Rapid re-identification of human samples using portable DNA sequencing
- New York Genome Center, United States
- Columbia University, United States
- New York University, United States
Figures
Figure 1
Schematic overview of MinION sketching.
A DNA sample is prepared for shotgun sequencing. Libraries are prepared either for 1D or 2D MinION sequencing (without and with hairpin, respectively). Variants observed in aligned MinION reads are …
Figure 2 with 1 supplement
Re-identification of three DNA samples against a database with 31,000 individuals.
(A) A Frappe plot showing the population structure of the database with a collection of 31,000 genome-wide SNP arrays. (B–D) The match probability is inferred by comparing a MinION sketch to its …
Figure 2—figure supplement 1
A prior representing a database larger than the world population still allows for identification power.
The match probability is inferred by comparing a MinION sketch of YE001 to its reference file as a function of the MinION sketching time. The prior probability for a match was modified as indicated.
Figure 3
Re-identification of HapMap sample NA12890.
The match probability is inferred by comparing a MinION sketch of NA12890 to the reference files of her own genome (red), her son’s genome (black), and her granddaughter’s genome (purple), as a …
Figure 4 with 1 supplement
Cell line authentication.
Barcoded DNA from the THP1 cell line is mixed 1:1 with a random, barcoded sample. Analysis of only the THP1 reads was used to infer ‘pure’ matches, while analyses of the mixture were used to …
Figure 4—figure supplement 1
Cell line authentication.
(A) 10,000 simulated runs of sketching SZ001 were matched against its reference file. The number of SNPs used to reach a 99.9% match is depicted in a histogram. (B) The number of mismatches …
Figure 5 with 1 supplement
Contamination simulations.
Random reads from a run with DNA from THP1 cells and a random, barcoded sample (the contaminant) are mixed in the indicated proportions and shuffled. This simulated MinION sketch is matched against …
Figure 5—figure supplement 1
Theoretical effect of differences in doubling time of contaminants in a cell culture.
We set the doubling time of our cell line of interest to 24 hr. We hypothesized that our culture (with a starting number of 106 cells) would be contaminated with 10 foreign cells. We considered a …
Figure 6 with 1 supplement
Rapid library preparation.
(A) Schematic of the steps from sample to MinION sketch. The current method requires ~55 min until the MinION starts to generate reads. (B) The match probability is inferred by comparing a MinION …
Figure 6—video 1
The movie depicts the rapid, on-site library preparation protocol using the Bento Lab (www.bento.bio) for DNA extraction and library preparation, prior to starting DNA sequencing as described in Figure 6.
https://doi.org/10.7554/eLife.27798.013Tables
Table 1
List of databases consulted and restrictions to access.
https://doi.org/10.7554/eLife.27798.006| Databases: | Restrictions to access | Dataset URL: |
|---|---|---|
| Opensnp.org | No | https://opensnp.org/ |
| HapMap* | No. The HapMap dataset has been discontinued (https://www.ncbi.nlm.nih.gov/variation/news/NCBI_retiring_HapMap/) and the archived HapMap data is available via FTP from ftp://ftp.ncbi.nlm.nih.gov/hapmap/. The relevant files used for this study have been downloaded from the latter in 2015. | http://www.completegenomics.com/documents/PublicGenomes.pdf and ftp://ftp.ncbi.nlm.nih.gov/hapmap/ |
| DNA.land | Yes. The 29,554 genomes provided by DNA.land are not available for distribution to ensure genomic privacy of the individuals who donated their genomes to DNA.land | https://dna.land/ |
| CCLE† | Yes. Public access is available by registration. The data made available on the Encyclopedia is for internal research purposes, as specified in CCLE Terms of Access (https://portals.broadinstitute.org/ccle/about). The SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE) is available on GEO under accession number GSE36139. | https://portals.broadinstitute.org/ccle/ and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36139 |
Additional files
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Supplementary file 1
Supplementary Tables.
Run statistics for the MinION sketch experiments.
- https://doi.org/10.7554/eLife.27798.014
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Transparent reporting form
- https://doi.org/10.7554/eLife.27798.015
