Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Kolker, Eugene; Özdemir, Vural; Martens, Lennart; Hancock, William S.; Anderson, Gordon A.; Anderson, Nathaniel; Aynacioglu, Sukru; Baranova, Ancha; Campagna, Shawn R.; Chen, Rui; Choiniere, John; Dearth, Stephen P.; Feng, Wu-chun; Ferguson, Lynnette R.; Fox, Geoffrey; Frishman, Dmitrij; Grossman, Robert L.; Heath, Allison P.; Higdon, Roger; Hutz, Mara Helena; Janko, Imre; Jiang, Lihua; Joshi, Sanjay; Kel, Alexander; Kemnitz, Joseph W.; Kohane, Isaac S.; Kolker, Natali; Lancet, Doron; Lee, Elaine; Li, Weizhong; Lisitsa, Andrey; LLerena, Adrián; MacNealy-Koch, Courtney; Marshall, Jean-Claude; Masuzzo, Paola; May, Amanda; Mias, George; Monroe, Matthew E.; Montague, Elizabeth; Mooney, Sean D.; Nesvizhskii, Alexey I.; Noronha, Santosh; Omenn, Gilbert S.; Rajasimha, Harsha; Ramamoorthy, Preveen; Sheehan, Jerry; Smarr, Larry; Smith, Charles V.; Smith, Todd; Snyder, M; Rapole, Srikanth; Srivastava, Sanjeeva; Stanberry, Larissa; Stewart, Elizabeth; Toppo, Stefano; Uetz, Peter; Verheggen, Kenneth; Voy, Brynn H.; Warnich, Louise; Wilhelm, Steven W.; Yandl, Gregory

doi:10.1089/big.2013.0039

Cited by 12 publications

(16 citation statements)

References 22 publications

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“…This limits the worldwide flow of bioinformatics knowledge necessary to build and train research groups with a solid bioinformatics background. Although there are several claims for more transparency and reproducibility of all the scientific process in biomedical literature (Sandve et al 2013;Kolker et al 2014;Iqbal et al 2016), advances Figure 1. Continental admixture of the EPIGEN-Brazil population-based cohorts.…”

Section: Addressing Lack Of Transparency and Reproducibility Of Genommentioning

confidence: 99%

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

et al. 2018

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EPIGEN-Brazil is one of the largest Latin American initiatives at the interface of human genomics, public health, and computational biology. Here, we present two resources to address two challenges to the global dissemination of precision medicine and the development of the bioinformatics know-how to support it. To address the underrepresentation of non-European individuals in human genome diversity studies, we present the EPIGEN-5M+1KGP imputation panel-the fusion of the public 1000 Genomes Project (1KGP) Phase 3 imputation panel with haplotypes derived from the EPIGEN-5M data set (a product of the genotyping of 4.3 million SNPs in 265 admixed individuals from the EPIGEN-Brazil Initiative). When we imputed a target SNPs data set (6487 admixed individuals genotyped for 2.2 million SNPs from the EPIGEN-Brazil project) with the EPIGEN-5M+1KGP panel, we gained 140,452 more SNPs in total than when using the 1KGP Phase 3 panel alone and 788,873 additional high confidence SNPs ( ≥ 0.8). Thus, the major effect of the inclusion of the EPIGEN-5M data set in this new imputation panel is not only to gain more SNPs but also to improve the quality of imputation. To address the lack of transparency and reproducibility of bioinformatics protocols, we present a conceptual Scientific Workflow in the form of a website that models the scientific process (by including publications, flowcharts, masterscripts, documents, and bioinformatics protocols), making it accessible and interactive. Its applicability is shown in the context of the development of our EPIGEN-5M+1KGP imputation panel. The Scientific Workflow also serves as a repository of bioinformatics resources.

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Section: Addressing Lack Of Transparency and Reproducibility Of Genommentioning

confidence: 99%

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

et al. 2018

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“…To this end, we have developed a multiomics metadata checklist. The checklist will not only be used for collecting metadata for MOPED but also has been made available to the community at large through DELSA (www.delsaglobal.org) [63]. The metadata checklist is a harmonization strategy for omics data integration, analysis and use.…”

Section: Meta-data Checklist and Data Submissionmentioning

confidence: 99%

MOPED Enables Discoveries through Consistently Processed Proteomics Data

Higdon

Stewart²,

Stanberry

et al. 2013

J. Proteome Res.

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The Model Organism Protein Expression Database (MOPED, http://moped.proteinspire.org), is an expanding proteomics resource to enable biological and biomedical discoveries. MOPED aggregates simple, standardized and consistently processed summaries of protein expression and metadata from proteomics (mass spectrometry) experiments from human and model organisms (mouse, worm and yeast). The latest version of MOPED adds new estimates of protein abundance and concentration, as well as relative (differential) expression data. MOPED provides a new updated query interface that allows users to explore information by organism, tissue, localization, condition, experiment, or keyword. MOPED supports the Human Proteome Project’s efforts to generate chromosome and diseases specific proteomes by providing links from proteins to chromosome and disease information, as well as many complementary resources. MOPED supports a new omics metadata checklist in order to harmonize data integration, analysis and use. MOPED’s development is driven by the user community, which spans 90 countries guiding future development that will transform MOPED into a multi-omics resource. MOPED encourages users to submit data in a simple format. They can use the metadata a checklist generate a data publication for this submission. As a result, MOPED will provide even greater insights into complex biological processes and systems and enable deeper and more comprehensive biological and biomedical discoveries.

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“…In the longer term, however, more complex omics studies that include genomics together with transcriptomics, proteomics, metabolomics, autoantibody profiles and various clinical parameters are likely to raise the same kind of reproducibility and credibility and veracity problems, and perhaps require more careful attention to metadata norms. 171 For patenting diagnostic method claims, this is going to remain a problem as IP Australia will never have the ability to independently assess the reproducibility and credibility and veracity of these claims.…”

Section: Discussionmentioning

confidence: 99%

Patenting Genetic Diagnostic Methods: NGS, GWAS, SNPs and Patents

Lawson

2015

SSRN Journal

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This article reviews the problems posed by patent claims to genetic diagnostic methods associated with genome-wide association studies (GWAS) adopting methodologies using next-generation sequencing (NGS) and single nucleotide polymorphisms (SNP). These problems are essentially about experimental reproducibility and the credibility and veracity of reported developments. An analysis of the relevant law demonstrates that the current Australian and United States laws about suitable patentable subject matter differ, and that the current reproducibility (sufficiency, enablement and inutility) standards are unlikely to address these problems. The article concludes that following the United States approach excluding these genetic diagnostic method claims from patenting is one solution. Failing this, improving analysis and quality controls that are now being adopted in the basic research will reduce the nature of the problems, although this will remain problematic for patent examiners and the broader public.

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Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Cited by 12 publications

References 22 publications

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

EPIGEN-Brazil Initiative resources: a Latin American imputation panel and the Scientific Workflow

MOPED Enables Discoveries through Consistently Processed Proteomics Data

Patenting Genetic Diagnostic Methods: NGS, GWAS, SNPs and Patents

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