ArticleAmerican journal of human genetics2017
Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy.
Article in American journal of human genetics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 169 papers, 3 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
169 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases.Nature communications · 2025Pooled it
- Fetal genetic factors in pregnancy loss: Insights from a meta-analysis and effectiveness of whole exome sequencing.PloS one · 2025Pooled it
- Pooled it
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- The landscape of allele-specific expression in human kidneys.Science advances · 2026Article
- Overlapping genetic etiology of pediatric and adult germ cell tumors.Journal of the National Cancer Institute · 2026Article
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- Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns.medRxiv : the preprint server for health sciences · 2026Article
- Analysis of whole genome sequencing and plasma metabolomics unveil genetic determinants and clinical implications for human health.Nature communications · 2026Article
- Search for the most precise diagnosis of monogenic diabetes - the usefulness of short-read NGS method in molecular testing in Polish patients.Acta diabetologica · 2026Article
- Rare protein-disrupting variants inmedRxiv : the preprint server for health sciences · 2026Article
- Variants in the ciliopathy gene SCLT1 are associated with non-syndromic and syndromic retinal degeneration of variable severity.NPJ genomic medicine · 2026Article
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- Joint Biochemical and Genetic Prostate Cancer Risk Stratification.The Journal of urology · 2026Article
- Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity in autism spectrum disorder.Genome biology · 2026Article
- Genetic diversity of infertile males in India.Journal of assisted reproduction and genetics · 2026Article
- Generalisability of Maternal Genetic Risk Score for Birth Weight Across Racial Identity and Ancestry: A Secondary Analysis of a Prospective Cohort Study.BJOG : an international journal of obstetrics and gynaecology · 2026Observational
- Identification of autosomal and sex chromosome aneuploidies using next generation sequencing.Bioinformatics (Oxford, England) · 2026Article
- Rare heterozygous missense variants in VSX2 are associated with retinal detachment.PLoS genetics · 2026Article
- Further Personalizing Medicine in Immune Disorders: Genomic Findings and Hematopoietic Cell Transplantation Survival.Transplantation · 2026Article
109 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.