Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Author:

Sirén Jouni1ORCID,Monlong Jean1ORCID,Chang Xian1ORCID,Novak Adam M.1ORCID,Eizenga Jordan M.1ORCID,Markello Charles1ORCID,Sibbesen Jonas A.1ORCID,Hickey Glenn1ORCID,Chang Pi-Chuan2ORCID,Carroll Andrew2ORCID,Gupta Namrata3ORCID,Gabriel Stacey4,Blackwell Thomas W.5,Ratan Aakrosh6ORCID,Taylor Kent D.7ORCID,Rich Stephen S.6ORCID,Rotter Jerome I.7ORCID,Haussler David18ORCID,Garrison Erik9,Paten Benedict1ORCID

Affiliation:

1. UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA.

2. Google Inc., Mountain View, CA, USA.

3. Genomics Platform, Broad Institute, Cambridge, MA, USA.

4. Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.

5. Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.

6. Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.

7. The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor–UCLA Medical Center, Torrance, CA, USA.

8. Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA.

9. Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.

Abstract

Giraffe pangenomes Genomes within a species often have a core, conserved component, as well as a variable set of genetic material among individuals or populations that is referred to as a “pangenome.” Inference of the relationships between pangenomes sequenced with short-read technology is often done computationally by mapping the sequences to a reference genome. The computational method affects genome assembly and comparisons, especially in cases of structural variants that are longer than an average sequenced region, for highly polymorphic loci, and for cross-species analyses. Siren et al . present a bioinformatic method called Giraffe, which improves mapping pangenomes in polymorphic regions of the genome containing single nucleotide polymorphisms and structural variants with standard computational resources, making large-scale genomic analyses more accessible. —LMZ

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Cited by 170 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3