ArticlePloS one2014
A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.NAR genomics and bioinformatics · 2026Article
- Prevalence and clinical implications of germline pathogenic variants in cancer predisposing genes in young patients across sarcoma subtypes.Journal of medical genetics · 2023Article
- Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants.Genome medicine · 2023Article
- Rare deleterious germline variants and risk of lung cancer.NPJ precision oncology · 2021Article
- Rapid, large-scale, and effective detection of COVID-19 via non-adaptive testing.Journal of theoretical biology · 2020Article
- Heterozygous rare genetic variants in non-syndromic early-onset obesity.International journal of obesity (2005) · 2020Article
- Article
- Investigation of Leukocyte Telomere Length and Genetic Variants in Chromosome 5p15.33 as Prognostic Markers in Lung Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2019Article
- Fine Mapping in Chromosome 3q28 Identified Two Variants Associated with Lung Cancer Risk in Asian Population.Journal of Cancer · 2019Article
- Decoding the chromatin proteome of a single genomic locus by DNA sequencing.PLoS biology · 2018Article
- Fine mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci.Carcinogenesis · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a method for pooling and sequencing DNA from a large number of individual samples while preserving information regarding sample identity. DNA from 576 individuals was arranged into four 12 row by 12 column matrices and then pooled by row and by column resulting in 96 total pools with 12 individuals in each pool. Pooling of DNA was carried out in a two-dimensional fashion, such that DNA from each individual is present in exactly one row pool and exactly one column pool. By considering the variants observed in the rows and columns of a matrix we are able to trace rare variants back to the specific individuals that carry them. The pooled DNA samples were enriched over a 250 kb region previously identified by GWAS to significantly predispose individuals to lung cancer. All 96 pools (12 row and 12 column pools from 4 matrices) were barcoded and sequenced on an Illumina HiSeq 2000 instrument with an average depth of coverage greater than 4,000×. Verification based on Ion PGM sequencing confirmed the presence of 91.4% of confidently classified SNVs assayed. In this way, each individual sample is sequenced in multiple pools providing more accurate variant calling than a single pool or a multiplexed approach. This provides a powerful method for rare variant detection in regions of interest at a reduced cost to the researcher.
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