Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy
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Abstract
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs, or scientists in the process of sequencing. We have developed a software package, peddy, to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing. Peddy predicts a sample's ancestry using a machine learning model trained on individuals of diverse ancestries from the 1000 Genomes Project reference panel. Peddy facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems that, if left undetected, would inhibit discovery.
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They identified participants with European genetic ancestry based on Peddy Pr(EUR) > 0.98 (n = 46,441).
“We identified the participants with European genetic ancestry based on Peddy60 Pr(EUR) > 0.98 (n = 46,441).”
From Rare variant associations with plasma protein levels in the UK Biobank (2023) · cites this paper as [60]
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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works
Flagged first, then by citations
Research works printed but not linked: 11
- [2]Miller C.A. Qiao Y. DiSera T. D’Astous B. Marth G.T. bam.iobio: a web-based, real-time, sequence alignment file inspector Nat. Methods 11 2014 1189 25423016 PMC4282680
- [3]Li H. Handsaker B. Wysoker A. Fennell T. Ruan J. Homer N. Marth G. Abecasis G. Durbin R. 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079 19505943 PMC2723002
- [4]Manichaikul A. Mychaleckyj J.C. Rich S.S. Daly K. Sale M. Chen W.-M. Robust relationship inference in genome-wide association studies Bioinformatics 26 2010 2867 2873 20926424 PMC3025716
- [5]Heinrich V. Kamphans T. Mundlos S. Robinson P.N. Krawitz P.M. A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data Bioinformatics 33 2017 72 78 27565584 PMC5408770
- [6]Staples J. Ekunwe L. Lange E. Wilson J.G. Nickerson D.A. Below J.E. PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes Bioinformatics 32 2016 596 598 26515822 PMC5963362
- [7]Danecek P. Auton A. Abecasis G. Albers C.A. Banks E. DePristo M.A. Handsaker R.E. Lunter G. Marth G.T. Sherry S.T. 1000 Genomes Project Analysis Group The variant call format and VCFtools Bioinformatics 27 2011 2156 2158 21653522 PMC3137218
- [8]Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files Bioinformatics 27 2011 718 719 21208982 PMC3042176
- [9]Eberle, M.A., Fritzilas, E., Krusche, P., Kallberg, M., Moore, B.L., Bekritsky, M.A., Iqbal, Z., Chuang, H.-Y., Humphray, S.J., Halpern, A.L., et al. (2016). A reference dataset of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. bioRxiv. http://biorxiv.org/lookup/doi/10.1101/055541. PMC5204340 27903644 · DOI
- [10]Blue E.M. Brown L.A. Conomos M.P. Kirk J.L. Nato A.Q. Popejoy A.B. Raffa J. Ranola J. Wijsman E.M. Thornton T. Estimating relationships between phenotypes and subjects drawn from admixed families BMC Proc. 10 2016 357 362 27980662 PMC5133521
- [11]Halko, N., Martinsson, P.-G., and Tropp, J.A. (2009). Finding structure with randomness: Probabilistic algorithms for constructing approximate matrix decompositions arXiv [math.NA]. http://arxiv.org/abs/0909.4061. · arXiv
- [13]Boada R. Janusz J. Hutaff-Lee C. Tartaglia N. The cognitive phenotype in Klinefelter syndrome: a review of the literature including genetic and hormonal factors Dev. Disabil. Res. Rev. 15 2009 284 294 20014369 PMC3056507
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Lemmelä, S., Wigmore, E. M., Benner, C., Havulinna, A. S., Ong, R. M., Kempf, T., Wollert, K. C., Blankenberg, S., Zeller, T., Peters, J. E., et al. (2022) · eLife · doi:10.7554/elife.76272 · Cited by 28 · see citing works
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- Authors
- Pedersen, B. S., & Quinlan, A. R.
- Affiliations
- University of Utah (US)
- Corresponding author
- Quinlan, Aaron R.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2017-03
- Volume
- 100
- Issue
- 3
- Pages
- 406-413
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC5339084
- OpenAlex
- W2586994065
- Cited by
- 237
- References
- 2
- Citations by year
- 2026: 22 · 2025: 31 · 2024: 42 · 2023: 30 · 2022: 27 · 2021: 33 · 2020: 24 · 2019: 17 · 2018: 9 · 2017: 2
- FWCI
- 9.22
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- US National Human Genome Research Institute (NIH R01HG006693)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- DNA contamination, sample quality control, ancestry inference, sex determination, relatedness inference, whole genome sequencing, exome sequencing, 1000 Genomes Project
- MeSH terms
- Machine Learning, Female, Genotype, Humans, Male, Pedigree, Software, Genome, Human, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Chromosomes, Human, X, Genetic Loci, Genetic Association Studies, Exome
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