Pangenomics enables genotyping of known structural variants in 5202 diverse genomes-Reference-Cited by-同舟云学术

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Published:2021-12-17 Issue:6574 Volume:374 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Sirén Jouni¹^ORCID,Monlong Jean¹^ORCID,Chang Xian¹^ORCID,Novak Adam M.¹^ORCID,Eizenga Jordan M.¹^ORCID,Markello Charles¹^ORCID,Sibbesen Jonas A.¹^ORCID,Hickey Glenn¹^ORCID,Chang Pi-Chuan²^ORCID,Carroll Andrew²^ORCID,Gupta Namrata³^ORCID,Gabriel Stacey⁴,Blackwell Thomas W.⁵,Ratan Aakrosh⁶^ORCID,Taylor Kent D.⁷^ORCID,Rich Stephen S.⁶^ORCID,Rotter Jerome I.⁷^ORCID,Haussler David¹⁸^ORCID,Garrison Erik⁹,Paten Benedict¹^ORCID

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

Reference79 articles.

1. A robust benchmark for detection of germline large deletions and insertions

2. Structural variant calling: the long and the short of it

3. Genotyping inversions and tandem duplications

4. Modernizing Reference Genome Assemblies

5. Computational pan-genomics: status, promises and challenges

Cited by 126 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

1. Co-linear chaining on pangenome graphs;Algorithms for Molecular Biology;2024-01-27

2. Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges;Briefings in Bioinformatics;2024-01-22

3. Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery;2024-01-11

4. Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms;2024-01-02

5. KAGE 2: Fast and accurate genotyping of structural variation using pangenomes;2023-12-23