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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...the sensitivity of structural variant (SV) discovery by ∼threefold by providing access to repetitive regions of s typically masked or excluded as part of short-read sequencing analyses (Chaisson et al. 2015, 2019; Audano et al. 2019) and by providing breakpoint resolution of variants previously inferred...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...Consortium (ICGC) (Zhang et al. 2019), and the Pan-Cancer Analysis of Whole Genomes (PCAWG) project (The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020) to characterize thousands of cancers across dozens of cancer types. Building on these population-scale efforts, the Catalogue Of Somatic...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...-read high-throughput sequencing (HTS) technologies, studies have revealed that somatic SVs can drive malignant phenotypes by altering the expression or function of oncogenes (The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020; Cosenza et al. 2022). Additionally, certain somatic SVs within...
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Research: Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia
- Xiao Gou,
- Zhen Wang,
- Ning Li,
- Feng Qiu,
- Ze Xu,
- Dawei Yan,
- Shuli Yang,
- Jia Jia,
- Xiaoyan Kong,
- Zehui Wei,
- Shaoxiong Lu,
- Linsheng Lian,
- Changxin Wu,
- Xueyan Wang,
- Guozhi Li,
- Teng Ma,
- Qiang Jiang,
- Xue Zhao,
- Jiaqiang Yang,
- Baohong Liu,
- Dongkai Wei,
- Hong Li,
- Jianfa Yang,
- Yulin Yan,
- Guiying Zhao,
- Xinxing Dong,
- Mingli Li,
- Weidong Deng,
- Jing Leng,
- Chaochun Wei,
- Chuan Wang,
- Huaming Mao,
- Hao Zhang,
- Guohui Ding,
- and Yixue Li
Genome Res. August 2014 24: 1308-1315; Published in Advance April 10, 2014, doi:10.1101/gr.171876.113
...to a starchrich diet. Nature 495: 360–364. Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37–48. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263–265. Beall CM...
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Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
- PingHsun Hsieh,
- August E. Woerner,
- Jeffrey D. Wall,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Ryan N. Gutenkunst,
- and Michael F. Hammer
Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
...history of the genus Homo . Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing model...
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Research: Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
- PingHsun Hsieh,
- Krishna R. Veeramah,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Jeffrey D. Wall,
- Michael F. Hammer,
- and Ryan N. Gutenkunst
Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115
...Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection PingHsun Hsieh 1 , Krishna R. Veeramah 2 , 3 , Joseph Lachance 4 , 5...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
...Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance Tim Downing 1 , 10 , Hideo Imamura 2 , 10 , Saskia Decuypere 2 , Taane G. Clark 3...
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PERSPECTIVE: Determinants of the success of whole-genome association testing
- Andrew G. Clark,
- Eric Boerwinkle,
- James Hixson,
- and Charles F. Sing
Genome Res. November 2005 15: 1463-1467; doi:10.1101/gr.4244005
...an impact on the efficacy of HapMap for providing guidelines for whole- association testing can be summarized as follows: 1. What is the population of inference? The first design issue in any study of complex disorders is to identify and characterize the population about which inferences are sought. Most...
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Method: An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data
- Goo Jun,
- Mary Kate Wing,
- Gonçalo R. Abecasis,
- and Hyun Min Kang
Genome Res. June 2015 25: 918-925; Published in Advance April 16, 2015, doi:10.1101/gr.176552.114
...alternatives. Experiments with whole-genome and exome-targeted sequence data generated by the 1000 Genomes Project show that the pipeline provides effective filtering against false positive variants and high power to detect true variants. Our pipeline has already contributed to variant detection and genotyping...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C...

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