دورية أكاديمية
أعرض في EDS

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.

التفاصيل البيبلوغرافية
العنوان: An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.
المؤلفون: Mc Cartney AM; NIH, Washington, USA., Mahmoud M; Baylor College of Medicine, Houston, USA., Jochum M; Baylor College of Medicine, Houston, USA., Agustinho DP; Washington University in St. Louis School of Medicine, St. Louis, USA., Zorman B; Baylor College of Medicine, Houston, USA., Al Khleifat A; King's College London, London, UK., Dabbaghie F; Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany., K Kesharwani R; Baylor College of Medicine, Houston, USA., Smolka M; University of Vienna, Vienna, Austria., Dawood M; Baylor College of Medicine, Houston, USA., Albin D; University of Colorado at Boulder, Boulder, USA., Aliyev E; Sidra Medicine, Doha, Qatar., Almabrazi H; Sidra Medicine, Doha, Qatar., Arslan A; Stanford University School of Medicine, California, USA., Balaji A; Rice University, Houston, USA., Behera S; Baylor College of Medicine, Houston, USA., Billingsley K; NIH, Washington, USA., L Cameron D; Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia., Daw J; NVIDIA Corporation, Santa Clara, California, USA., T Dawson E; NVIDIA Corporation, Santa Clara, California, USA., De Coster W; VIB Center for Molecular Neurology, Antwerp, Belgium., Du H; Baylor College of Medicine, Houston, USA., Dunn C; Pacific Biosciences, Menlo Park, USA., Esteban R; Oxford Nanopore Technologies Ltd, Oxford, UK., Jolly A; Baylor College of Medicine, Houston, USA., Kalra D; Baylor College of Medicine, Houston, USA., Liao C; Rice University, Houston, USA., Liu Y; Rice University, Houston, USA., Lu TY; USC, Los Angeles, USA., M Havrilla J; Children's Hospital of Philadelphia, Philadelphia, USA., M Khayat M; Baylor College of Medicine, Houston, USA., Marin M; Harvard Medical School, Boston, USA., Monlong J; UC Santa Cruz Genomics Institute, Santa Cruz, USA., Price S; Carnegie Mellon University, Pittsburgh, USA., Rafael Gener A; Baylor College of Medicine, Houston, USA., Ren J; USC, Los Angeles, USA., Sagayaradj S; University of California, Davis, USA., Sapoval N; Rice University, Houston, USA., Sinner C; University of Texas at Dallas, Richardson, USA., C Soto D; University of California, Davis, USA., Soylev A; Konya Food and Agriculture University, Konya, Turkey., Subramaniyan A; University of Michigan, Ann Arbor, USA., Syed N; Sidra Medicine, Doha, Qatar., Tadimeti N; NVIDIA Corporation, Santa Clara, California, USA., Tater P; DNAnexus, Mountain View, USA., Vats P; NVIDIA Corporation, Santa Clara, California, USA., Vaughn J; USDA-ARS, Athens, USA., Walker K; Baylor College of Medicine, Houston, USA., Wang G; Max Planck Institute for Molecular Genetics, Berlin, Germany., Zeng Q; Laboratory Corporation of America Holdings, Westborough, USA., Zhang S; Lanzhou University, Lanzhou, China., Zhao T; University of Pittsburgh, Pittsburgh, USA., Kille B; Rice University, Houston, USA., Biederstedt E; Harvard Medical School, Boston, USA., Chaisson M; USC, Los Angeles, USA., English A; Baylor College of Medicine, Houston, USA., Kronenberg Z; Pacific Biosciences, Menlo Park, USA., J Treangen T; Rice University, Houston, USA., Hefferon T; NIH, Washington, USA., Chin CS; DNAnexus, Mountain View, USA., Busby B; DNAnexus, Mountain View, USA., J Sedlazeck F; Baylor College of Medicine, Houston, USA.
المصدر: F1000Research [F1000Res] 2021 Mar 26; Vol. 10, pp. 246. Date of Electronic Publication: 2021 Mar 26 (Print Publication: 2021).
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, N.I.H., Intramural
اللغة: English
بيانات الدورية: Publisher: F1000 Research Ltd Country of Publication: England NLM ID: 101594320 Publication Model: eCollection Cited Medium: Internet ISSN: 2046-1402 (Electronic) Linking ISSN: 20461402 NLM ISO Abbreviation: F1000Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : F1000 Research Ltd
مواضيع طبية MeSH: COVID-19* , SARS-CoV-2*, Animals ; Genome, Viral ; Humans ; Vertebrates
مستخلص: In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research.   The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at  https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
Competing Interests: Competing interests: Wouter De Coster has received free sequencing consumables and travel reimbursement to speak at conferences from Oxford Nanopore Technologies. Jason Chin and Ben Busby are employees of DNAnexus. Zev Kronenberg is an employee and shareholder of Pacific BioSciences; is a shareholder of Phase Genomics. Christopher Dunn is an employee and shareholder of Pacific BioSciences. FS received travel and conference reimbursements from Oxford Nanopore and PacBio. Qiandong Zeng is an employee of Laboratory Corporation of America Holdings, a company providing clinical diagnostics services.
(Copyright: © 2021 Mc Cartney AM et al.)
References: Expert Rev Mol Diagn. 2017 Jan;17(1):95-103. (PMID: 27917695)
J Comput Biol. 2015 May;22(5):336-52. (PMID: 25629448)
Nat Biotechnol. 2017 Nov;35(11):1026-1028. (PMID: 29035372)
Nucleic Acids Res. 2020 Jan 8;48(D1):D835-D844. (PMID: 31777943)
Bioinformatics. 2019 Aug 15;35(16):2853-2855. (PMID: 30596893)
Nat Rev Genet. 2011 May;12(5):363-76. (PMID: 21358748)
Comput Struct Biotechnol J. 2019 Dec 23;18:83-92. (PMID: 32099591)
PLoS One. 2021 Jan 27;16(1):e0245362. (PMID: 33503040)
Genome Res. 2020 Sep;30(9):1291-1305. (PMID: 32801147)
Sci Rep. 2020 Aug 19;10(1):14004. (PMID: 32814791)
Bioinformatics. 2012 Sep 15;28(18):i333-i339. (PMID: 22962449)
Genome Biol. 2019 Dec 19;20(1):291. (PMID: 31856913)
Nature. 2020 Feb;578(7793):112-121. (PMID: 32025012)
Bioinformatics. 2017 Jun 15;33(12):1867-1869. (PMID: 28165109)
Oncotarget. 2016 Dec 13;7(50):82733-82740. (PMID: 27716627)
Nat Biotechnol. 2020 Nov;38(11):1347-1355. (PMID: 32541955)
Genome Biol. 2020 Nov 9;21(1):274. (PMID: 33168059)
Nat Methods. 2018 Jun;15(6):461-468. (PMID: 29713083)
J Virol. 2016 Jul 11;90(15):6884-95. (PMID: 27194763)
Cancer Cell. 2020 Apr 13;37(4):431-442. (PMID: 32289268)
Bioinformatics. 2014 Aug 1;30(15):2114-20. (PMID: 24695404)
Nature. 2020 May;581(7809):434-443. (PMID: 32461654)
Nat Commun. 2020 Sep 22;11(1):4794. (PMID: 32963235)
Nat Rev Genet. 2020 Jan;21(1):44-62. (PMID: 31548659)
Nat Commun. 2019 Oct 11;10(1):4660. (PMID: 31604920)
PLoS Genet. 2018 Nov 12;14(11):e1007758. (PMID: 30419019)
Nat Rev Genet. 2006 Feb;7(2):85-97. (PMID: 16418744)
Nat Rev Genet. 2011 Sep 27;12(11):745-55. (PMID: 21946919)
Methods. 2017 Oct 1;129:3-7. (PMID: 28583483)
BMC Genomics. 2021 Jan 19;22(1):62. (PMID: 33468057)
Genome Biol. 2014 Jun 26;15(6):R84. (PMID: 24970577)
Bioinformatics. 2012 Feb 15;28(4):593-4. (PMID: 22199392)
Brief Funct Genomics. 2020 Jul 29;19(4):243-258. (PMID: 32393978)
Bioinformatics. 2018 Mar 1;34(5):867-868. (PMID: 29096012)
Bioinformatics. 2016 Apr 15;32(8):1220-2. (PMID: 26647377)
Nature. 2021 Feb;590(7847):679-681. (PMID: 33619406)
Bioinformatics. 2017 Apr 1;33(7):1083-1085. (PMID: 28031184)
Nat Biotechnol. 2019 Oct;37(10):1155-1162. (PMID: 31406327)
Nat Genet. 2013 Jun;45(6):580-5. (PMID: 23715323)
Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. (PMID: 23193291)
Genome Res. 2015 Mar;25(3):402-12. (PMID: 25609572)
Nature. 2019 Nov;575(7781):210-216. (PMID: 31645765)
Genome Res. 2017 Dec;27(12):2050-2060. (PMID: 29097403)
Genome Biol. 2020 Feb 12;21(1):35. (PMID: 32051000)
Bioinformatics. 2011 Mar 1;27(5):718-9. (PMID: 21208982)
Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153)
Nat Commun. 2019 Jul 19;10(1):3240. (PMID: 31324872)
Nat Commun. 2017 Jan 24;8:14061. (PMID: 28117401)
Genome Biol. 2020 Aug 3;21(1):189. (PMID: 32746918)
Genome Biol. 2019 Nov 20;20(1):246. (PMID: 31747936)
Genome Biol. 2021 May 25;22(1):161. (PMID: 34034781)
Bioinformatics. 2019 Oct 1;35(19):3599-3607. (PMID: 30851095)
Lancet. 2020 Aug 29;396(10251):603-611. (PMID: 32822564)
Nat Rev Genet. 2020 Mar;21(3):171-189. (PMID: 31729472)
Bioinformatics. 2002 Mar;18(3):452-64. (PMID: 11934745)
Gigascience. 2020 Dec 21;9(12):. (PMID: 33347570)
Nat Rev Genet. 2018 Jun;19(6):329-346. (PMID: 29599501)
Science. 2012 Aug 17;337(6096):816-21. (PMID: 22745249)
Nat Cancer. 2020 Aug;1(8):774-783. (PMID: 35122052)
Sci Data. 2016 Jun 07;3:160025. (PMID: 27271295)
Nat Commun. 2019 Apr 16;10(1):1784. (PMID: 30992455)
Genome Med. 2018 Dec 7;10(1):95. (PMID: 30526634)
Sci Rep. 2019 Dec 18;9(1):19365. (PMID: 31852928)
Bioinformatics. 2018 Dec 15;34(24):4205-4212. (PMID: 29945233)
Genome Res. 2018 Apr;28(4):581-591. (PMID: 29535149)
Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943)
Bioinformatics. 2018 Oct 15;34(20):3572-3574. (PMID: 29669011)
Genome Res. 2021 Apr;31(4):635-644. (PMID: 33602693)
Gigascience. 2020 Jul 1;9(7):. (PMID: 32706368)
Cancer Biol Ther. 2016;17(3):246-53. (PMID: 26787508)
معلومات مُعتمدة: UM1 HG008898 United States HG NHGRI NIH HHS; T32 HD098068 United States HD NICHD NIH HHS; R01 GM132713 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: CNV; NextGeneration Sequencing; SARS-CoV-2; Structural variant
تواريخ الأحداث: Date Created: 20211011 Date Completed: 20211013 Latest Revision: 20231107
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8479851.2
DOI: 10.12688/f1000research.51477.2
PMID: 34621504.2. Version: 2. Publisher Version ID: 2. Version Date: 2021/09/03
قاعدة البيانات: MEDLINE
الوصف
تدمد:2046-1402
DOI:10.12688/f1000research.51477.2