapping method to sub-threshold SNP signals, the molecular constraints on these signals would result in a set of SNPs that are plausibly related to the biology of the trait in question, thereby bypassing the requirement of a larger GWAS to implicate these signals.

To test this hypothesis, we leveraged multiple GWAS data sets, increasing in sample size over time, to determine whether our sub-threshold implicated leads became genome-wide significant in a subsequent larger study. We chose to test this method utilizing GWAS data sets for body mass index (BMI) and waist-to-hip ratio adjusted for BMI (WHRadjBMI) as initial traits because they have both been the subject of particularly large GWAS efforts by the GIANT consortium. Additionally, both traits have implicated a large number of loci and therefore provide optimal statistical power for our purposes. With respect to variant-to-gene mapping, we utilized our existing 3D genomic data sets for adipocytes as well as hypothalamic neurons as previous studies have implicated these cell types in BMI-associated variants (Locke et al., 2015).

Results

Suggestive proxy SNP identification

We first applied our chromatin-based variant-to-gene mapping approach to predict BMI loci that would be subsequently reported as genome-wide significant in a 2015 GWAS (n = 339,224) but were only suggestive in 2010 (n = 249,796). Because the sentinel SNPs reported from a GWAS are not necessarily causal with regard to phenotype, but very likely in linkage disequilibrium (LD) with the responsible allele, we first identified proxy SNPs (r2 > 0.8) for each of the 2010 suggestive SNPs, 5×10−8≤p<5×10−4. Here, we detected 26,343 proxy SNPs; however, some of these proxy signals were in LD with an already established genome-wide significant signal. Given the purpose of this analysis was to identify new signals that were not yet genome-wide significant, we eliminated all proxies that were in even very modest LD, with an already genome-wide significant signal using an r2 > 0.1. This filtering left a residual of 23,197 signals.

ATAC-seq and promoter-focused capture C

We generated ATAC-seq and promoter-focused Capture C libraries from mesenchymal stem cell (MSC)-derived adipocytes and leveraged our existing comparable data from human ESC-derived hypothalamic neurons to query open chromatin maps for open sub-threshold SNPs that contact open gene promoters (Pahl et al., 2020). The adipocytes were derived from mesenchymal stem cells. Three ATAC-seq libraries were sequenced and analyzed with the ENCODE pipeline (https://github.com/kundajelab/atac_dnase_pipelines). Peaks from all replicates were merged by bedtools (v2.25.0) provided peaks were present in at least two biological replicates. These resulted in 2,225,635 adipocyte peaks and 179,212 hypothalamic neuron peaks.

The adipose capture C libraries had an average of 1.4 billion reads per adipose library, with an average of 41% valid read pairs and 89% capture efficiency. We then called significant interactions using the CHiCAGO pipeline and performed analyses at a 1-fragment resolution to identify short-distance interactions (258,882 interactions) and at 4-fragment resolution to identify long-distance interactions (278,040) (Cairns et al., 2016).

Variant-to-gene mapping reveals suggestive 2010 BMI loci that subsequently achieved genome-wide significance in 2015

We next identified physical contacts between any of the remaining proxy SNPs and gene promoters, with the additional constraint that both points of contact were within regions of open chromatin and that the SNP itself did not map to a gene promoter. This approach favors SNPs most likely to have a functional role in the regulation of genes relevant to a given trait and is therefore dependent on the cell type utilized to make such inferences. For BMI variant-to-gene mapping, we used data derived from MSC-derived adipocytes and human ESC-derived hypothalamic neurons because of the known roles of these cell types in BMI. To identify the point at which this approach is no longer viable due to noise, that is, at point of negligible return and excessive false positives, we stratified the suggestive regions into several bins: 5×10−8≤p<5×10−7, 5×10−8≤p<5×10−6, 5×10−8≤p<5×10−5, and 5×10−8≤p<5×10−4. Note that each successive bin is inclusive of the SNPs from the previous bin.

Upon identifying loci that passed these filters, we quantified those that had reached genome-wide significance by 2015. To avoid redundant inclusion of SNPs in LD with one another, we collapsed all biologically constrained SNPs into independent SNP clusters, designated here as separate independent ‘loci’. We defined such loci as the set of SNPs surviving the variant-to-gene mapping filter that were in LD with one another at a relatively relaxed r2 threshold of >0.4.

One hundred and sixty-one of the 23,197 suggestive proxy SNPs survived these biological filters at our most relaxed p-value threshold. These SNPs corresponded to 78 loci, of which 11 achieved genome-wide significance by 2015 (Table 1); these are annotated on the 2015 BMI Manhattan plot (Figure 1). Four of these loci were highlighted in the 2010 study, but the associations were only considered ‘suggestive’ within the stage one discovery set at that time, that is at p>5×10−8. Across all suggestive bins and cell types, the positive predictive value was low through 2015, and the proportion of constrained signals actually achieving genome-wide significance (GWS) did not differ significantly from the proportion of the unconstrained signals achieving GWS within the corresponding p-value bin (Figure 2). This is likely a function of the relatively modest increase in sample size (+89,428) between 2010 and 2015. At the relatively relaxed p-value threshold of 5×10−8≤p<5×10−5, we observed that 6/15 2010 biologically constrained loci were GWS in 2015, whereas 43/163 unconstrained loci were GWS by 2015. A flowchart describing this pipeline using the 2010–2015 BMI data is available in Figure 3.

Figure 1
Download asset Open asset
2015 BMI Manhattan plot depicting loci identified with 2010 salvaged SNPs 2015 BMI loci identifiable with 2010 salvaged SNPs.

Cell type where locus was identified indicated below locus name. Color indicates the p-value threshold where the locus became implicated (Locke et al., 2015). Color key: Green – 5×10−8≤p<5×10−7, blue – 5×10−7≤p<5×10−6, orange – 5×10−6≤p<5×10−5, red – 5×10−5≤p<5×10−4.

Figure 2
Download asset Open asset
Independent 2010 BMI SNPs identified via variant-to-gene mapping that go on to reach genome-wide significance by 2015, as well as the set of unconstrained 2010 suggestive SNPs that achieve genome-wide significance by 2015.

Positive predictive value is depicted as a percentage for each bar. Above these percentages, the p-value, as identified through Fisher’s exact test, is posted. These p-values depict the probability that the proportions of salvaged SNPs using variant-to-gene mapping differ from simply salvaging all suggestive SNPs within the same suggestive bin.

Figure 2—source data 1

Number of 2010 loci identified by constrained method and the number that achieved GWS by 2015 in each cell type.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig2-data1-v2.csv
Figure 2—source data 2

Number of 2010 loci identified with no constraint and the number that achieved GWS by 2015.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig2-data2-v2.csv
Figure 3
Download asset Open asset
Flowchart of the pipeline describing each computational step.

BMI 2010–2015 data is utilized here as an example to report the number of SNPs and loci that occur at each step of the analysis.

Table 1
2015 BMI loci that were implicated with our method in the 2010 data set.

The 2015 genome-wide significant BMI loci whose sentinel SNP was in LD with SNPs implicated from suggestive association in the 2010 BMI GWAS. Key: Notable genes from biological relevance to obesity (B); copy number variation (C); DEPICT analyses (D); GRAIL results (G); BMI-associated variant is in strong LD (r2 ≥ 0.8) with a missense variant in the indicated gene (M); gene nearest to index SNP (N); association and eQTL data converge to affect gene expression (Q) (Locke et al., 2015).

Novel as of 2015 (Locke et al.)
2015 sentinel SNP2010 implicated SNPs2015 assigned locus nameInteracting gene
rs4740619rs10810462C9orf93(C,M,N)TCONS_00015651
rs17094222rs117597828HIF1AN(N)PAX2
rs2820292rs12086240, rs2820315NAV1(N)TIMM17A
rs758747rs2238435NLRC3(N)TCONS_00024950, TCONS_00024564, TCONS_00024949, TCONS_00024562, RP11-462G12.1, TCONS_00024568, TCONS_00024570, RP11-95P2.1, TCONS_00024567, TCONS_00024569, TCONS_00024320, TCONS_00024952
rs3736485rs7183479SCG3(B,D); DMXL2(M,N)LYSMD2, SCG3, CTD-2308G16.1, TMOD2
Identified between 2010 (Speliotes et al.) and 2015 (Locke et al.)
2015 Sentinel SNP2010 Implicated SNPs2015 Assigned locus nameInteracting gene
rs17024393rs72705210GNAT2(N); AMPD2(D)GSTM3, AHCYL1
rs4256980rs10840079, rs10840087, rs11041999, rs11042023, rs12803166, rs4256980,TRIM66(D,M,N); TUB(B)PBLD, RPL27A, TRIM66
Identified in 2010 (Speliotes et al.), but was not genome-wide significant
2015 Sentinel SNP2010 Implicated SNPs2015 Assigned Locus NameInteracting gene
rs10182181rs12713419, rs13012304, rs6718510, rs7597332, rs7608976ADCY3(B,M,N,Q); POMC(B,G); NCOA1(B); SH2B1(B,M,Q); APOBR(M,Q);ADCY3, TCONS_00003602
rs12016871rs7988412,MTIF3(N); GTF3A(Q) *~1 Mb from sentinelMTIF3
rs1808579rs1788783NPC1(B,G,M,Q); C18orf8(N,Q)NPC1
rs2287019rs11672660, rs34783010QPCTL(N); GIPR(B,M)GIPR

BMI GWAS variant-to-gene mapping constraints between 2010 and 2018

Using the same set of 2010 surviving SNPs from the previous section, we next identified how many of these SNPs reached GWS by the 2018 BMI GWAS (N = 681,275), representing a nearly tripling in cohort size compared to 2010. Here, we observed that 45 of the 78 2010 biologically constrained loci achieved genome-wide significance by 2018 at the most relaxed p-value threshold (Table 2).

Table 2
2018 BMI loci that were identified using 2010 salvaged.

SNPs 2018 BMI loci identified as genes nearest to genome-wide significant SNPs that could be identified using SNPs salvaged from suggestive regions of the 2010 BMI GWAS.

Nearest gene to sentinelSurviving proxy SNPsLowest threshold found
ABHD17Ars893543, rs893542, rs116713475 × 10−4
AC007879.5rs11677847, rs72951700, rs11689163, rs72966483, rs11694560, rs11692026, rs964621, rs9646225 × 10−4
ADCY3rs6718510, rs7597332, rs7608976, rs13012304, rs127134195 × 10−4
ADCY9rs710893, rs2531993, rs22384355 × 10−5
AK5rs127299145 × 10−5
AP000439.5rs116057295 × 10−4
BCL7Ars72998425 × 10−4
C10orf32rs70851045 × 10−4
C18orf8rs17888265 × 10−4
C1orf61rs112644835 × 10−4
CCDC171rs108104625 × 10−4
CNNM2rs19260325 × 10−4
COQ4rs14686485 × 10−4
CRTC1rs4808845, rs48088445 × 10−4
DPYDrs120774425 × 10−4
EIF2B5rs3914188, rs356374225 × 10−4
EXOSC10rs1884429, rs120417405 × 10−4
FAIM2rs4220225 × 10−4
GAB2rs8692025 × 10−4
GIPRrs34783010, rs116726605 × 10−7
GPR61rs727052105 × 10−4
HIF1ANrs1175978285 × 10−4
HOXB1rs23260135 × 10−4
IFNGR1rs172587505 × 10−4
IPO9rs28203155 × 10−5
KCNJ12rs99060725 × 10−4
LMOD1rs20472645 × 10−4
MAP2K3rs2001651, rs37855425 × 10−4
MAP3K7CLrs9282775 × 10−4
MEF2Drs2274319, rs1925950, rs12038396, rs3818463, rs2274320, rs22743175 × 10−4
MLNrs11752353, rs6921487, rs72880511, rs1887340, rs737465095 × 10−4
MLXIPrs28530689, rs10773037, rs28737311, rs36158849, rs22805735 × 10−4
MST1Rrs3774758, rs2252833, rs64461875 × 10^−4
MTIF3rs79884125 × 10−7
MTORrs11581010, rs108644905 × 10−4
NAV1rs120862405 × 10−5
NPC1rs17887835 × 10−4
RASA2rs20428645 × 10−4
RCAN2rs39343935 × 10−5
RNU6-543Prs107616895 × 10−4
RP11-493K19.3rs131009035 × 10−4
RP11-562L8.1rs128876365 × 10−5
RP11-68I18.10rs107888005 × 10−5
RP11-707P17.1rs71834795 × 10−4
SAE1rs4664775 × 10−4
SKAP1rs16951519, rs22401215 × 10−5
STK33rs10840087, rs11041999, rs340099215 × 10−4
TNRC6Brs6001834, rs48204095 × 10−4
TRIM66rs10840079, rs4256980, rs11042023, rs128031665 × 10−6
TTC34rs64240625 × 10−5
URM1rs7859557, rs22409485 × 10−4
XXYLT1rs584349655 × 10−4

The proportion of 2010 suggestive SNPs meeting these criteria that achieved GWS by 2018 within suggestive bin 5×10−8≤p<5×10−5 was particularly striking (Figure 4). At this threshold, 86.7% (13/15) of biologically constrained loci identified achieved genome-wide significance by 2018, whereas only 40% (6/15) had achieved genome-wide significance by 2015 (Figure 2); clearly, this improvement is a function of relative cohort size. While an increase was also observed with loci identified with no constraint (43/163 suggestive 2010 loci achieving GWS by 2015 and 105/163 achieving GWS by 2018), the precision was significantly higher with the biological constraint than without.

Figure 4 with 1 supplement see all
Download asset Open asset
Independent 2010.

BMI SNPs salvaged via variant-to-gene mapping that go on to reach genome-wide significance by 2018, as well as the set of unconstrained 2010 suggestive SNPs that achieve genome-wide significance by 2018. Positive predictive value is depicted for each bar. Above these percentages, the p-value, as identified through Fisher’s exact test, is posted. These p-values depict the probability that the proportions of salvaged SNPs using variant-to-gene mapping differ from simply salvaging all suggestive SNPs within the same suggestive bin.

Figure 4—source data 1

Number of 2010 loci identified by constrained method and the number that achieved GWS by 2018 in each cell type.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig4-data1-v2.csv
Figure 4—source data 2

Number of 2010 loci identified with no constraint and the number that achieved GWS by 2018.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig4-data2-v2.csv

We assessed the positive predictive capability of this method across the stratified p-value bins to determine at which level of significance this biologically constrained analytic no longer outperformed randomly selected signals from the same bin. As shown in Figure 4—figure supplement 1, there is no point across either cell type or p-value bin where randomly sampled SNPs outperform the chromatin-constrained approach. Forty-four of 78 suggestive loci were identified in the 5×10−8≤p<5×10−4 bin, with a positive predictive value approximately 1.2-fold higher than random selection. As anticipated, fewer novel chromatin-implicated loci were detected in the 5×10−8≤p<5×10−5 bin, though the positive predictive value was approximately 1.5-fold higher than random. Taken together, these results suggest that this chromatin-constrained approach consistently performs better than random within these serial data sets, though there are diminishing returns as the p-value threshold is made increasingly less stringent.

BMI GWAS variant-to-gene mapping constraints between 2015 and 2018

We also applied the chromatin-based variant-to-gene mapping approach to the 2015 BMI GWAS data to assess the efficiency of this analysis in identifying loci that would achieve genome-wide significance by 2018. The identified proxy SNPs, their nearest 2018 GWS proxy, and the nearest gene to those proxies are described in Supplementary file 1 (see Supplementary file 2 for the implicated genes). We observed that across all cell types with 5×10−8≤p<5×10−4, 117 of the implicated 184 loci reached GWS in 2018. At the 5×10−8≤p<5×10−5 threshold, 80% (57/71) of the constrained 2015 implicated loci reached GWS in 2018, while 59% (148/248) of the unconstrained 2015 loci reached GWS in 2018 (Figure 5).

Figure 5
Download asset Open asset
Independent 2015.

BMI SNPs salvaged via variant-to-gene mapping that go on to reach genome-wide significance by 2018, as well as the set of unconstrained 2015 suggestive SNPs that achieve genome-wide significance by 2018. Positive predictive value is depicted for each bar. The posterior probability that loci identified by our chromatin-based constraint more often achieve GWS than loci with no constraint is posted above these percentages.

Figure 5—source data 1

Number of 2015 loci identified by constrained method and the number that achieved GWS by 2018 in each cell type.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig5-data1-v2.csv
Figure 5—source data 2

Number of 2015 loci identified with no constraint and the number that achieved GWS by 2018.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig5-data2-v2.csv

The results from the analyses at these years present the greatest levels of significance observed thus far. Given the presence of many more loci in each bin, we observed significance at the 5×10−8≤p<5×10−6 threshold in both cell types, where 93% (26/28) of the surviving signals reached GWS by 2018 in both cell types. This appears to be principally due to the larger sample sizes at this bin size relative to 2010, which provided additional power to observe such differences. Considering the results of all BMI retrospective analyses through 2018, we found that this method positively identified sub-threshold BMI signals that went on to achieve GWS at a later date significantly more often than when we apply no biological constraint.

Constraining WHRadjBMI GWAS reports: 2010–2018

We also assessed the performance of this method in the 2010 WHRadjBMI GWAS (n = 77,167) relative to 2018 (n = 694,649) (The results of the WHRadjBMI 2010 WHRadjBMI relative to 2015 [n = 224,459,459], and 2015 WHRadjBMI relative to 2018, are available in our Figure 6—figure supplement 2, Figure 6—figure supplement 2, and Supplementary file 2). Here, we found 15,457 proxies within the most relaxed p-value threshold of 5×10−8≤p<5×10−4. One hundred and fifty-seven of these proxies survived our biological constraints, corresponding to 71 independent loci. Thirty-six of these ultimately achieved GWS by the 2018 GWAS (Figure 6).

Figure 6 with 3 supplements see all
Download asset Open asset
Independent 2010.

WHRadjBMI SNPs salvaged via variant-to-gene mapping that go on to reach genome-wide significance by 2018, as well as the set of unconstrained 2010 suggestive SNPs that achieve genome-wide significance by 2018. Positive predictive value is depicted for each bar. Above these percentages, the p-value, as identified through Fisher’s exact test, is posted. These p-values depict the probability that the proportions of salvaged SNPs using variant-to-gene mapping differ from simply salvaging all suggestive SNPs within the same suggestive bin.

Figure 6—source data 1

Number of 2010 loci identified by constrained method and the number that achieved GWS by 2018 in each cell type.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig6-data1-v2.csv
Figure 6—source data 2

Number of 2010 loci identified with no constraint and the number that achieved GWS by 2018.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig6-data2-v2.csv

Precision of the biologically constrained 2010 loci reaching genome-wide significance in 2018 for both traits through 5×10−8≤p<5×10−6 was 100% for each cell type, except for the 2010 WHRadjBMI SNPs constrained by adipose chromatin data which equals 83% (Figure 6—figure supplement 1). This represents a 1.3- to 1.6-fold increase over the mean PPV of a randomly sampled unconstrained SNP set at the same p-value threshold. The number of loci surviving this constraint present in this p-value threshold is quite modest (BMI: 4/4 vs WHRadjBMI: 5/6). The threshold may be further relaxed (5×10−8<p<5×10−5) to identify additional loci: BMI: 13/15 vs WHRadjBMI: 13/20. Relaxing even further to p<5×10−4 yielded far more loci, but brought in more potential false positives (BMI: 44/78 vs WHRadjBMI: 36/71), although they could still become GWS at a future time point. Despite the larger rate of false positives at a threshold of 5×10−8<p<5×10−5 in WHRadjBMI relative to BMI, we still observe that the chromatin-constraint surviving sub-threshold WHRadjBMI signals went on to achieve GWS at a later date significantly more often than when we apply no constraint.

Predictive power of negative control does not differ from the unconstrained set

We assessed whether there was any period (2010–2018) in which PPV for the set of SNPs that do not physically contact gene promoters or are not located within regions of open chromatin differed significantly from the unconstrained signals, that is, if there was any period in which such a negative control outperformed, the unconstrained signals. We found that there was no p-value bin, cell type or trait for which there was a difference between this negative set and the unconstrained set (Figure 7 and Figure 8). The absence of observable differences between the negative control and unconstrained sets supports the inference that the differences observed between our biological constrained data and the unconstrained data are in fact attributable to the chromatin-constrained analytic strategy.

Figure 7
Download asset Open asset
Independent 2010.

BMI SNPs failing the variant-to-gene mapping filter that go on to reach genome-wide significance by 2018. Positive predictive value is depicted for each bar. The posterior probability that loci identified by our chromatin-based constraint more often achieve GWS than loci with no constraint is posted above these percentages. There is no threshold where this data differs significantly from the unconstrained set.

Figure 7—source data 1

Number of 2010 loci identified by constrained method and the number that achieved GWS by 2018 in each cell type.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig7-data1-v2.csv
Figure 8
Download asset Open asset
Independent 2010.

WHRadjBMI SNPs failing the variant-to-gene mapping filter that go on to reach genome-wide significance by 2018. Positive predictive value is depicted for each bar. The posterior probability that loci identified by our chromatin-based constraint more often achieve GWS than loci with no constraint is posted above these percentages. There is no threshold where this data differs significantly from the unconstrained set.

Figure 8—source data 1

Number of 2010 loci identified by constrained method and the number that achieved GWS by 2018 in each cell type.

https://cdn.elifesciences.org/articles/62206/elife-62206-fig8-data1-v2.csv

Finally, we assessed the classification rates of this approach for both traits in all testable years. At each threshold for prior GWAS significance, we used our biological constraints to predict whether an implicated locus would achieve GWS in a subsequent GWAS. We found that, across all thresholds and chromatin-constrained loci in each cell type, sensitivity was generally less than 25%, indicating a high rate of false negatives. This is expected because the chromatin-constrained data represent effects that are only captured by the cell-types (and their respective developmental maturities) that were profiled. By combining the loci identified in either adipose or hypothalamic neurons, sensitivity was increased, though the increment was modest. Specificity, however, was consistently >80%, and often >90%, indicating few false positives. The precision was particularly high through 5×10−8<p<5×10−5; however, expanding through to 5×10−8<p<5×10−4 resulted in relatively high proportions of false positives in most analyses, although always at a lower rate than without a chromatin-constraint. As a control, we analyzed classifications of a negative control set in which loci failed to survive the variant-to-gene mapping filter for each cell type and suggestive threshold. There was no instance across trait, cell type, or p-value bin in which the specificity of the negative control outperformed the variant-to-gene mapping filter (Source data 1). All together, the consistently high specificity and precision observed conveys the capacity of this chromatin-constraint to preferentially retain signals that are likely to achieve GWS in larger data sets while minimizing the presence of false positives through 5×10−8<p<5×10−5.

Discussion

In this study, we used our recently described variant-to-gene structural mapping approach (Chesi et al., 2019; Su et al., 2020) to conduct retrospective biologically constrained analyses of previous sequential GWAS reports to determine whether we could implicate statistically suggestive SNPs that would subsequently achieve GWS in incrementally larger data sets. Using a combination of high-resolution promoter-focused Capture C and ATAC-seq, this method enables the prioritization of statistically suggestive loci.

We assessed the extent to which this method can be applied to ‘salvage’ sub-threshold loci for possible consideration. We used BMI and WHR adjusted for BMI because of the relatively large number of loci identified in GWAS efforts conducted in large cohorts that continued to increase over time. The number of SNPs surviving these filters for each cell type and trait at each successively relaxed statistical cutoff are described in Source data 1.

Given the fairly modest increase in sample size between 2010 (N = 249,796) and 2015 (N = 339,224) for BMI, it was not particularly surprising that majority of the surviving 2010 BMI signals did not achieve GWS until 2018 (N = 681,275). Only six of the 15 surviving signals achieved GWS by 2015, but 13 eventually achieved GWS by 2018. Reaching deeper into the 2010 suggestive signals through p<5×10−4 showed a much clearer trend for both traits: roughly 20% of the surviving 2010 signals achieved GWS by 2015 and nearly 50% achieved GWS by 2018. Despite positive predictive values consistently greater than 80% for loci with 5×10−8≤p<5×10−6, it remains to be seen how many of the remaining surviving SNPs with less significant p-values will achieve GWS by the publication of the next GWAS in the future for each corresponding trait.

In this study, we never identified a particular sub-threshold bin where no constraint was as precise as this chromatin-based constraint. We did, however, find that the precision observed for loci in data sets between 2010 and 2018 varied by trait. While the positive predictive value was nearly 90% for 2010 BMI constrained loci reaching GWS by 2018 at 5×10−8≤p<5×10−5, only 65% of the surviving 2010 WHRadjBMI achieved GWS by the subsequent 2018 study. At the next, more restrictive, threshold, 5×10−8≤p<5×10−6, we found that nearly all of the surviving loci for both traits of the same years reached GWS by their respective 2018 study, although the number of loci within this threshold is small (BMI: 4/4, WHRadjBMI: 5/6). Thus, our findings suggest that this strategy is capable of identifying loci that will achieve GWS at 5×10−8≤p<5×10−6. Additional loci can be identified at 5×10−8≤p<5×10−5, at the expense of a degree of false positives. Although as noted above, such false-positive signals could possibly go on to be GWS in a future study.

We also observed that across all suggestive thresholds, specificity was consistently >80%, and often >90%. The consistently high specificity and precision, at least through 5×10−8≤p<5×10−6, suggest that true negatives are largely properly identified without the generation of large amounts of false positives. The low false-positive rate did come at a cost, however. Sensitivity was extremely low at all thresholds, often below 20% (Source data 1). The lack of sensitivity conveys high levels of false negatives, meaning many signals that would eventually achieve GWS would not be properly classified with this method.

The strength of this method is in its ability to attach biological relevance to sub-threshold SNPs in individual cell types, but this can also serve as its weakness. However, given the cost in time and resources to test candidate loci, we believe that high specificity and precision are more important characteristics for such a classifier. While we believe this trade-off is acceptable for the identification of novel biologically relevant loci prior to their confirmation via GWAS, we recognize that there are many loci that are falsely identified as not relevant. In utilizing the chromatin state of individual cell types in such a manner, we may reject loci that are biologically relevant in a different cell type or those that simply lack such an epigenetic mechanism. Provided a more comprehensive library of chromatin state in a much more diverse set of cell types, or the inclusion of additional biological filters that could identify loci that lack this epigenetic mechanism, we could potentially increase sensitivity in a substantial manner while retaining high rates of precision and specificity.

Despite any such limitations, we implicated loci most likely to become significant in the context of larger data sets with just our chromatin-based constraint approach. Using this variant-to-gene mapping approach, one can prioritize loci/genes of borderline statistical significance that may have important candidacy based upon functional considerations. Confirmation could come via larger data sets and/or by direct molecular physiological analyses of the candidates.

Materials and methods

ATAC-seq library generation and peak calls

Request a detailed protocol

Tn5 transposase transposition (Illumina Cat #FC-121–1030, Nextera) and purification of the Tn5 transposase derived DNA from 100,000 cells of each investigated cell type. The samples were then shipped to the Center of Spatial and Functional Genomics at CHOP where the ATAC-seq process was completed. Live cells were harvested via trypsinization, followed by a series of wash steps. One hundred thousand cells from each sample were pelleted at 550 × g for 5 min at 4°C. The cell pellet was then resuspended in 50 μl cold lysis buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged immediately at 550 × g for 10 min at 4°C. The nuclei were resuspended in the transposition reaction mix (2× TD Buffer [Illumina Cat #FC-121–1030, Nextera], 2.5 µl Tn5 transposase [Illumina Cat #FC-121–1030, Nextera], and nuclease-free H2O) on ice and then incubated for 45 min at 37°C. The transposed DNA was then purified using the MinElute Kit (Qiagen), eluted with 10.5 μl elution buffer (EB), frozen, and sent to the Center for Spatial and Functional Genomics at CHOP. The transposed DNA was PCR amplified using Nextera primers for 12 cycles to generate each library. The PCR was subsequently cleaned up using AMPureXP beads (Agencourt), and libraries were paired-end sequenced on an Illumina HiSeq 4000 (100 bp read length) and the Illumina NovaSeq platform. Open chromatin regions were called using the ENCODE ATAC-seq pipeline (https://www.encodeproject.org/atac-seq/), selecting the resulting IDR conservative peaks (with all coordinates referring to hg19). We define a genomic region open if it has 1 bp overlap with an ATAC-seq peak.

Cell fixation for chromatin capture

Request a detailed protocol

The protocol used for cell fixation was similar to previous methods (Hughes et al., 2014). Cells were collected and single-cell suspension were made with aliquots of 107 cells in 10 ml media (e.g. RPMI + 10% FCS). Five hundred and forty microliters of 37% formaldehyde was added and incubated for 10 min at RT on a platform rocker. The reaction was quenched by adding 1.5 ml 1 M cold glycine (4°C) for a total volume of 12 ml. Fixed cells were centrifuged at 1000 rpm for 5 min at 4°C and supernatant removed. The cell pellets were washed in 10 ml cold PBS (4°C) followed by centrifugation as above. Supernatant was removed and cell pellets were resuspended in 5 ml of cold lysis buffer (10 mM Tris pH8, 10 mM NaCl, 0.2% NP-40 [Igepal] supplemented with protease inhibitor cocktails). Resuspended cells were incubated for 20 min on ice, centrifuged as above, and the lysis buffer removed. Finally, cell pellets were resuspended in 1 ml fresh lysis buffer, transferred to 1.5 ml Eppendorf tubes, and snap frozen (ethanol/dry ice or liquid nitrogen). Cells were stored at −80°C until they were thawed for 3C library generation.

Capture C

Request a detailed protocol

Custom capture baits were designed using an Agilent SureSelect library design targeting both ends of DpnII restriction fragments encompassing promoters (including alternative promoters) of all human coding genes, noncoding RNA, antisense RNA, snRNA, miRNA, snoRNA, and lincRNA transcripts, totaling 36,691 RNA-baited fragments. The library was designed using scripts generously provided by Dr. Hughes (Oxford, UK), utilizing the RefSeq, lincRNA transcripts, and sno/miRNA tracks in the hg19 assembly downloaded from the UCSC Table Browser on 16 September 2015. The capture library design covered 95% of all coding RNA promoters and 88% of RNA types described above. The missing 5% of coding genes that could not be designed were either duplicated genes or contained highly repetitive DNA in their promoter regions.

The isolated DNA from the 3C libraries was quantified using a Qubit fluorometer (Life Technologies), and 10 μg of each library was sheared in dH2O using a QSonica Q800R to an average DNA fragment size of 350 bp. QSonica settings used were 60% amplitude, 30 s on, 30 s off, 2 min intervals, for a total of five intervals at 4°C. After shearing, DNA was purified using AMPureXP beads (Agencourt). Sample concentration was checked via Qubit fluorometer and DNA size was assessed on a Bioanalyzer 2100 using a 1000 DNA Chip. Agilent SureSelect XT Library Prep Kit (Agilent) was used to repair DNA ends and for adaptor ligation following the standard protocol. Excess adaptors were removed using AMPureXP beads. Size and concentration were checked again before hybridization. One microgram of adaptor ligated library was used as input for the SureSelect XT capture kit using their standard protocol and our custom-designed Capture C library. The quantity and quality of the captured library were assessed by Qubit fluorometer and Bioanalyser using a high-sensitivity DNA Chip. Each SureSelect XT library was initially sequenced on one lane HiSeq 4000 paired-end sequencing (100 bp read length) for QC. All six Capture C promoter interactome libraries were then sequenced three at a time on an S2 flow cells on an Illumina NovaSeq, generating ~1.6 billion paired-end reads per sample (50 bp read length).

Analysis of promoter-focused capture C data

Request a detailed protocol

Quality control of the raw fastq files was performed with FastQC. Paired-end reads were pre-processed with the HiCUP pipeline (Wingett et al., 2015), with bowtie2 as aligner and hg19 as reference genome. Significant promoter interactions at 1-DpnII fragment resolution were called using CHiCAGO (Cairns et al., 2016), with default parameters except for binsize which was set to 2500. Significant interactions at 4-DpnII fragment resolution were also called with CHiCAGO using artificial .baitmap and .rmap files where DpnII fragments were grouped into four consecutively and using default parameters except for removeAdjacent that was set to false. We define PIR a promoter-interacting region, irrespective of whether it is a baited region or not. The CHiCAGO function peakEnrichment4Features() was used to assess enrichment of genomic features in promoter-interacting regions at both 1-fragment and 4-fragment resolution.

Variant-to-gene mapping pipeline

Request a detailed protocol

BMI and WHRadjBMI GWAS summary statistics derived from European ancestry, each from 2010, 2015, and 2018, were downloaded from the Genetic Investigation of Anthropometric Traits (GIANT) consortium https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files (Heid et al., 2010a; Locke et al., 2015; Pulit et al., 2019; Shungin et al., 2015; Speliotes et al., 2010b; Yengo et al., 2018). We identified all genome-wide significant variants from each data set as any SNP with p<5×10−8. We then identified the sets of variants in the varying suggestive bins of 5×10−8≤p<5×10−7, 5 × 10−8 ≤ p<5×10−6, 5 × 10−8 ≤ p<5×10−5, and 5 × 10−8 ≤ p<5×10−4. Upon the identification of these variants within each bin, we utilized SNiPA v3.3 (Arnold et al., 2015) to find their proxy SNPs, which we define as any SNP with r2 > 0.8 in Europeans for each region. Only signals with LD information within SNiPA were considered.

We next conducted a variant-to-gene mapping for each cell type within each of the suggestive bins to identify the gene promoters that are in contact with these SNPs. Promoter Capture C libraries are utilized to identify the genes with which these variants have interactions. Significant interactions were called using the CHiCAGO pipeline (Cairns et al., 2016) utilizing both 1-fragment and 4-fragment resolutions. We chose to focus on non-gene-to-gene interactions; thus, we ignored interactions that were identified as bait-to-bait as these represent the interactions between gene promoters. ATAC-seq libraries were also utilized to identify only those gene promoters that interact with SNPs in regions of open chromatin. Genes within the annotated MHC region were removed due to its highly polymorphic nature.

We next removed SNPs within the suggestive bins that were in linkage disequilibrium with any SNP that was significant genome wide. This was done to determine an entirely novel set of variant interacting genes that are entirely independent of those that are already known. To accomplish this, we removed all variants that were found to be in LD with a variant that is significant at a genome level. Thus, we identified all proxies of genome-wide significant variants at r2 > 0.1 and remove any variant within the suggestive region that is found to be a proxy of these genome-wide significant variants. This provides a filtered set of SNPs that are independent of any SNP that is significant at a genome-wide scale.

Retrospective analysis

Request a detailed protocol

Interacting SNP-gene promoter pairs were identified by the variant-to-gene mapping pipeline described above for each GWAS across all suggestive zones for each cell type. Of these SNP-gene promoter pairs, we identify those that are in tight LD (r2 >0.8) with an SNP that is genome-wide significant in a future study. The implicated genes derived from our variant-to-gene mapping approach were frequently different from the locus ‘names’ traditionally used in publications reporting GWAS findings, typically based on the nearest gene. In contrast, our variant-to-gene mapping used the integration of ATAC-seq and promoter-focused Capture C data to identify the gene promotor(s) physically in contact with a genomic region (almost always non-coding) harboring an associated variant. However, in order to assess the 2015 loci that were identifiable in 2010 with this method, for consistency’s sake, we annotated the implicated 2010 loci with the published locus ‘name’ annotation from the respective 2015 GWAS report. However, unlike the 2015 efforts, the 2018 studies did not annotate the reported loci with an arbitrary gene notation; thus, we simply labeled the nearest gene to the 2018 sentinel SNP in which the surviving signals were in tight LD. The gene promoters in contact with each surviving signal are also available in Source data 1. The surviving SNPs that were in tight LD with an SNP that achieved GWS in 2015 were annotated with the published 2015 locus name of a sentinel SNP residing up to 1 MB away. We indicate the locus name that was provided in each 2015 study, as well as provide the set of gene promoters that were identified by the variant-to-gene mapping pipeline. Manhattan plots were generated in R (R Development Core Team, 2019), utilizing p-values of SNPs from the corresponding summary statistics. SNP positions were identified with dbSNP Build 151 to plot the relative location of the SNPs on the Manhattan plot. The highlighted loci point to the SNP with the lowest p-value identified at each locus.

In the case of all remaining comparisons, retrospective annotation was performed differently. Rather than trying to provide a locus name to the set of SNPs that were identified to be in tight LD with a genome-wide significant SNP in a later year, we elected to identify the surviving SNP, the gene promoters it physically contacts, and its best proxy that reached GWS (as defined by both r2 and p-value in the summary statistics).

To assess the predictive power of this method, we identified the positive predictive value of each set of salvaged SNPs across each retrospective analysis. To accurately quantify the number of loci that are identifiable using salvaged suggestive SNPs, we group the surviving variants based on their LD (r2 > 0.4) to one another as a locus. We extend this one additional time to include the proxies (r2 > 0.4) of each previously identified proxy SNP as a component of each locus. This allows SNPs that failed to be identified as a proxy of the lead SNP to be included within the locus via the transitive property, but only via one iteration of this process. The resulting loci identified are independent from one another, which prevents double counting of loci. We count these loci for each cell type across each suggestive bin, and we also identify the number of distinct loci regardless of cell type. We then identify the set of true positives as a locus that is in tight LD with a genome-wide significant SNP in a future GWAS. Those failing to meet these criteria are deemed false positives. We also identified loci of all genome-wide significant independent suggestive SNPs (r2 < 0.4) for each retrospective analysis and identified true-positive, false-positive, false-negative, and true-negative counts for this set using the same metrics as the constrained data sets. We used a beta-binomial model and used Monte Carlo approximation over 100,000 iterations to identify the posterior probability that loci identified by our chromatin-based constraint more often achieve GWS than loci with no constraint. We also assessed significance of the positive predictive values by calculating an empirical distribution from 10,000 iterations of a randomly sampled population of the unconstrained suggestive signals within each p-value threshold bin. At each iteration, we randomly selected N loci, where N is the corresponding number of loci surviving our chromatin-constraints from either cell type, and quantified the positive predictive value from this sampling. We then plotted the location where the positive predictive values fell for each cell type to determine whether these different significantly from the random population.

We calculated sensitivity, specificity, false-negative rate, and false positive rate of this approach across both traits for all testable years. To do this, we identified binary classifications of sub-threshold loci that were predicted to either reach or not reach GWS by the future year in each cell type separately. We then created confusion matrices for each cell type and p-value bin to calculate each binary classification performance metric. Additionally, we identified these values for the previously described negative control data (the effective inverse of the biological constrained data) as well as the randomly sampled data. For both of these data sets, we identified these metrics across 10,000 randomly sampled populations where we randomly selected N loci, where N is the corresponding number of loci surviving our chromatin-constraints from either cell type at the corresponding p-value threshold.

All source code available on Github: https://github.com/rkweku/SubThresholdProjectScripts.

Data availability

Adipose ATAC-seq and promoter-focused capture C data will be made available on GEO prior to publication. Hypothalamic Neuron ATAC-eq and promoter-focused capture C data is the subject of another atlas-based manuscript currently under peer review and through that process that dataset will be made available once the paper is published- the corresponding hypothalamus preprint can be found at: https://doi.org/10.1101/2020.07.06.146951v1.full.

The following data sets were generated
The following previously published data sets were used

References

    1. Heid IM
    2. Jackson AU
    3. Randall JC
    4. Winkler TW
    5. Qi L
    6. Steinthorsdottir V
    7. Thorleifsson G
    8. Zillikens MC
    9. Speliotes EK
    10. Mägi R
    11. Workalemahu T
    12. White CC
    13. Bouatia-Naji N
    14. Harris TB
    15. Berndt SI
    16. Ingelsson E
    17. Willer CJ
    18. Weedon MN
    19. Luan J
    20. Vedantam S
    21. Esko T
    22. Kilpeläinen TO
    23. Kutalik Z
    24. Li S
    25. Monda KL
    26. Dixon AL
    27. Holmes CC
    28. Kaplan LM
    29. Liang L
    30. Min JL
    31. Moffatt MF
    32. Molony C
    33. Nicholson G
    34. Schadt EE
    35. Zondervan KT
    36. Feitosa MF
    37. Ferreira T
    38. Lango Allen H
    39. Weyant RJ
    40. Wheeler E
    41. Wood AR
    42. Estrada K
    43. Goddard ME
    44. Lettre G
    45. Mangino M
    46. Nyholt DR
    47. Purcell S
    48. Smith AV
    49. Visscher PM
    50. Yang J
    51. McCarroll SA
    52. Nemesh J
    53. Voight BF
    54. Absher D
    55. Amin N
    56. Aspelund T
    57. Coin L
    58. Glazer NL
    59. Hayward C
    60. Heard-Costa NL
    61. Hottenga JJ
    62. Johansson A
    63. Johnson T
    64. Kaakinen M
    65. Kapur K
    66. Ketkar S
    67. Knowles JW
    68. Kraft P
    69. Kraja AT
    70. Lamina C
    71. Leitzmann MF
    72. McKnight B
    73. Morris AP
    74. Ong KK
    75. Perry JR
    76. Peters MJ
    77. Polasek O
    78. Prokopenko I
    79. Rayner NW
    80. Ripatti S
    81. Rivadeneira F
    82. Robertson NR
    83. Sanna S
    84. Sovio U
    85. Surakka I
    86. Teumer A
    87. van Wingerden S
    88. Vitart V
    89. Zhao JH
    90. Cavalcanti-Proença C
    91. Chines PS
    92. Fisher E
    93. Kulzer JR
    94. Lecoeur C
    95. Narisu N
    96. Sandholt C
    97. Scott LJ
    98. Silander K
    99. Stark K
    100. Tammesoo ML
    101. Teslovich TM
    102. Timpson NJ
    103. Watanabe RM
    104. Welch R
    105. Chasman DI
    106. Cooper MN
    107. Jansson JO
    108. Kettunen J
    109. Lawrence RW
    110. Pellikka N
    111. Perola M
    112. Vandenput L
    113. Alavere H
    114. Almgren P
    115. Atwood LD
    116. Bennett AJ
    117. Biffar R
    118. Bonnycastle LL
    119. Bornstein SR
    120. Buchanan TA
    121. Campbell H
    122. Day IN
    123. Dei M
    124. Dörr M
    125. Elliott P
    126. Erdos MR
    127. Eriksson JG
    128. Freimer NB
    129. Fu M
    130. Gaget S
    131. Geus EJ
    132. Gjesing AP
    133. Grallert H
    134. Grässler J
    135. Groves CJ
    136. Guiducci C
    137. Hartikainen AL
    138. Hassanali N
    139. Havulinna AS
    140. Herzig KH
    141. Hicks AA
    142. Hui J
    143. Igl W
    144. Jousilahti P
    145. Jula A
    146. Kajantie E
    147. Kinnunen L
    148. Kolcic I
    149. Koskinen S
    150. Kovacs P
    151. Kroemer HK
    152. Krzelj V
    153. Kuusisto J
    154. Kvaloy K
    155. Laitinen J
    156. Lantieri O
    157. Lathrop GM
    158. Lokki ML
    159. Luben RN
    160. Ludwig B
    161. McArdle WL
    162. McCarthy A
    163. Morken MA
    164. Nelis M
    165. Neville MJ
    166. Paré G
    167. Parker AN
    168. Peden JF
    169. Pichler I
    170. Pietiläinen KH
    171. Platou CG
    172. Pouta A
    173. Ridderstråle M
    174. Samani NJ
    175. Saramies J
    176. Sinisalo J
    177. Smit JH
    178. Strawbridge RJ
    179. Stringham HM
    180. Swift AJ
    181. Teder-Laving M
    182. Thomson B
    183. Usala G
    184. van Meurs JB
    185. van Ommen GJ
    186. Vatin V
    187. Volpato CB
    188. Wallaschofski H
    189. Walters GB
    190. Widen E
    191. Wild SH
    192. Willemsen G
    193. Witte DR
    194. Zgaga L
    195. Zitting P
    196. Beilby JP
    197. James AL
    198. Kähönen M
    199. Lehtimäki T
    200. Nieminen MS
    201. Ohlsson C
    202. Palmer LJ
    203. Raitakari O
    204. Ridker PM
    205. Stumvoll M
    206. Tönjes A
    207. Viikari J
    208. Balkau B
    209. Ben-Shlomo Y
    210. Bergman RN
    211. Boeing H
    212. Smith GD
    213. Ebrahim S
    214. Froguel P
    215. Hansen T
    216. Hengstenberg C
    217. Hveem K
    218. Isomaa B
    219. Jørgensen T
    220. Karpe F
    221. Khaw KT
    222. Laakso M
    223. Lawlor DA
    224. Marre M
    225. Meitinger T
    226. Metspalu A
    227. Midthjell K
    228. Pedersen O
    229. Salomaa V
    230. Schwarz PE
    231. Tuomi T
    232. Tuomilehto J
    233. Valle TT
    234. Wareham NJ
    235. Arnold AM
    236. Beckmann JS
    237. Bergmann S
    238. Boerwinkle E
    239. Boomsma DI
    240. Caulfield MJ
    241. Collins FS
    242. Eiriksdottir G
    243. Gudnason V
    244. Gyllensten U
    245. Hamsten A
    246. Hattersley AT
    247. Hofman A
    248. Hu FB
    249. Illig T
    250. Iribarren C
    251. Jarvelin MR
    252. Kao WH
    253. Kaprio J
    254. Launer LJ
    255. Munroe PB
    256. Oostra B
    257. Penninx BW
    258. Pramstaller PP
    259. Psaty BM
    260. Quertermous T
    261. Rissanen A
    262. Rudan I
    263. Shuldiner AR
    264. Soranzo N
    265. Spector TD
    266. Syvanen AC
    267. Uda M
    268. Uitterlinden A
    269. Völzke H
    270. Vollenweider P
    271. Wilson JF
    272. Witteman JC
    273. Wright AF
    274. Abecasis GR
    275. Boehnke M
    276. Borecki IB
    277. Deloukas P
    278. Frayling TM
    279. Groop LC
    280. Haritunians T
    281. Hunter DJ
    282. Kaplan RC
    283. North KE
    284. O'Connell JR
    285. Peltonen L
    286. Schlessinger D
    287. Strachan DP
    288. Hirschhorn JN
    289. Assimes TL
    290. Wichmann HE
    291. Thorsteinsdottir U
    292. van Duijn CM
    293. Stefansson K
    294. Cupples LA
    295. Loos RJ
    296. Barroso I
    297. McCarthy MI
    298. Fox CS
    299. Mohlke KL
    300. Lindgren CM
    301. MAGIC
    (2010a) Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution
    Nature Genetics 42:949–960.
    https://doi.org/10.1038/ng.685
    1. Locke AE
    2. Kahali B
    3. Berndt SI
    4. Justice AE
    5. Pers TH
    6. Day FR
    7. Powell C
    8. Vedantam S
    9. Buchkovich ML
    10. Yang J
    11. Croteau-Chonka DC
    12. Esko T
    13. Fall T
    14. Ferreira T
    15. Gustafsson S
    16. Kutalik Z
    17. Luan J
    18. Mägi R
    19. Randall JC
    20. Winkler TW
    21. Wood AR
    22. Workalemahu T
    23. Faul JD
    24. Smith JA
    25. Zhao JH
    26. Zhao W
    27. Chen J
    28. Fehrmann R
    29. Hedman ÅK
    30. Karjalainen J
    31. Schmidt EM
    32. Absher D
    33. Amin N
    34. Anderson D
    35. Beekman M
    36. Bolton JL
    37. Bragg-Gresham JL
    38. Buyske S
    39. Demirkan A
    40. Deng G
    41. Ehret GB
    42. Feenstra B
    43. Feitosa MF
    44. Fischer K
    45. Goel A
    46. Gong J
    47. Jackson AU
    48. Kanoni S
    49. Kleber ME
    50. Kristiansson K
    51. Lim U
    52. Lotay V
    53. Mangino M
    54. Leach IM
    55. Medina-Gomez C
    56. Medland SE
    57. Nalls MA
    58. Palmer CD
    59. Pasko D
    60. Pechlivanis S
    61. Peters MJ
    62. Prokopenko I
    63. Shungin D
    64. Stančáková A
    65. Strawbridge RJ
    66. Sung YJ
    67. Tanaka T
    68. Teumer A
    69. Trompet S
    70. van der Laan SW
    71. van Setten J
    72. Van Vliet-Ostaptchouk JV
    73. Wang Z
    74. Yengo L
    75. Zhang W
    76. Isaacs A
    77. Albrecht E
    78. Ärnlöv J
    79. Arscott GM
    80. Attwood AP
    81. Bandinelli S
    82. Barrett A
    83. Bas IN
    84. Bellis C
    85. Bennett AJ
    86. Berne C
    87. Blagieva R
    88. Blüher M
    89. Böhringer S
    90. Bonnycastle LL
    91. Böttcher Y
    92. Boyd HA
    93. Bruinenberg M
    94. Caspersen IH
    95. Chen YI
    96. Clarke R
    97. Daw EW
    98. de Craen AJM
    99. Delgado G
    100. Dimitriou M
    101. Doney ASF
    102. Eklund N
    103. Estrada K
    104. Eury E
    105. Folkersen L
    106. Fraser RM
    107. Garcia ME
    108. Geller F
    109. Giedraitis V
    110. Gigante B
    111. Go AS
    112. Golay A
    113. Goodall AH
    114. Gordon SD
    115. Gorski M
    116. Grabe HJ
    117. Grallert H
    118. Grammer TB
    119. Gräßler J
    120. Grönberg H
    121. Groves CJ
    122. Gusto G
    123. Haessler J
    124. Hall P
    125. Haller T
    126. Hallmans G
    127. Hartman CA
    128. Hassinen M
    129. Hayward C
    130. Heard-Costa NL
    131. Helmer Q
    132. Hengstenberg C
    133. Holmen O
    134. Hottenga JJ
    135. James AL
    136. Jeff JM
    137. Johansson Å
    138. Jolley J
    139. Juliusdottir T
    140. Kinnunen L
    141. Koenig W
    142. Koskenvuo M
    143. Kratzer W
    144. Laitinen J
    145. Lamina C
    146. Leander K
    147. Lee NR
    148. Lichtner P
    149. Lind L
    150. Lindström J
    151. Lo KS
    152. Lobbens S
    153. Lorbeer R
    154. Lu Y
    155. Mach F
    156. Magnusson PKE
    157. Mahajan A
    158. McArdle WL
    159. McLachlan S
    160. Menni C
    161. Merger S
    162. Mihailov E
    163. Milani L
    164. Moayyeri A
    165. Monda KL
    166. Morken MA
    167. Mulas A
    168. Müller G
    169. Müller-Nurasyid M
    170. Musk AW
    171. Nagaraja R
    172. Nöthen MM
    173. Nolte IM
    174. Pilz S
    175. Rayner NW
    176. Renstrom F
    177. Rettig R
    178. Ried JS
    179. Ripke S
    180. Robertson NR
    181. Rose LM
    182. Sanna S
    183. Scharnagl H
    184. Scholtens S
    185. Schumacher FR
    186. Scott WR
    187. Seufferlein T
    188. Shi J
    189. Smith AV
    190. Smolonska J
    191. Stanton AV
    192. Steinthorsdottir V
    193. Stirrups K
    194. Stringham HM
    195. Sundström J
    196. Swertz MA
    197. Swift AJ
    198. Syvänen AC
    199. Tan ST
    200. Tayo BO
    201. Thorand B
    202. Thorleifsson G
    203. Tyrer JP
    204. Uh HW
    205. Vandenput L
    206. Verhulst FC
    207. Vermeulen SH
    208. Verweij N
    209. Vonk JM
    210. Waite LL
    211. Warren HR
    212. Waterworth D
    213. Weedon MN
    214. Wilkens LR
    215. Willenborg C
    216. Wilsgaard T
    217. Wojczynski MK
    218. Wong A
    219. Wright AF
    220. Zhang Q
    221. Brennan EP
    222. Choi M
    223. Dastani Z
    224. Drong AW
    225. Eriksson P
    226. Franco-Cereceda A
    227. Gådin JR
    228. Gharavi AG
    229. Goddard ME
    230. Handsaker RE
    231. Huang J
    232. Karpe F
    233. Kathiresan S
    234. Keildson S
    235. Kiryluk K
    236. Kubo M
    237. Lee JY
    238. Liang L
    239. Lifton RP
    240. Ma B
    241. McCarroll SA
    242. McKnight AJ
    243. Min JL
    244. Moffatt MF
    245. Montgomery GW
    246. Murabito JM
    247. Nicholson G
    248. Nyholt DR
    249. Okada Y
    250. Perry JRB
    251. Dorajoo R
    252. Reinmaa E
    253. Salem RM
    254. Sandholm N
    255. Scott RA
    256. Stolk L
    257. Takahashi A
    258. Tanaka T
    259. van 't Hooft FM
    260. Vinkhuyzen AAE
    261. Westra HJ
    262. Zheng W
    263. Zondervan KT
    264. Heath AC
    265. Arveiler D
    266. Bakker SJL
    267. Beilby J
    268. Bergman RN
    269. Blangero J
    270. Bovet P
    271. Campbell H
    272. Caulfield MJ
    273. Cesana G
    274. Chakravarti A
    275. Chasman DI
    276. Chines PS
    277. Collins FS
    278. Crawford DC
    279. Cupples LA
    280. Cusi D
    281. Danesh J
    282. de Faire U
    283. den Ruijter HM
    284. Dominiczak AF
    285. Erbel R
    286. Erdmann J
    287. Eriksson JG
    288. Farrall M
    289. Felix SB
    290. Ferrannini E
    291. Ferrières J
    292. Ford I
    293. Forouhi NG
    294. Forrester T
    295. Franco OH
    296. Gansevoort RT
    297. Gejman PV
    298. Gieger C
    299. Gottesman O
    300. Gudnason V
    301. Gyllensten U
    302. Hall AS
    303. Harris TB
    304. Hattersley AT
    305. Hicks AA
    306. Hindorff LA
    307. Hingorani AD
    308. Hofman A
    309. Homuth G
    310. Hovingh GK
    311. Humphries SE
    312. Hunt SC
    313. Hyppönen E
    314. Illig T
    315. Jacobs KB
    316. Jarvelin MR
    317. Jöckel KH
    318. Johansen B
    319. Jousilahti P
    320. Jukema JW
    321. Jula AM
    322. Kaprio J
    323. Kastelein JJP
    324. Keinanen-Kiukaanniemi SM
    325. Kiemeney LA
    326. Knekt P
    327. Kooner JS
    328. Kooperberg C
    329. Kovacs P
    330. Kraja AT
    331. Kumari M
    332. Kuusisto J
    333. Lakka TA
    334. Langenberg C
    335. Marchand LL
    336. Lehtimäki T
    337. Lyssenko V
    338. Männistö S
    339. Marette A
    340. Matise TC
    341. McKenzie CA
    342. McKnight B
    343. Moll FL
    344. Morris AD
    345. Morris AP
    346. Murray JC
    347. Nelis M
    348. Ohlsson C
    349. Oldehinkel AJ
    350. Ong KK
    351. Madden PAF
    352. Pasterkamp G
    353. Peden JF
    354. Peters A
    355. Postma DS
    356. Pramstaller PP
    357. Price JF
    358. Qi L
    359. Raitakari OT
    360. Rankinen T
    361. Rao DC
    362. Rice TK
    363. Ridker PM
    364. Rioux JD
    365. Ritchie MD
    366. Rudan I
    367. Salomaa V
    368. Samani NJ
    369. Saramies J
    370. Sarzynski MA
    371. Schunkert H
    372. Schwarz PEH
    373. Sever P
    374. Shuldiner AR
    375. Sinisalo J
    376. Stolk RP
    377. Strauch K
    378. Tönjes A
    379. Trégouët DA
    380. Tremblay A
    381. Tremoli E
    382. Virtamo J
    383. Vohl MC
    384. Völker U
    385. Waeber G
    386. Willemsen G
    387. Witteman JC
    388. Zillikens MC
    389. Adair LS
    390. Amouyel P
    391. Asselbergs FW
    392. Assimes TL
    393. Bochud M
    394. Boehm BO
    395. Boerwinkle E
    396. Bornstein SR
    397. Bottinger EP
    398. Bouchard C
    399. Cauchi S
    400. Chambers JC
    401. Chanock SJ
    402. Cooper RS
    403. de Bakker PIW
    404. Dedoussis G
    405. Ferrucci L
    406. Franks PW
    407. Froguel P
    408. Groop LC
    409. Haiman CA
    410. Hamsten A
    411. Hui J
    412. Hunter DJ
    413. Hveem K
    414. Kaplan RC
    415. Kivimaki M
    416. Kuh D
    417. Laakso M
    418. Liu Y
    419. Martin NG
    420. März W
    421. Melbye M
    422. Metspalu A
    423. Moebus S
    424. Munroe PB
    425. Njølstad I
    426. Oostra BA
    427. Palmer CNA
    428. Pedersen NL
    429. Perola M
    430. Pérusse L
    431. Peters U
    432. Power C
    433. Quertermous T
    434. Rauramaa R
    435. Rivadeneira F
    436. Saaristo TE
    437. Saleheen D
    438. Sattar N
    439. Schadt EE
    440. Schlessinger D
    441. Slagboom PE
    442. Snieder H
    443. Spector TD
    444. Thorsteinsdottir U
    445. Stumvoll M
    446. Tuomilehto J
    447. Uitterlinden AG
    448. Uusitupa M
    449. van der Harst P
    450. Walker M
    451. Wallaschofski H
    452. Wareham NJ
    453. Watkins H
    454. Weir DR
    455. Wichmann HE
    456. Wilson JF
    457. Zanen P
    458. Borecki IB
    459. Deloukas P
    460. Fox CS
    461. Heid IM
    462. O'Connell JR
    463. Strachan DP
    464. Stefansson K
    465. van Duijn CM
    466. Abecasis GR
    467. Franke L
    468. Frayling TM
    469. McCarthy MI
    470. Visscher PM
    471. Scherag A
    472. Willer CJ
    473. Boehnke M
    474. Mohlke KL
    475. Lindgren CM
    476. Beckmann JS
    477. Barroso I
    478. North KE
    479. Ingelsson E
    480. Hirschhorn JN
    481. Loos RJF
    482. Speliotes EK
    483. LifeLines Cohort Study
    484. ADIPOGen Consortium
    485. AGEN-BMI Working Group
    486. CARDIOGRAMplusC4D Consortium
    487. CKDGen Consortium
    488. GLGC
    489. ICBP
    490. MAGIC Investigators
    491. MuTHER Consortium
    492. MIGen Consortium
    493. PAGE Consortium
    494. ReproGen Consortium
    495. GENIE Consortium
    496. International Endogene Consortium
    (2015) Genetic studies of body mass index yield new insights for obesity biology
    Nature 518:197–206.
    https://doi.org/10.1038/nature14177
  15. Software
    1. R Development Core Team
    (2019) R: A Language and Environment for Statistical Computing
    R Foundation for Statistical Computing, Vienna, Austria.
    http://www.R-project.org
    1. Shungin D
    2. Winkler TW
    3. Croteau-Chonka DC
    4. Ferreira T
    5. Locke AE
    6. Mägi R
    7. Strawbridge RJ
    8. Pers TH
    9. Fischer K
    10. Justice AE
    11. Workalemahu T
    12. Wu JMW
    13. Buchkovich ML
    14. Heard-Costa NL
    15. Roman TS
    16. Drong AW
    17. Song C
    18. Gustafsson S
    19. Day FR
    20. Esko T
    21. Fall T
    22. Kutalik Z
    23. Luan J
    24. Randall JC
    25. Scherag A
    26. Vedantam S
    27. Wood AR
    28. Chen J
    29. Fehrmann R
    30. Karjalainen J
    31. Kahali B
    32. Liu CT
    33. Schmidt EM
    34. Absher D
    35. Amin N
    36. Anderson D
    37. Beekman M
    38. Bragg-Gresham JL
    39. Buyske S
    40. Demirkan A
    41. Ehret GB
    42. Feitosa MF
    43. Goel A
    44. Jackson AU
    45. Johnson T
    46. Kleber ME
    47. Kristiansson K
    48. Mangino M
    49. Leach IM
    50. Medina-Gomez C
    51. Palmer CD
    52. Pasko D
    53. Pechlivanis S
    54. Peters MJ
    55. Prokopenko I
    56. Stančáková A
    57. Sung YJ
    58. Tanaka T
    59. Teumer A
    60. Van Vliet-Ostaptchouk JV
    61. Yengo L
    62. Zhang W
    63. Albrecht E
    64. Ärnlöv J
    65. Arscott GM
    66. Bandinelli S
    67. Barrett A
    68. Bellis C
    69. Bennett AJ
    70. Berne C
    71. Blüher M
    72. Böhringer S
    73. Bonnet F
    74. Böttcher Y
    75. Bruinenberg M
    76. Carba DB
    77. Caspersen IH
    78. Clarke R
    79. Daw EW
    80. Deelen J
    81. Deelman E
    82. Delgado G
    83. Doney AS
    84. Eklund N
    85. Erdos MR
    86. Estrada K
    87. Eury E
    88. Friedrich N
    89. Garcia ME
    90. Giedraitis V
    91. Gigante B
    92. Go AS
    93. Golay A
    94. Grallert H
    95. Grammer TB
    96. Gräßler J
    97. Grewal J
    98. Groves CJ
    99. Haller T
    100. Hallmans G
    101. Hartman CA
    102. Hassinen M
    103. Hayward C
    104. Heikkilä K
    105. Herzig KH
    106. Helmer Q
    107. Hillege HL
    108. Holmen O
    109. Hunt SC
    110. Isaacs A
    111. Ittermann T
    112. James AL
    113. Johansson I
    114. Juliusdottir T
    115. Kalafati IP
    116. Kinnunen L
    117. Koenig W
    118. Kooner IK
    119. Kratzer W
    120. Lamina C
    121. Leander K
    122. Lee NR
    123. Lichtner P
    124. Lind L
    125. Lindström J
    126. Lobbens S
    127. Lorentzon M
    128. Mach F
    129. Magnusson PK
    130. Mahajan A
    131. McArdle WL
    132. Menni C
    133. Merger S
    134. Mihailov E
    135. Milani L
    136. Mills R
    137. Moayyeri A
    138. Monda KL
    139. Mooijaart SP
    140. Mühleisen TW
    141. Mulas A
    142. Müller G
    143. Müller-Nurasyid M
    144. Nagaraja R
    145. Nalls MA
    146. Narisu N
    147. Glorioso N
    148. Nolte IM
    149. Olden M
    150. Rayner NW
    151. Renstrom F
    152. Ried JS
    153. Robertson NR
    154. Rose LM
    155. Sanna S
    156. Scharnagl H
    157. Scholtens S
    158. Sennblad B
    159. Seufferlein T
    160. Sitlani CM
    161. Smith AV
    162. Stirrups K
    163. Stringham HM
    164. Sundström J
    165. Swertz MA
    166. Swift AJ
    167. Syvänen AC
    168. Tayo BO
    169. Thorand B
    170. Thorleifsson G
    171. Tomaschitz A
    172. Troffa C
    173. van Oort FV
    174. Verweij N
    175. Vonk JM
    176. Waite LL
    177. Wennauer R
    178. Wilsgaard T
    179. Wojczynski MK
    180. Wong A
    181. Zhang Q
    182. Zhao JH
    183. Brennan EP
    184. Choi M
    185. Eriksson P
    186. Folkersen L
    187. Franco-Cereceda A
    188. Gharavi AG
    189. Hedman ÅK
    190. Hivert MF
    191. Huang J
    192. Kanoni S
    193. Karpe F
    194. Keildson S
    195. Kiryluk K
    196. Liang L
    197. Lifton RP
    198. Ma B
    199. McKnight AJ
    200. McPherson R
    201. Metspalu A
    202. Min JL
    203. Moffatt MF
    204. Montgomery GW
    205. Murabito JM
    206. Nicholson G
    207. Nyholt DR
    208. Olsson C
    209. Perry JR
    210. Reinmaa E
    211. Salem RM
    212. Sandholm N
    213. Schadt EE
    214. Scott RA
    215. Stolk L
    216. Vallejo EE
    217. Westra HJ
    218. Zondervan KT
    219. Amouyel P
    220. Arveiler D
    221. Bakker SJ
    222. Beilby J
    223. Bergman RN
    224. Blangero J
    225. Brown MJ
    226. Burnier M
    227. Campbell H
    228. Chakravarti A
    229. Chines PS
    230. Claudi-Boehm S
    231. Collins FS
    232. Crawford DC
    233. Danesh J
    234. de Faire U
    235. de Geus EJ
    236. Dörr M
    237. Erbel R
    238. Eriksson JG
    239. Farrall M
    240. Ferrannini E
    241. Ferrières J
    242. Forouhi NG
    243. Forrester T
    244. Franco OH
    245. Gansevoort RT
    246. Gieger C
    247. Gudnason V
    248. Haiman CA
    249. Harris TB
    250. Hattersley AT
    251. Heliövaara M
    252. Hicks AA
    253. Hingorani AD
    254. Hoffmann W
    255. Hofman A
    256. Homuth G
    257. Humphries SE
    258. Hyppönen E
    259. Illig T
    260. Jarvelin MR
    261. Johansen B
    262. Jousilahti P
    263. Jula AM
    264. Kaprio J
    265. Kee F
    266. Keinanen-Kiukaanniemi SM
    267. Kooner JS
    268. Kooperberg C
    269. Kovacs P
    270. Kraja AT
    271. Kumari M
    272. Kuulasmaa K
    273. Kuusisto J
    274. Lakka TA
    275. Langenberg C
    276. Le Marchand L
    277. Lehtimäki T
    278. Lyssenko V
    279. Männistö S
    280. Marette A
    281. Matise TC
    282. McKenzie CA
    283. McKnight B
    284. Musk AW
    285. Möhlenkamp S
    286. Morris AD
    287. Nelis M
    288. Ohlsson C
    289. Oldehinkel AJ
    290. Ong KK
    291. Palmer LJ
    292. Penninx BW
    293. Peters A
    294. Pramstaller PP
    295. Raitakari OT
    296. Rankinen T
    297. Rao DC
    298. Rice TK
    299. Ridker PM
    300. Ritchie MD
    301. Rudan I
    302. Salomaa V
    303. Samani NJ
    304. Saramies J
    305. Sarzynski MA
    306. Schwarz PE
    307. Shuldiner AR
    308. Staessen JA
    309. Steinthorsdottir V
    310. Stolk RP
    311. Strauch K
    312. Tönjes A
    313. Tremblay A
    314. Tremoli E
    315. Vohl MC
    316. Völker U
    317. Vollenweider P
    318. Wilson JF
    319. Witteman JC
    320. Adair LS
    321. Bochud M
    322. Boehm BO
    323. Bornstein SR
    324. Bouchard C
    325. Cauchi S
    326. Caulfield MJ
    327. Chambers JC
    328. Chasman DI
    329. Cooper RS
    330. Dedoussis G
    331. Ferrucci L
    332. Froguel P
    333. Grabe HJ
    334. Hamsten A
    335. Hui J
    336. Hveem K
    337. Jöckel KH
    338. Kivimaki M
    339. Kuh D
    340. Laakso M
    341. Liu Y
    342. März W
    343. Munroe PB
    344. Njølstad I
    345. Oostra BA
    346. Palmer CN
    347. Pedersen NL
    348. Perola M
    349. Pérusse L
    350. Peters U
    351. Power C
    352. Quertermous T
    353. Rauramaa R
    354. Rivadeneira F
    355. Saaristo TE
    356. Saleheen D
    357. Sinisalo J
    358. Slagboom PE
    359. Snieder H
    360. Spector TD
    361. Stefansson K
    362. Stumvoll M
    363. Tuomilehto J
    364. Uitterlinden AG
    365. Uusitupa M
    366. van der Harst P
    367. Veronesi G
    368. Walker M
    369. Wareham NJ
    370. Watkins H
    371. Wichmann HE
    372. Abecasis GR
    373. Assimes TL
    374. Berndt SI
    375. Boehnke M
    376. Borecki IB
    377. Deloukas P
    378. Franke L
    379. Frayling TM
    380. Groop LC
    381. Hunter DJ
    382. Kaplan RC
    383. O'Connell JR
    384. Qi L
    385. Schlessinger D
    386. Strachan DP
    387. Thorsteinsdottir U
    388. van Duijn CM
    389. Willer CJ
    390. Visscher PM
    391. Yang J
    392. Hirschhorn JN
    393. Zillikens MC
    394. McCarthy MI
    395. Speliotes EK
    396. North KE
    397. Fox CS
    398. Barroso I
    399. Franks PW
    400. Ingelsson E
    401. Heid IM
    402. Loos RJ
    403. Cupples LA
    404. Morris AP
    405. Lindgren CM
    406. Mohlke KL
    407. ADIPOGen Consortium
    408. CARDIOGRAMplusC4D Consortium
    409. CKDGen Consortium
    410. GEFOS Consortium
    411. GENIE Consortium
    412. GLGC
    413. ICBP
    414. International Endogene Consortium
    415. LifeLines Cohort Study
    416. MAGIC Investigators
    417. MuTHER Consortium
    418. PAGE Consortium
    419. ReproGen Consortium
    (2015) New genetic loci link adipose and insulin biology to body fat distribution
    Nature 518:187–196.
    https://doi.org/10.1038/nature14132
    1. Speliotes EK
    2. Willer CJ
    3. Berndt SI
    4. Monda KL
    5. Thorleifsson G
    6. Jackson AU
    7. Lango Allen H
    8. Lindgren CM
    9. Luan J
    10. Mägi R
    11. Randall JC
    12. Vedantam S
    13. Winkler TW
    14. Qi L
    15. Workalemahu T
    16. Heid IM
    17. Steinthorsdottir V
    18. Stringham HM
    19. Weedon MN
    20. Wheeler E
    21. Wood AR
    22. Ferreira T
    23. Weyant RJ
    24. Segrè AV
    25. Estrada K
    26. Liang L
    27. Nemesh J
    28. Park JH
    29. Gustafsson S
    30. Kilpeläinen TO
    31. Yang J
    32. Bouatia-Naji N
    33. Esko T
    34. Feitosa MF
    35. Kutalik Z
    36. Mangino M
    37. Raychaudhuri S
    38. Scherag A
    39. Smith AV
    40. Welch R
    41. Zhao JH
    42. Aben KK
    43. Absher DM
    44. Amin N
    45. Dixon AL
    46. Fisher E
    47. Glazer NL
    48. Goddard ME
    49. Heard-Costa NL
    50. Hoesel V
    51. Hottenga JJ
    52. Johansson A
    53. Johnson T
    54. Ketkar S
    55. Lamina C
    56. Li S
    57. Moffatt MF
    58. Myers RH
    59. Narisu N
    60. Perry JR
    61. Peters MJ
    62. Preuss M
    63. Ripatti S
    64. Rivadeneira F
    65. Sandholt C
    66. Scott LJ
    67. Timpson NJ
    68. Tyrer JP
    69. van Wingerden S
    70. Watanabe RM
    71. White CC
    72. Wiklund F
    73. Barlassina C
    74. Chasman DI
    75. Cooper MN
    76. Jansson JO
    77. Lawrence RW
    78. Pellikka N
    79. Prokopenko I
    80. Shi J
    81. Thiering E
    82. Alavere H
    83. Alibrandi MT
    84. Almgren P
    85. Arnold AM
    86. Aspelund T
    87. Atwood LD
    88. Balkau B
    89. Balmforth AJ
    90. Bennett AJ
    91. Ben-Shlomo Y
    92. Bergman RN
    93. Bergmann S
    94. Biebermann H
    95. Blakemore AI
    96. Boes T
    97. Bonnycastle LL
    98. Bornstein SR
    99. Brown MJ
    100. Buchanan TA
    101. Busonero F
    102. Campbell H
    103. Cappuccio FP
    104. Cavalcanti-Proença C
    105. Chen YD
    106. Chen CM
    107. Chines PS
    108. Clarke R
    109. Coin L
    110. Connell J
    111. Day IN
    112. den Heijer M
    113. Duan J
    114. Ebrahim S
    115. Elliott P
    116. Elosua R
    117. Eiriksdottir G
    118. Erdos MR
    119. Eriksson JG
    120. Facheris MF
    121. Felix SB
    122. Fischer-Posovszky P
    123. Folsom AR
    124. Friedrich N
    125. Freimer NB
    126. Fu M
    127. Gaget S
    128. Gejman PV
    129. Geus EJ
    130. Gieger C
    131. Gjesing AP
    132. Goel A
    133. Goyette P
    134. Grallert H
    135. Grässler J
    136. Greenawalt DM
    137. Groves CJ
    138. Gudnason V
    139. Guiducci C
    140. Hartikainen AL
    141. Hassanali N
    142. Hall AS
    143. Havulinna AS
    144. Hayward C
    145. Heath AC
    146. Hengstenberg C
    147. Hicks AA
    148. Hinney A
    149. Hofman A
    150. Homuth G
    151. Hui J
    152. Igl W
    153. Iribarren C
    154. Isomaa B
    155. Jacobs KB
    156. Jarick I
    157. Jewell E
    158. John U
    159. Jørgensen T
    160. Jousilahti P
    161. Jula A
    162. Kaakinen M
    163. Kajantie E
    164. Kaplan LM
    165. Kathiresan S
    166. Kettunen J
    167. Kinnunen L
    168. Knowles JW
    169. Kolcic I
    170. König IR
    171. Koskinen S
    172. Kovacs P
    173. Kuusisto J
    174. Kraft P
    175. Kvaløy K
    176. Laitinen J
    177. Lantieri O
    178. Lanzani C
    179. Launer LJ
    180. Lecoeur C
    181. Lehtimäki T
    182. Lettre G
    183. Liu J
    184. Lokki ML
    185. Lorentzon M
    186. Luben RN
    187. Ludwig B
    188. Manunta P
    189. Marek D
    190. Marre M
    191. Martin NG
    192. McArdle WL
    193. McCarthy A
    194. McKnight B
    195. Meitinger T
    196. Melander O
    197. Meyre D
    198. Midthjell K
    199. Montgomery GW
    200. Morken MA
    201. Morris AP
    202. Mulic R
    203. Ngwa JS
    204. Nelis M
    205. Neville MJ
    206. Nyholt DR
    207. O'Donnell CJ
    208. O'Rahilly S
    209. Ong KK
    210. Oostra B
    211. Paré G
    212. Parker AN
    213. Perola M
    214. Pichler I
    215. Pietiläinen KH
    216. Platou CG
    217. Polasek O
    218. Pouta A
    219. Rafelt S
    220. Raitakari O
    221. Rayner NW
    222. Ridderstråle M
    223. Rief W
    224. Ruokonen A
    225. Robertson NR
    226. Rzehak P
    227. Salomaa V
    228. Sanders AR
    229. Sandhu MS
    230. Sanna S
    231. Saramies J
    232. Savolainen MJ
    233. Scherag S
    234. Schipf S
    235. Schreiber S
    236. Schunkert H
    237. Silander K
    238. Sinisalo J
    239. Siscovick DS
    240. Smit JH
    241. Soranzo N
    242. Sovio U
    243. Stephens J
    244. Surakka I
    245. Swift AJ
    246. Tammesoo ML
    247. Tardif JC
    248. Teder-Laving M
    249. Teslovich TM
    250. Thompson JR
    251. Thomson B
    252. Tönjes A
    253. Tuomi T
    254. van Meurs JB
    255. van Ommen GJ
    256. Vatin V
    257. Viikari J
    258. Visvikis-Siest S
    259. Vitart V
    260. Vogel CI
    261. Voight BF
    262. Waite LL
    263. Wallaschofski H
    264. Walters GB
    265. Widen E
    266. Wiegand S
    267. Wild SH
    268. Willemsen G
    269. Witte DR
    270. Witteman JC
    271. Xu J
    272. Zhang Q
    273. Zgaga L
    274. Ziegler A
    275. Zitting P
    276. Beilby JP
    277. Farooqi IS
    278. Hebebrand J
    279. Huikuri HV
    280. James AL
    281. Kähönen M
    282. Levinson DF
    283. Macciardi F
    284. Nieminen MS
    285. Ohlsson C
    286. Palmer LJ
    287. Ridker PM
    288. Stumvoll M
    289. Beckmann JS
    290. Boeing H
    291. Boerwinkle E
    292. Boomsma DI
    293. Caulfield MJ
    294. Chanock SJ
    295. Collins FS
    296. Cupples LA
    297. Smith GD
    298. Erdmann J
    299. Froguel P
    300. Grönberg H
    301. Gyllensten U
    302. Hall P
    303. Hansen T
    304. Harris TB
    305. Hattersley AT
    306. Hayes RB
    307. Heinrich J
    308. Hu FB
    309. Hveem K
    310. Illig T
    311. Jarvelin MR
    312. Kaprio J
    313. Karpe F
    314. Khaw KT
    315. Kiemeney LA
    316. Krude H
    317. Laakso M
    318. Lawlor DA
    319. Metspalu A
    320. Munroe PB
    321. Ouwehand WH
    322. Pedersen O
    323. Penninx BW
    324. Peters A
    325. Pramstaller PP
    326. Quertermous T
    327. Reinehr T
    328. Rissanen A
    329. Rudan I
    330. Samani NJ
    331. Schwarz PE
    332. Shuldiner AR
    333. Spector TD
    334. Tuomilehto J
    335. Uda M
    336. Uitterlinden A
    337. Valle TT
    338. Wabitsch M
    339. Waeber G
    340. Wareham NJ
    341. Watkins H
    342. Wilson JF
    343. Wright AF
    344. Zillikens MC
    345. Chatterjee N
    346. McCarroll SA
    347. Purcell S
    348. Schadt EE
    349. Visscher PM
    350. Assimes TL
    351. Borecki IB
    352. Deloukas P
    353. Fox CS
    354. Groop LC
    355. Haritunians T
    356. Hunter DJ
    357. Kaplan RC
    358. Mohlke KL
    359. O'Connell JR
    360. Peltonen L
    361. Schlessinger D
    362. Strachan DP
    363. van Duijn CM
    364. Wichmann HE
    365. Frayling TM
    366. Thorsteinsdottir U
    367. Abecasis GR
    368. Barroso I
    369. Boehnke M
    370. Stefansson K
    371. North KE
    372. McCarthy MI
    373. Hirschhorn JN
    374. Ingelsson E
    375. Loos RJ
    376. MAGIC
    377. Procardis Consortium
    (2010b) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
    Nature Genetics 42:937–948.
    https://doi.org/10.1038/ng.686
    1. Turcot V
    2. Lu Y
    3. Highland HM
    4. Schurmann C
    5. Justice AE
    6. Fine RS
    7. Bradfield JP
    8. Esko T
    9. Giri A
    10. Graff M
    11. Guo X
    12. Hendricks AE
    13. Karaderi T
    14. Lempradl A
    15. Locke AE
    16. Mahajan A
    17. Marouli E
    18. Sivapalaratnam S
    19. Young KL
    20. Alfred T
    21. Feitosa MF
    22. Masca NGD
    23. Manning AK
    24. Medina-Gomez C
    25. Mudgal P
    26. Ng MCY
    27. Reiner AP
    28. Vedantam S
    29. Willems SM
    30. Winkler TW
    31. Abecasis G
    32. Aben KK
    33. Alam DS
    34. Alharthi SE
    35. Allison M
    36. Amouyel P
    37. Asselbergs FW
    38. Auer PL
    39. Balkau B
    40. Bang LE
    41. Barroso I
    42. Bastarache L
    43. Benn M
    44. Bergmann S
    45. Bielak LF
    46. Blüher M
    47. Boehnke M
    48. Boeing H
    49. Boerwinkle E
    50. Böger CA
    51. Bork-Jensen J
    52. Bots ML
    53. Bottinger EP
    54. Bowden DW
    55. Brandslund I
    56. Breen G
    57. Brilliant MH
    58. Broer L
    59. Brumat M
    60. Burt AA
    61. Butterworth AS
    62. Campbell PT
    63. Cappellani S
    64. Carey DJ
    65. Catamo E
    66. Caulfield MJ
    67. Chambers JC
    68. Chasman DI
    69. Chen YI
    70. Chowdhury R
    71. Christensen C
    72. Chu AY
    73. Cocca M
    74. Collins FS
    75. Cook JP
    76. Corley J
    77. Corominas Galbany J
    78. Cox AJ
    79. Crosslin DS
    80. Cuellar-Partida G
    81. D'Eustacchio A
    82. Danesh J
    83. Davies G
    84. Bakker PIW
    85. Groot MCH
    86. Mutsert R
    87. Deary IJ
    88. Dedoussis G
    89. Demerath EW
    90. Heijer M
    91. Hollander AI
    92. Ruijter HM
    93. Dennis JG
    94. Denny JC
    95. Di Angelantonio E
    96. Drenos F
    97. Du M
    98. Dubé MP
    99. Dunning AM
    100. Easton DF
    101. Edwards TL
    102. Ellinghaus D
    103. Ellinor PT
    104. Elliott P
    105. Evangelou E
    106. Farmaki AE
    107. Farooqi IS
    108. Faul JD
    109. Fauser S
    110. Feng S
    111. Ferrannini E
    112. Ferrieres J
    113. Florez JC
    114. Ford I
    115. Fornage M
    116. Franco OH
    117. Franke A
    118. Franks PW
    119. Friedrich N
    120. Frikke-Schmidt R
    121. Galesloot TE
    122. Gan W
    123. Gandin I
    124. Gasparini P
    125. Gibson J
    126. Giedraitis V
    127. Gjesing AP
    128. Gordon-Larsen P
    129. Gorski M
    130. Grabe HJ
    131. Grant SFA
    132. Grarup N
    133. Griffiths HL
    134. Grove ML
    135. Gudnason V
    136. Gustafsson S
    137. Haessler J
    138. Hakonarson H
    139. Hammerschlag AR
    140. Hansen T
    141. Harris KM
    142. Harris TB
    143. Hattersley AT
    144. Have CT
    145. Hayward C
    146. He L
    147. Heard-Costa NL
    148. Heath AC
    149. Heid IM
    150. Helgeland Ø
    151. Hernesniemi J
    152. Hewitt AW
    153. Holmen OL
    154. Hovingh GK
    155. Howson JMM
    156. Hu Y
    157. Huang PL
    158. Huffman JE
    159. Ikram MA
    160. Ingelsson E
    161. Jackson AU
    162. Jansson JH
    163. Jarvik GP
    164. Jensen GB
    165. Jia Y
    166. Johansson S
    167. Jørgensen ME
    168. Jørgensen T
    169. Jukema JW
    170. Kahali B
    171. Kahn RS
    172. Kähönen M
    173. Kamstrup PR
    174. Kanoni S
    175. Kaprio J
    176. Karaleftheri M
    177. Kardia SLR
    178. Karpe F
    179. Kathiresan S
    180. Kee F
    181. Kiemeney LA
    182. Kim E
    183. Kitajima H
    184. Komulainen P
    185. Kooner JS
    186. Kooperberg C
    187. Korhonen T
    188. Kovacs P
    189. Kuivaniemi H
    190. Kutalik Z
    191. Kuulasmaa K
    192. Kuusisto J
    193. Laakso M
    194. Lakka TA
    195. Lamparter D
    196. Lange EM
    197. Lange LA
    198. Langenberg C
    199. Larson EB
    200. Lee NR
    201. Lehtimäki T
    202. Lewis CE
    203. Li H
    204. Li J
    205. Li-Gao R
    206. Lin H
    207. Lin KH
    208. Lin LA
    209. Lin X
    210. Lind L
    211. Lindström J
    212. Linneberg A
    213. Liu CT
    214. Liu DJ
    215. Liu Y
    216. Lo KS
    217. Lophatananon A
    218. Lotery AJ
    219. Loukola A
    220. Luan J
    221. Lubitz SA
    222. Lyytikäinen LP
    223. Männistö S
    224. Marenne G
    225. Mazul AL
    226. McCarthy MI
    227. McKean-Cowdin R
    228. Medland SE
    229. Meidtner K
    230. Milani L
    231. Mistry V
    232. Mitchell P
    233. Mohlke KL
    234. Moilanen L
    235. Moitry M
    236. Montgomery GW
    237. Mook-Kanamori DO
    238. Moore C
    239. Mori TA
    240. Morris AD
    241. Morris AP
    242. Müller-Nurasyid M
    243. Munroe PB
    244. Nalls MA
    245. Narisu N
    246. Nelson CP
    247. Neville M
    248. Nielsen SF
    249. Nikus K
    250. Njølstad PR
    251. Nordestgaard BG
    252. Nyholt DR
    253. O'Connel JR
    254. O'Donoghue ML
    255. Olde Loohuis LM
    256. Ophoff RA
    257. Owen KR
    258. Packard CJ
    259. Padmanabhan S
    260. Palmer CNA
    261. Palmer ND
    262. Pasterkamp G
    263. Patel AP
    264. Pattie A
    265. Pedersen O
    266. Peissig PL
    267. Peloso GM
    268. Pennell CE
    269. Perola M
    270. Perry JA
    271. Perry JRB
    272. Pers TH
    273. Person TN
    274. Peters A
    275. Petersen ERB
    276. Peyser PA
    277. Pirie A
    278. Polasek O
    279. Polderman TJ
    280. Puolijoki H
    281. Raitakari OT
    282. Rasheed A
    283. Rauramaa R
    284. Reilly DF
    285. Renström F
    286. Rheinberger M
    287. Ridker PM
    288. Rioux JD
    289. Rivas MA
    290. Roberts DJ
    291. Robertson NR
    292. Robino A
    293. Rolandsson O
    294. Rudan I
    295. Ruth KS
    296. Saleheen D
    297. Salomaa V
    298. Samani NJ
    299. Sapkota Y
    300. Sattar N
    301. Schoen RE
    302. Schreiner PJ
    303. Schulze MB
    304. Scott RA
    305. Segura-Lepe MP
    306. Shah SH
    307. Sheu WH
    308. Sim X
    309. Slater AJ
    310. Small KS
    311. Smith AV
    312. Southam L
    313. Spector TD
    314. Speliotes EK
    315. Starr JM
    316. Stefansson K
    317. Steinthorsdottir V
    318. Stirrups KE
    319. Strauch K
    320. Stringham HM
    321. Stumvoll M
    322. Sun L
    323. Surendran P
    324. Swift AJ
    325. Tada H
    326. Tansey KE
    327. Tardif JC
    328. Taylor KD
    329. Teumer A
    330. Thompson DJ
    331. Thorleifsson G
    332. Thorsteinsdottir U
    333. Thuesen BH
    334. Tönjes A
    335. Tromp G
    336. Trompet S
    337. Tsafantakis E
    338. Tuomilehto J
    339. Tybjaerg-Hansen A
    340. Tyrer JP
    341. Uher R
    342. Uitterlinden AG
    343. Uusitupa M
    344. Laan SW
    345. Duijn CM
    346. Leeuwen N
    347. van Setten J
    348. Vanhala M
    349. Varbo A
    350. Varga TV
    351. Varma R
    352. Velez Edwards DR
    353. Vermeulen SH
    354. Veronesi G
    355. Vestergaard H
    356. Vitart V
    357. Vogt TF
    358. Völker U
    359. Vuckovic D
    360. Wagenknecht LE
    361. Walker M
    362. Wallentin L
    363. Wang F
    364. Wang CA
    365. Wang S
    366. Wang Y
    367. Ware EB
    368. Wareham NJ
    369. Warren HR
    370. Waterworth DM
    371. Wessel J
    372. White HD
    373. Willer CJ
    374. Wilson JG
    375. Witte DR
    376. Wood AR
    377. Wu Y
    378. Yaghootkar H
    379. Yao J
    380. Yao P
    381. Yerges-Armstrong LM
    382. Young R
    383. Zeggini E
    384. Zhan X
    385. Zhang W
    386. Zhao JH
    387. Zhao W
    388. Zhao W
    389. Zhou W
    390. Zondervan KT
    391. Rotter JI
    392. Pospisilik JA
    393. Rivadeneira F
    394. Borecki IB
    395. Deloukas P
    396. Frayling TM
    397. Lettre G
    398. North KE
    399. Lindgren CM
    400. Hirschhorn JN
    401. Loos RJF
    402. CHD Exome+ Consortium
    403. EPIC-CVD Consortium
    404. ExomeBP Consortium
    405. Global Lipids Genetic Consortium
    406. GoT2D Genes Consortium
    407. EPIC InterAct Consortium
    408. INTERVAL Study
    409. ReproGen Consortium
    410. T2D-Genes Consortium
    411. MAGIC Investigators
    412. Understanding Society Scientific Group
    (2018) Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity
    Nature Genetics 50:26–41.
    https://doi.org/10.1038/s41588-017-0011-x
    1. Wood AR
    2. Esko T
    3. Yang J
    4. Vedantam S
    5. Pers TH
    6. Gustafsson S
    7. Chu AY
    8. Estrada K
    9. Luan J
    10. Kutalik Z
    11. Amin N
    12. Buchkovich ML
    13. Croteau-Chonka DC
    14. Day FR
    15. Duan Y
    16. Fall T
    17. Fehrmann R
    18. Ferreira T
    19. Jackson AU
    20. Karjalainen J
    21. Lo KS
    22. Locke AE
    23. Mägi R
    24. Mihailov E
    25. Porcu E
    26. Randall JC
    27. Scherag A
    28. Vinkhuyzen AA
    29. Westra HJ
    30. Winkler TW
    31. Workalemahu T
    32. Zhao JH
    33. Absher D
    34. Albrecht E
    35. Anderson D
    36. Baron J
    37. Beekman M
    38. Demirkan A
    39. Ehret GB
    40. Feenstra B
    41. Feitosa MF
    42. Fischer K
    43. Fraser RM
    44. Goel A
    45. Gong J
    46. Justice AE
    47. Kanoni S
    48. Kleber ME
    49. Kristiansson K
    50. Lim U
    51. Lotay V
    52. Lui JC
    53. Mangino M
    54. Mateo Leach I
    55. Medina-Gomez C
    56. Nalls MA
    57. Nyholt DR
    58. Palmer CD
    59. Pasko D
    60. Pechlivanis S
    61. Prokopenko I
    62. Ried JS
    63. Ripke S
    64. Shungin D
    65. Stancáková A
    66. Strawbridge RJ
    67. Sung YJ
    68. Tanaka T
    69. Teumer A
    70. Trompet S
    71. van der Laan SW
    72. van Setten J
    73. Van Vliet-Ostaptchouk JV
    74. Wang Z
    75. Yengo L
    76. Zhang W
    77. Afzal U
    78. Arnlöv J
    79. Arscott GM
    80. Bandinelli S
    81. Barrett A
    82. Bellis C
    83. Bennett AJ
    84. Berne C
    85. Blüher M
    86. Bolton JL
    87. Böttcher Y
    88. Boyd HA
    89. Bruinenberg M
    90. Buckley BM
    91. Buyske S
    92. Caspersen IH
    93. Chines PS
    94. Clarke R
    95. Claudi-Boehm S
    96. Cooper M
    97. Daw EW
    98. De Jong PA
    99. Deelen J
    100. Delgado G
    101. Denny JC
    102. Dhonukshe-Rutten R
    103. Dimitriou M
    104. Doney AS
    105. Dörr M
    106. Eklund N
    107. Eury E
    108. Folkersen L
    109. Garcia ME
    110. Geller F
    111. Giedraitis V
    112. Go AS
    113. Grallert H
    114. Grammer TB
    115. Gräßler J
    116. Grönberg H
    117. de Groot LC
    118. Groves CJ
    119. Haessler J
    120. Hall P
    121. Haller T
    122. Hallmans G
    123. Hannemann A
    124. Hartman CA
    125. Hassinen M
    126. Hayward C
    127. Heard-Costa NL
    128. Helmer Q
    129. Hemani G
    130. Henders AK
    131. Hillege HL
    132. Hlatky MA
    133. Hoffmann W
    134. Hoffmann P
    135. Holmen O
    136. Houwing-Duistermaat JJ
    137. Illig T
    138. Isaacs A
    139. James AL
    140. Jeff J
    141. Johansen B
    142. Johansson Å
    143. Jolley J
    144. Juliusdottir T
    145. Junttila J
    146. Kho AN
    147. Kinnunen L
    148. Klopp N
    149. Kocher T
    150. Kratzer W
    151. Lichtner P
    152. Lind L
    153. Lindström J
    154. Lobbens S
    155. Lorentzon M
    156. Lu Y
    157. Lyssenko V
    158. Magnusson PK
    159. Mahajan A
    160. Maillard M
    161. McArdle WL
    162. McKenzie CA
    163. McLachlan S
    164. McLaren PJ
    165. Menni C
    166. Merger S
    167. Milani L
    168. Moayyeri A
    169. Monda KL
    170. Morken MA
    171. Müller G
    172. Müller-Nurasyid M
    173. Musk AW
    174. Narisu N
    175. Nauck M
    176. Nolte IM
    177. Nöthen MM
    178. Oozageer L
    179. Pilz S
    180. Rayner NW
    181. Renstrom F
    182. Robertson NR
    183. Rose LM
    184. Roussel R
    185. Sanna S
    186. Scharnagl H
    187. Scholtens S
    188. Schumacher FR
    189. Schunkert H
    190. Scott RA
    191. Sehmi J
    192. Seufferlein T
    193. Shi J
    194. Silventoinen K
    195. Smit JH
    196. Smith AV
    197. Smolonska J
    198. Stanton AV
    199. Stirrups K
    200. Stott DJ
    201. Stringham HM
    202. Sundström J
    203. Swertz MA
    204. Syvänen AC
    205. Tayo BO
    206. Thorleifsson G
    207. Tyrer JP
    208. van Dijk S
    209. van Schoor NM
    210. van der Velde N
    211. van Heemst D
    212. van Oort FV
    213. Vermeulen SH
    214. Verweij N
    215. Vonk JM
    216. Waite LL
    217. Waldenberger M
    218. Wennauer R
    219. Wilkens LR
    220. Willenborg C
    221. Wilsgaard T
    222. Wojczynski MK
    223. Wong A
    224. Wright AF
    225. Zhang Q
    226. Arveiler D
    227. Bakker SJ
    228. Beilby J
    229. Bergman RN
    230. Bergmann S
    231. Biffar R
    232. Blangero J
    233. Boomsma DI
    234. Bornstein SR
    235. Bovet P
    236. Brambilla P
    237. Brown MJ
    238. Campbell H
    239. Caulfield MJ
    240. Chakravarti A
    241. Collins R
    242. Collins FS
    243. Crawford DC
    244. Cupples LA
    245. Danesh J
    246. de Faire U
    247. den Ruijter HM
    248. Erbel R
    249. Erdmann J
    250. Eriksson JG
    251. Farrall M
    252. Ferrannini E
    253. Ferrières J
    254. Ford I
    255. Forouhi NG
    256. Forrester T
    257. Gansevoort RT
    258. Gejman PV
    259. Gieger C
    260. Golay A
    261. Gottesman O
    262. Gudnason V
    263. Gyllensten U
    264. Haas DW
    265. Hall AS
    266. Harris TB
    267. Hattersley AT
    268. Heath AC
    269. Hengstenberg C
    270. Hicks AA
    271. Hindorff LA
    272. Hingorani AD
    273. Hofman A
    274. Hovingh GK
    275. Humphries SE
    276. Hunt SC
    277. Hypponen E
    278. Jacobs KB
    279. Jarvelin MR
    280. Jousilahti P
    281. Jula AM
    282. Kaprio J
    283. Kastelein JJ
    284. Kayser M
    285. Kee F
    286. Keinanen-Kiukaanniemi SM
    287. Kiemeney LA
    288. Kooner JS
    289. Kooperberg C
    290. Koskinen S
    291. Kovacs P
    292. Kraja AT
    293. Kumari M
    294. Kuusisto J
    295. Lakka TA
    296. Langenberg C
    297. Le Marchand L
    298. Lehtimäki T
    299. Lupoli S
    300. Madden PA
    301. Männistö S
    302. Manunta P
    303. Marette A
    304. Matise TC
    305. McKnight B
    306. Meitinger T
    307. Moll FL
    308. Montgomery GW
    309. Morris AD
    310. Morris AP
    311. Murray JC
    312. Nelis M
    313. Ohlsson C
    314. Oldehinkel AJ
    315. Ong KK
    316. Ouwehand WH
    317. Pasterkamp G
    318. Peters A
    319. Pramstaller PP
    320. Price JF
    321. Qi L
    322. Raitakari OT
    323. Rankinen T
    324. Rao DC
    325. Rice TK
    326. Ritchie M
    327. Rudan I
    328. Salomaa V
    329. Samani NJ
    330. Saramies J
    331. Sarzynski MA
    332. Schwarz PE
    333. Sebert S
    334. Sever P
    335. Shuldiner AR
    336. Sinisalo J
    337. Steinthorsdottir V
    338. Stolk RP
    339. Tardif JC
    340. Tönjes A
    341. Tremblay A
    342. Tremoli E
    343. Virtamo J
    344. Vohl MC
    345. Amouyel P
    346. Asselbergs FW
    347. Assimes TL
    348. Bochud M
    349. Boehm BO
    350. Boerwinkle E
    351. Bottinger EP
    352. Bouchard C
    353. Cauchi S
    354. Chambers JC
    355. Chanock SJ
    356. Cooper RS
    357. de Bakker PI
    358. Dedoussis G
    359. Ferrucci L
    360. Franks PW
    361. Froguel P
    362. Groop LC
    363. Haiman CA
    364. Hamsten A
    365. Hayes MG
    366. Hui J
    367. Hunter DJ
    368. Hveem K
    369. Jukema JW
    370. Kaplan RC
    371. Kivimaki M
    372. Kuh D
    373. Laakso M
    374. Liu Y
    375. Martin NG
    376. März W
    377. Melbye M
    378. Moebus S
    379. Munroe PB
    380. Njølstad I
    381. Oostra BA
    382. Palmer CN
    383. Pedersen NL
    384. Perola M
    385. Pérusse L
    386. Peters U
    387. Powell JE
    388. Power C
    389. Quertermous T
    390. Rauramaa R
    391. Reinmaa E
    392. Ridker PM
    393. Rivadeneira F
    394. Rotter JI
    395. Saaristo TE
    396. Saleheen D
    397. Schlessinger D
    398. Slagboom PE
    399. Snieder H
    400. Spector TD
    401. Strauch K
    402. Stumvoll M
    403. Tuomilehto J
    404. Uusitupa M
    405. van der Harst P
    406. Völzke H
    407. Walker M
    408. Wareham NJ
    409. Watkins H
    410. Wichmann HE
    411. Wilson JF
    412. Zanen P
    413. Deloukas P
    414. Heid IM
    415. Lindgren CM
    416. Mohlke KL
    417. Speliotes EK
    418. Thorsteinsdottir U
    419. Barroso I
    420. Fox CS
    421. North KE
    422. Strachan DP
    423. Beckmann JS
    424. Berndt SI
    425. Boehnke M
    426. Borecki IB
    427. McCarthy MI
    428. Metspalu A
    429. Stefansson K
    430. Uitterlinden AG
    431. van Duijn CM
    432. Franke L
    433. Willer CJ
    434. Price AL
    435. Lettre G
    436. Loos RJ
    437. Weedon MN
    438. Ingelsson E
    439. O'Connell JR
    440. Abecasis GR
    441. Chasman DI
    442. Goddard ME
    443. Visscher PM
    444. Hirschhorn JN
    445. Frayling TM
    446. Electronic Medical Records and Genomics (eMEMERGEGE) Consortium
    447. MIGen Consortium
    448. PAGEGE Consortium
    449. LifeLines Cohort Study
    (2014) Defining the role of common variation in the genomic and biological architecture of adult human height
    Nature Genetics 46:1173–1186.
    https://doi.org/10.1038/ng.3097

Article and author information

Author details

  1. Reza K Hammond

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Conceptualization, Data curation, Software, Formal analysis, Validation, Investigation, Methodology, Writing - original draft, Writing - review and editing
    Competing interests
    No competing interests declared

  2. Matthew C Pahl

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Formal analysis, Investigation, Writing - review and editing
    Competing interests
    No competing interests declared

  3. Chun Su

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Investigation, Writing - review and editing
    Competing interests
    No competing interests declared

  4. Diana L Cousminer

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Investigation, Writing - review and editing
    Competing interests
    No competing interests declared

  5. Michelle E Leonard

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Data curation, Writing - review and editing
    Competing interests
    No competing interests declared

  6. Sumei Lu

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Data curation, Writing - review and editing
    Competing interests
    No competing interests declared

  7. Claudia A Doege

    1. Naomi Berrie Diabetes Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, United States
    2. Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, United States
    3. Columbia Stem Cell Initiative, Vagelos College of Physicians and Surgeons, Columbia University, New York, United States
    Contribution
    Resources, Writing - review and editing
    Competing interests
    No competing interests declared

  8. Yadav Wagley

    Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, United States
    Contribution
    Writing - review and editing
    Competing interests
    No competing interests declared

  9. Kenyaita M Hodge

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Data curation, Writing - review and editing
    Competing interests
    No competing interests declared

  10. Chiara Lasconi

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Data curation, Writing - review and editing
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4684-704X

  11. Matthew E Johnson

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Data curation, Writing - review and editing
    Competing interests
    No competing interests declared

  12. James A Pippin

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Data curation, Writing - review and editing
    Competing interests
    No competing interests declared

  13. Kurt D Hankenson

    Department of Orthopaedic Surgery, University of Michigan Medical School, Ann Arbor, United States
    Contribution
    Writing - review and editing
    Competing interests
    No competing interests declared

  14. Rudolph L Leibel

    Division of Molecular Genetics (Pediatrics) and the Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, United States
    Contribution
    Writing - review and editing
    Competing interests
    No competing interests declared

  15. Alessandra Chesi

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Formal analysis, Investigation, Writing - review and editing
    Competing interests
    No competing interests declared

  16. Andrew D Wells

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Department of Pathology, The Children’s Hospital of Philadelphia, Philadelphia, United States
    3. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
    Contribution
    Investigation, Writing - review and editing
    Competing interests
    No competing interests declared

  17. Struan FA Grant

    1. Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, United States
    2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, United States
    3. Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
    4. Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
    5. Division of Diabetes and Endocrinology, The Children’s Hospital of Philadelphia, Philadelphia, United States
    Contribution
    Conceptualization, Supervision, Investigation, Writing - original draft, Project administration, Writing - review and editing
    For correspondence
    grants@email.chop.edu
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2025-5302

Funding

Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01-HD056465)

  • Struan FA Grant

National Human Genome Research Institute (R01-HG010067)

  • Struan FA Grant

Children's Hospital of Philadelphia (Daniel B. Burke Endowed Chair for Diabetes Research)

  • Struan FA Grant

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Version history

  1. Received: August 18, 2020
  2. Accepted: January 8, 2021
  3. Accepted Manuscript published: January 18, 2021 (version 1)
  4. Version of Record published: January 18, 2021 (version 2)

Copyright

© 2021, Hammond et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,586
    views
  • 192
    downloads
  • 28
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Reza K Hammond
  2. Matthew C Pahl
  3. Chun Su
  4. Diana L Cousminer
  5. Michelle E Leonard
  6. Sumei Lu
  7. Claudia A Doege
  8. Yadav Wagley
  9. Kenyaita M Hodge
  10. Chiara Lasconi
  11. Matthew E Johnson
  12. James A Pippin
  13. Kurt D Hankenson
  14. Rudolph L Leibel
  15. Alessandra Chesi
  16. Andrew D Wells
  17. Struan FA Grant
(2021)
Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci
eLife 10:e62206.
https://doi.org/10.7554/eLife.62206

Share this article

https://doi.org/10.7554/eLife.62206

Categories and tags

Research organism

Further reading

    1. Computational and Systems Biology
    2. Developmental Biology

    A logic-incorporated gene regulatory network deciphers principles in cell fate decisions

    Gang Xue, Xiaoyi Zhang ... Zhiyuan Li
    Research Article

    Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding question in this field is how these tangled interactions synergistically contribute to decision-making procedures. To comprehensively understand the role of regulatory logic in cell fate decisions, we constructed a logic-incorporated GRN model and examined its behavior under two distinct driving forces (noise-driven and signal-driven). Under the noise-driven mode, we distilled the relationship among fate bias, regulatory logic, and noise profile. Under the signal-driven mode, we bridged regulatory logic and progression-accuracy trade-off, and uncovered distinctive trajectories of reprogramming influenced by logic motifs. In differentiation, we characterized a special logic-dependent priming stage by the solution landscape. Finally, we applied our findings to decipher three biological instances: hematopoiesis, embryogenesis, and trans-differentiation. Orthogonal to the classical analysis of expression profile, we harnessed noise patterns to construct the GRN corresponding to fate transition. Our work presents a generalizable framework for top-down fate-decision studies and a practical approach to the taxonomy of cell fate decisions.

    1. Computational and Systems Biology
    2. Genetics and Genomics

    Haplotype function score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

    Weichen Song, Yongyong Shi, Guan Ning Lin
    Tools and Resources

    We propose a new framework for human genetic association studies: at each locus, a deep learning model (in this study, Sei) is used to calculate the functional genomic activity score for two haplotypes per individual. This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3619 independent HFS–trait associations with a significance of p < 5 × 10−8. Fine-mapping revealed 2699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with single-nucleotide polymorphism (SNP)-based analysis. HFS-based enrichment analysis uncovered 727 pathway–trait associations and 153 tissue–trait associations with strong biological interpretability, including ‘circadian pathway-chronotype’ and ‘arachidonic acid-intelligence’. Lastly, we applied least absolute shrinkage and selection operator (LASSO) regression to integrate HFS prediction score with SNP-based polygenic risk scores, which showed an improvement of 16.1–39.8% in cross-ancestry polygenic prediction. We concluded that HFS is a promising strategy for understanding the genetic basis of human complex traits.

    1. Computational and Systems Biology

    Genome-scale annotation of protein binding sites via language model and geometric deep learning

    Qianmu Yuan, Chong Tian, Yuedong Yang
    Tools and Resources

    Revealing protein binding sites with other molecules, such as nucleic acids, peptides, or small ligands, sheds light on disease mechanism elucidation and novel drug design. With the explosive growth of proteins in sequence databases, how to accurately and efficiently identify these binding sites from sequences becomes essential. However, current methods mostly rely on expensive multiple sequence alignments or experimental protein structures, limiting their genome-scale applications. Besides, these methods haven’t fully explored the geometry of the protein structures. Here, we propose GPSite, a multi-task network for simultaneously predicting binding residues of DNA, RNA, peptide, protein, ATP, HEM, and metal ions on proteins. GPSite was trained on informative sequence embeddings and predicted structures from protein language models, while comprehensively extracting residual and relational geometric contexts in an end-to-end manner. Experiments demonstrate that GPSite substantially surpasses state-of-the-art sequence-based and structure-based approaches on various benchmark datasets, even when the structures are not well-predicted. The low computational cost of GPSite enables rapid genome-scale binding residue annotations for over 568,000 sequences, providing opportunities to unveil unexplored associations of binding sites with molecular functions, biological processes, and genetic variants. The GPSite webserver and annotation database can be freely accessed at https://bio-web1.nscc-gz.cn/app/GPSite.