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Method: Identifying crossovers and shared genetic material in whole genome sequencing data from families
- Kelley Paskov,
- Brianna Chrisman,
- Nathaniel Stockham,
- Peter Yigitcan Washington,
- Kaitlyn Dunlap,
- Jae-Yoon Jung,
- and Dennis P. Wall
Genome Res. October 2023 33: 1747-1756; Published in Advance October 25, 2023, doi:10.1101/gr.277172.122
..., as well as shared genetic material in families. In fact, using genetic data from families is one of the only ways to identify individual crossover events. We provide an open-source tool to identify these events in any type of genetic data, including microarray or high-throughput sequencing data...
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Research: Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia
- Sanchita Bhattacharya,
- Jian Li,
- Alexandra Sockell,
- Matthew J. Kan,
- Felice A. Bava,
- Shann-Ching Chen,
- María C. Ávila-Arcos,
- Xuhuai Ji,
- Emery Smith,
- Narges B. Asadi,
- Ralph S. Lachman,
- Hugo Y.K. Lam,
- Carlos D. Bustamante,
- Atul J. Butte,
- and Garry P. Nolan
Genome Res. April 2018 28: 423-431; Published in Advance March 22, 2018, doi:10.1101/gr.223693.117
..., Sensenbrenner syndrome, is a ciliopathy caused by mutations in the IFT122 gene. Am J Hum Genet 86: 949–956. ↵Wang K, Li M, Hakonarson H. 2010. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38: e164. ↵Wang J, Duncan D, Shi Z, Zhang B. 2013. WEB...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...of the nonreference allele (DePristo et al. 2011; Raczy et al. 2013). For variants that deviate significantly from the reference, alternative methods such as de novo assembly can be used if the variant is not highly repetitive (Iqbal et al. 2012; Weisenfeld et al. 2014; Li 2015; Chen et al. 2016). Because high-throughput...
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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
..., Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, et al. 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898–902. Wang K, Li M, Hakonarson H. 2010. ANNOVAR: functional annotation of genetic variants from high-throughput...
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Research: Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
- Elena Helman,
- Michael S. Lawrence,
- Chip Stewart,
- Carrie Sougnez,
- Gad Getz,
- and Matthew Meyerson
Genome Res. July 2014 24: 1053-1063; Published in Advance May 13, 2014, doi:10.1101/gr.163659.113
...Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing Elena Helman 1 , 2 , Michael S. Lawrence 2 , Chip Stewart 2 , Carrie Sougnez 2 , Gad Getz 2 , 3 and Matthew Meyerson 1 , 2 , 4 , 5 , 6...
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Resource: SNP detection for massively parallel whole-genome resequencing
- Ruiqiang Li,
- Yingrui Li,
- Xiaodong Fang,
- Huanming Yang,
- Jian Wang,
- Karsten Kristiansen,
- and Jun Wang
Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108
...SNP detection for massively parallel whole-genome resequencing Ruiqiang Li 1 , 2 , 3 , Yingrui Li 1 , 3 , Xiaodong Fang 1 , Huanming Yang 1 , Jian Wang 1 , Karsten Kristiansen 1 , 2 and Jun Wang 1 , 2 , 4...
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Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
- Adam D. Ewing and
- Haig H. Kazazian, Jr.
Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
...Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans Adam D. Ewing 1 , 2 and Haig H. Kazazian Jr. 1 , 3 1The McKusick-Nathans Institute for Genetic Medicine, The Johns Hopkins University School of Medicine...
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Research: Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
- Hoon Kim,
- Siyuan Zheng,
- Seyed S. Amini,
- Selene M. Virk,
- Tom Mikkelsen,
- Daniel J. Brat,
- Jonna Grimsby,
- Carrie Sougnez,
- Florian Muller,
- Jian Hu,
- Andrew E. Sloan,
- Mark L. Cohen,
- Erwin G. Van Meir,
- Lisa Scarpace,
- Peter W. Laird,
- John N. Weinstein,
- Eric S. Lander,
- Stacey Gabriel,
- Gad Getz,
- Matthew Meyerson,
- Lynda Chin,
- Jill S. Barnholtz-Sloan,
- and Roel G.W. Verhaak
Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114
...Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution Hoon Kim 1 , 12 , Siyuan Zheng 1 , 2 , 12 , Seyed S. Amini 1 , Selene M. Virk 3 , Tom Mikkelsen 4...
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Method: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
- Nadin Rohland and
- David Reich
Genome Res. May 2012 22: 939-946; Published in Advance January 20, 2012, doi:10.1101/gr.128124.111
...Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture Nadin Rohland 1 and David Reich Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Harvard and MIT, Cambridge...
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Method: Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren,
- Marjo de Ruiter,
- Taco Jesse,
- Hein van der Poel,
- Jifeng Tang,
- Feyruz Yalcin,
- Antoine Janssen,
- Hanne Volpin,
- Keith E. Stormo,
- Robert Bogden,
- Michiel J.T. van Eijk,
- and Marcel Prins
Genome Res. April 2011 21: 618-625; Published in Advance February 1, 2011, doi:10.1101/gr.112094.110
...with results from previous studies on the effect of read length ondetermining uniquepositions in the (Whiteford et al. 2005; Chaisson et al. 2009). A 20-nt tag length, even when adding 6 nt for a pool identifier, is well within the sequence length output of contemporary high-throughput sequencing machines...

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