Literature DB >> 32694666

Responsible, practical genomic data sharing that accelerates research.

James Brian Byrd1, Anna C Greene2, Deepashree Venkatesh Prasad3, Xiaoqian Jiang4, Casey S Greene5,6.   

Abstract

Data sharing anchors reproducible science, but expectations and best practices are often nebulous. Communities of funders, researchers and publishers continue to grapple with what should be required or encouraged. To illuminate the rationales for sharing data, the technical challenges and the social and cultural challenges, we consider the stakeholders in the scientific enterprise. In biomedical research, participants are key among those stakeholders. Ethical sharing requires considering both the value of research efforts and the privacy costs for participants. We discuss current best practices for various types of genomic data, as well as opportunities to promote ethical data sharing that accelerates science by aligning incentives.

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Year:  2020        PMID: 32694666      PMCID: PMC7974070          DOI: 10.1038/s41576-020-0257-5

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  82 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  Predicting genetic modifier loci using functional gene networks.

Authors:  Insuk Lee; Ben Lehner; Tanya Vavouri; Junha Shin; Andrew G Fraser; Edward M Marcotte
Journal:  Genome Res       Date:  2010-06-09       Impact factor: 9.043

3.  Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

Authors:  Jie Tan; Georgia Doing; Kimberley A Lewis; Courtney E Price; Kathleen M Chen; Kyle C Cady; Barret Perchuk; Michael T Laub; Deborah A Hogan; Casey S Greene
Journal:  Cell Syst       Date:  2017-07-12       Impact factor: 10.304

Review 4.  Genotyping technologies for genetic research.

Authors:  Jiannis Ragoussis
Journal:  Annu Rev Genomics Hum Genet       Date:  2009       Impact factor: 8.929

5.  Reliable identification of genomic variants from RNA-seq data.

Authors:  Robert Piskol; Gokul Ramaswami; Jin Billy Li
Journal:  Am J Hum Genet       Date:  2013-09-26       Impact factor: 11.025

6.  MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease.

Authors:  Jaclyn N Taroni; Peter C Grayson; Qiwen Hu; Sean Eddy; Matthias Kretzler; Peter A Merkel; Casey S Greene
Journal:  Cell Syst       Date:  2019-05-22       Impact factor: 10.304

7.  Exploring the human genome with functional maps.

Authors:  Curtis Huttenhower; Erin M Haley; Matthew A Hibbs; Vanessa Dumeaux; Daniel R Barrett; Hilary A Coller; Olga G Troyanskaya
Journal:  Genome Res       Date:  2009-02-26       Impact factor: 9.043

Review 8.  The methylome: approaches for global DNA methylation profiling.

Authors:  Stephan Beck; Vardhman K Rakyan
Journal:  Trends Genet       Date:  2008-03-05       Impact factor: 11.639

9.  Discovery of biological networks from diverse functional genomic data.

Authors:  Chad L Myers; Drew Robson; Adam Wible; Matthew A Hibbs; Camelia Chiriac; Chandra L Theesfeld; Kara Dolinski; Olga G Troyanskaya
Journal:  Genome Biol       Date:  2005-12-19       Impact factor: 13.583

10.  GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function.

Authors:  Sara Mostafavi; Debajyoti Ray; David Warde-Farley; Chris Grouios; Quaid Morris
Journal:  Genome Biol       Date:  2008-06-27       Impact factor: 13.583

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  17 in total

1.  Blood-based biomarkers of antidepressant response to ketamine and esketamine: A systematic review and meta-analysis.

Authors:  Gustavo C Medeiros; Todd D Gould; William L Prueitt; Julie Nanavati; Michael F Grunebaum; Nuri B Farber; Balwinder Singh; Sudhakar Selvaraj; Rodrigo Machado-Vieira; Eric D Achtyes; Sagar V Parikh; Mark A Frye; Carlos A Zarate; Fernando S Goes
Journal:  Mol Psychiatry       Date:  2022-06-27       Impact factor: 15.992

2.  Reproducibility standards for machine learning in the life sciences.

Authors:  Benjamin J Heil; Michael M Hoffman; Florian Markowetz; Su-In Lee; Casey S Greene; Stephanie C Hicks
Journal:  Nat Methods       Date:  2021-10       Impact factor: 47.990

Review 3.  Opportunities and challenges for the use of common controls in sequencing studies.

Authors:  Genevieve L Wojcik; Jessica Murphy; Jacob L Edelson; Christopher R Gignoux; Alexander G Ioannidis; Alisa Manning; Manuel A Rivas; Steven Buyske; Audrey E Hendricks
Journal:  Nat Rev Genet       Date:  2022-05-17       Impact factor: 59.581

Review 4.  Public availability of HIV-1 drug resistance sequence and treatment data: a systematic review.

Authors:  Soo-Yon Rhee; Seble G Kassaye; Michael R Jordan; Vinie Kouamou; David Katzenstein; Robert W Shafer
Journal:  Lancet Microbe       Date:  2022-01-19

5.  Improving the completeness of public metadata accompanying omics studies.

Authors:  Anushka Rajesh; Yutong Chang; Malak S Abedalthagafi; Annie Wong-Beringer; Michael I Love; Serghei Mangul
Journal:  Genome Biol       Date:  2021-04-15       Impact factor: 13.583

6.  Demonstrating trustworthiness when collecting and sharing genomic data: public views across 22 countries.

Authors:  Richard Milne; Katherine I Morley; Mohamed A Almarri; Shamim Anwer; Jerome Atutornu; Elena E Baranova; Paul Bevan; Maria Cerezo; Yali Cong; Alessia Costa; Christine Critchley; Josepine Fernow; Peter Goodhand; Qurratulain Hasan; Aiko Hibino; Gry Houeland; Heidi C Howard; S Zakir Hussain; Charlotta Ingvoldstad Malmgren; Vera L Izhevskaya; Aleksandra Jędrzejak; Cao Jinhong; Megumi Kimura; Erika Kleiderman; Brandi Leach; Keying Liu; Deborah Mascalzoni; Álvaro Mendes; Jusaku Minari; Dianne Nicol; Emilia Niemiec; Christine Patch; Jack Pollard; Barbara Prainsack; Marie Rivière; Lauren Robarts; Jonathan Roberts; Virginia Romano; Haytham A Sheerah; James Smith; Alexandra Soulier; Claire Steed; Vigdis Stefànsdóttir; Cornelia Tandre; Adrian Thorogood; Torsten H Voigt; Nan Wang; Anne V West; Go Yoshizawa; Anna Middleton
Journal:  Genome Med       Date:  2021-05-25       Impact factor: 11.117

7.  Reproducible Single-Cell Genomic Research in Pulmonary and Critical Care Medicine.

Authors:  Oliver Eickelberg; Alexander V Misharin; Patricia J Sime
Journal:  Am J Respir Crit Care Med       Date:  2020-12-01       Impact factor: 21.405

8.  Apropos Data Sharing: Abandon the Distrust and Embrace the Opportunity.

Authors:  Giorgia Brambilla Pisoni; Mariarosaria Taddeo
Journal:  DNA Cell Biol       Date:  2021-12-23       Impact factor: 3.311

9.  Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer.

Authors:  Anthony R Kerlavage; Anne C Kirchhoff; Jaime M Guidry Auvil; Norman E Sharpless; Kara L Davis; Karlyne Reilly; Gregory Reaman; Lynne Penberthy; Dennis Deapen; Amie Hwang; Eric B Durbin; Sara L Gallotto; Richard Aplenc; Samuel L Volchenboum; Allison P Heath; Bruce J Aronow; Jinghui Zhang; Olena Vaske; Todd A Alonzo; Paul C Nathan; Jenny N Poynter; Greg Armstrong; Erin E Hahn; Karen J Wernli; Casey Greene; Jack DiGiovanna; Adam C Resnick; Eve R Shalley; Sorena Nadaf; Warren A Kibbe
Journal:  JCO Clin Cancer Inform       Date:  2021-08

Review 10.  Expanding and Remixing the Metadata Landscape.

Authors:  Ariel A Hippen; Casey S Greene
Journal:  Trends Cancer       Date:  2020-11-20
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