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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
.... The EN-TEx resource of multi-tissue personal epis & variant-impact models. Cell 186: 1493–1511.e40. doi:10.1016/j.cell.2023.02.018 ↵Rubinacci S, Hofmeister RJ, Sousa da Mota B, Delaneau O. 2023. Imputation of low-coverage sequencing data from 150,119 UK Biobank s. Nat Genet 55: 1088–1090. doi:10.1038/s...
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Resource: Low-coverage sequencing: Implications for design of complex trait association studies
- Yun Li,
- Carlo Sidore,
- Hyun Min Kang,
- Michael Boehnke,
- and Gonçalo R. Abecasis
Genome Res. June 2011 21: 940-951; Published in Advance April 1, 2011, doi:10.1101/gr.117259.110
...systematically compare study designs based on genotyping of tagSNPs, sequencing of many individuals at depths ranging between 23 and 303 and imputation of variants discovered by sequencing in a subset of individuals into the remainder of the sample. Our results show that low-coverage sequencing provides...
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Method: An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
- Yi Wang,
- James Lu,
- Jin Yu,
- Richard A. Gibbs,
- and Fuli Yu
Genome Res. May 2013 23: 833-842; Published in Advance January 7, 2013, doi:10.1101/gr.146084.112
...and genotyping of population SNPs. We herein provide an integrative pipeline, SNPTools, that applies novel algorithms to detect, impute, and phase SNPs. It has achieved high sensitivity and specificity from low-coverage, whole- sequencing in the 1000G data set. We have designed our pipeline to be flexible...
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Method: Genotype calling and haplotyping in parent-offspring trios
- Wei Chen,
- Bingshan Li,
- Zhen Zeng,
- Serena Sanna,
- Carlo Sidore,
- Fabio Busonero,
- Hyun Min Kang,
- Yun Li,
- and Gonçalo R. Abecasis
Genome Res. January 2013 23: 142-151; Published in Advance October 11, 2012, doi:10.1101/gr.142455.112
...analyses (such as genotype imputation) that rely on phased haplotypes. To further evaluate our approach, we analyzed data on the first 508 individuals sequenced by the SardiNIA sequencing project. Our results show that our method reduces the genotyping error rate by 50% compared with analysis using...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...face validity to construct validity and improve translational relevance. In addition to the biomedical implications, knowledge of intraspecies genetic variation in this widely distributed primate will inform analyses of the ecological, demographic, and population genetic factors that drive differences...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
..., and Arabidopsis. Before the availability of such data, several -wide studies have been completed using Sanger sequencing (e.g., Bustamante et al. 2005; Begun et al. 2007) or SNP genotyping (Hinds et al. 2005; The International HapMap Consortium 2005, 2007; Jakobsson et al. 2008; JZ Li et al. 2008). The low-coverage...
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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. March 5, 2026 gr.280989.125; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
...and HET calls. For single-nucleotide variants (SNVs), both imputation methods performed comparably across all coverage levels, with each achieving F1 scores above 0.9 even at low coverage. For indel variants, a similar pattern was observed, though Beagle showed slightly higher F1 scores at higher...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...sequencing in a natural population (the “ Drosophila melanogaster Genetic Reference Panel,” DGRP). Most SVs (&gt;90%) were inferred at nucleotide resolution, and a large fraction was genotyped across all samples. Comprehensive analyses of SV formation mechanisms using the short-read data revealed...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...restrictive permissions, the 1kGP and HGDP s remain the most uniquely valuable resources for many of the most common genetic analyses. These include genetic simulations, ancestry analysis including local ancestry inference (Maples et al. 2013), genotype refinement of low-coverage s (Rubinacci et al. 2021...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...), most recent analyses are consistent with a dual origin of domestication from east and west Eurasia that continues to shape the population structure of modern dogs today (Bergström et al. 2022).Breed-associated differences in morphology and behavior have garnered particular interest and are often...
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