Evidence map›Paper›PMID 34621504›Full record

ArticleF1000Research2021

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

Ann M Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood and 52 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in F1000Research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

62 authors.

Ann M Mc CartneyNIH, Washington, USA.ORCID 0000-0003-3191-3200
Medhat MahmoudBaylor College of Medicine, Houston, USA.ORCID 0000-0002-2553-4231
Michael JochumBaylor College of Medicine, Houston, USA.ORCID 0000-0002-2398-356X
Daniel Paiva AgustinhoWashington University in St. Louis School of Medicine, St. Louis, USA.ORCID 0000-0003-2242-4798
Barry ZormanBaylor College of Medicine, Houston, USA.
Ahmad Al KhleifatKing's College London, London, UK.
Fawaz DabbaghieInstitute for Medical Biometry and Bioinformatics, Düsseldorf, Germany.
Rupesh K KesharwaniBaylor College of Medicine, Houston, USA.
Moritz SmolkaUniversity of Vienna, Vienna, Austria.ORCID 0000-0002-8621-600X
Moez DawoodBaylor College of Medicine, Houston, USA.
Dreycey AlbinUniversity of Colorado at Boulder, Boulder, USA.
Elbay AliyevSidra Medicine, Doha, Qatar.ORCID 0000-0002-6469-1854
Hakeem AlmabraziSidra Medicine, Doha, Qatar.
Ahmed ArslanStanford University School of Medicine, California, USA.ORCID 0000-0002-5325-6558
Advait BalajiRice University, Houston, USA.
Sairam BeheraBaylor College of Medicine, Houston, USA.
Kimberley BillingsleyNIH, Washington, USA.
Daniel L CameronWalter and Eliza Hall Institute of Medical Research, Melbourne, Australia.ORCID 0000-0002-0951-7116
Joyjit DawNVIDIA Corporation, Santa Clara, California, USA.
Eric T DawsonNVIDIA Corporation, Santa Clara, California, USA.
Wouter De CosterVIB Center for Molecular Neurology, Antwerp, Belgium.
Haowei DuBaylor College of Medicine, Houston, USA.ORCID 0000-0001-9052-1587
Christopher DunnPacific Biosciences, Menlo Park, USA.ORCID 0000-0002-0601-3254
Rocio EstebanOxford Nanopore Technologies Ltd, Oxford, UK.
Angad JollyBaylor College of Medicine, Houston, USA.
Divya KalraBaylor College of Medicine, Houston, USA.
Chunxiao LiaoRice University, Houston, USA.ORCID 0000-0003-0344-7134
Yunxi LiuRice University, Houston, USA.
Tsung-Yu LuUSC, Los Angeles, USA.
James M HavrillaChildren's Hospital of Philadelphia, Philadelphia, USA.
Michael M KhayatBaylor College of Medicine, Houston, USA.
Maximillian MarinHarvard Medical School, Boston, USA.
Jean MonlongUC Santa Cruz Genomics Institute, Santa Cruz, USA.ORCID 0000-0002-9737-5516
Stephen PriceCarnegie Mellon University, Pittsburgh, USA.ORCID 0000-0001-9072-7518
Alejandro Rafael GenerBaylor College of Medicine, Houston, USA.
Jingwen RenUSC, Los Angeles, USA.
Sagayamary SagayaradjUniversity of California, Davis, USA.
Nicolae SapovalRice University, Houston, USA.
Claude SinnerUniversity of Texas at Dallas, Richardson, USA.
Daniela C SotoUniversity of California, Davis, USA.ORCID 0000-0002-6292-655X
Arda SoylevKonya Food and Agriculture University, Konya, Turkey.
Arun SubramaniyanUniversity of Michigan, Ann Arbor, USA.
Najeeb SyedSidra Medicine, Doha, Qatar.
Neha TadimetiNVIDIA Corporation, Santa Clara, California, USA.
Pamella TaterDNAnexus, Mountain View, USA.
Pankaj VatsNVIDIA Corporation, Santa Clara, California, USA.
Justin VaughnUSDA-ARS, Athens, USA.
Kimberly WalkerBaylor College of Medicine, Houston, USA.
Gaojianyong WangMax Planck Institute for Molecular Genetics, Berlin, Germany.
Qiandong ZengLaboratory Corporation of America Holdings, Westborough, USA.ORCID 0000-0002-1885-7892
Shangzhe ZhangLanzhou University, Lanzhou, China.ORCID 0000-0003-2064-4287
Tingting ZhaoUniversity of Pittsburgh, Pittsburgh, USA.
Bryce KilleRice University, Houston, USA.
Evan BiederstedtHarvard Medical School, Boston, USA.
Mark ChaissonUSC, Los Angeles, USA.
Adam EnglishBaylor College of Medicine, Houston, USA.
Zev KronenbergPacific Biosciences, Menlo Park, USA.
Todd J TreangenRice University, Houston, USA.
Timothy HefferonNIH, Washington, USA.
Chen-Shan ChinDNAnexus, Mountain View, USA.
Ben BusbyDNAnexus, Mountain View, USA.
Fritz J SedlazeckBaylor College of Medicine, Houston, USA.ORCID 0000-0001-6040-2691

Funding

Genomic Architecture of Common Disease in Diverse Populations: WGS of Ongoing Hemorrhagic Stroke Study SupplementUM1HG008898 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2016 to 2020
$77.0M
Comprehensive Mechanisms in Reproductive SciencesT32HD098068 · NICHD · BAYLOR COLLEGE OF MEDICINE · PI STEPHANIE A. PANGAS · 2020 to 2026
$2.4M
Detection and annotation of structural variants from long-read sequencingR01GM132713 · NIGMS · CHILDREN'S HOSP OF PHILADELPHIA · PI WANG, KAI · 2019 to 2022
$1.9M
NHGRI NIH HHS UM1 HG008898NICHD NIH HHS T32 HD098068NIGMS NIH HHS R01 GM132713
6 · The paper itself

Abstract

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.

Indexed as

COVID-19SARS-CoV-2AnimalsGenome, ViralHumansVertebratesCNVNextGeneration SequencingSARS-CoV-2Structural variant

Identifiers

PMID34621504
PMCPMC8479851.2

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.