ArticleHuman genetics2018
High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation.
Article in Human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras.Genomics, proteomics & bioinformatics · 2025Review
- Genome wide association study and genomic risk prediction of age related macular degeneration in Israel.Scientific reports · 2024Article
- Imputation accuracy across global human populations.American journal of human genetics · 2024Article
- The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population.Bioinformatics (Oxford, England) · 2024Article
- Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14Cell · 2022Article
- SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2022Article
- Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia.Neuron · 2021Article
- IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes.Nucleic acids research · 2021Article
- Welfare Genome Project: A Participatory Korean Personal Genome Project With Free Health Check-Up and Genetic Report Followed by Counseling.Frontiers in genetics · 2021Article
- Similar burden of pathogenic coding variants in exceptionally long-lived individuals and individuals without exceptional longevity.Aging cell · 2020Article
- Sequencing and imputation in GWAS: Cost-effective strategies to increase power and genomic coverage across diverse populations.Genetic epidemiology · 2020Article
- Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling.Genetics, selection, evolution : GSE · 2020Article
- Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations.Genetics, selection, evolution : GSE · 2020Article
- Preconception carrier screening yield: effect of variants of unknown significance in partners of carriers with clinically significant variants.Genetics in medicine : official journal of the American College of Medical Genetics · 2020Article
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- Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications.Journal of assisted reproduction and genetics · 2019Article
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Corrections and comments
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Authors and funding
20 authors.
Funding
Abstract
While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. Here, we sequenced at full-depth (≥ 30×), across two platforms (Illumina X Ten and Complete Genomics, Inc.), a moderately large (n = 738) cohort of samples drawn from the Ashkenazi Jewish population. We developed a series of quality control steps to optimize sensitivity, specificity, and comprehensiveness of variant calls in the reference panel, and then tested the accuracy of imputation against target cohorts drawn from the same population. Quality control (QC) thresholds for the Illumina X Ten platform were identified that permitted highly accurate calling of single nucleotide variants across 94% of the genome. QC procedures also identified numerous regions that are poorly mapped using current reference or alternate assemblies. After stringent QC, the population-specific reference panel produced more accurate and comprehensive imputation results relative to publicly available, large cosmopolitan reference panels, especially in the range of rare variants that may be most critical to further progress in mapping of complex phenotypes. The population-specific reference panel also permitted enhanced filtering of clinically irrelevant variants from personal genomes.
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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.