Literature DB >> 31161416

Mind the gap: resources required to receive, process and interpret research-returned whole genome data.

Dana C Crawford1,2,3, Jessica N Cooke Bailey4,5, Farren B S Briggs4,5.   

Abstract

Most genotype-phenotype studies have historically lacked population diversity, impacting the generalizability of findings and thereby limiting the ability to equitably implement precision medicine. This well-documented problem has generated much interest in the ascertainment of new cohorts with an emphasis on multiple dimensions of diversity, including race/ethnicity, gender, age, socioeconomic status, disability, and geography. The most well known of these new cohort efforts is arguably All of Us, formerly known as the Precision Medicine Cohort Initiative Program. All of Us intends to ascertain at least one million participants in the United States representative of the multiple dimensions of diversity. As an incentive to participate, All of Us is offering the return of research results, including whole genome sequencing data, as well as the opportunity to contribute to the scientific process as non-scientists. The scale and scope of the proposed return of research results are unprecedented. Here, we briefly review possible return of genetic data models, including the likely data file formats and modes of data transfer or access. We also review the resources required to access and interpret the genetic or genomic data once received by the average participant, highlighting the nuanced anticipated barriers that will challenge both the digitally, computationally literate and illiterate participant alike. This inventory of resources required to receive, process, and interpret return of research results exposes the potential for access disparities and warns the scientific community to mind the gap so that all participants have equal access and understanding of the benefits of human genetic research.

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Year:  2019        PMID: 31161416      PMCID: PMC6767905          DOI: 10.1007/s00439-019-02033-5

Source DB:  PubMed          Journal:  Hum Genet        ISSN: 0340-6717            Impact factor:   4.132


  66 in total

1.  Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.

Authors:  Jamie K Teer; Lori L Bonnycastle; Peter S Chines; Nancy F Hansen; Natsuyo Aoyama; Amy J Swift; Hatice Ozel Abaan; Thomas J Albert; Elliott H Margulies; Eric D Green; Francis S Collins; James C Mullikin; Leslie G Biesecker
Journal:  Genome Res       Date:  2010-09-01       Impact factor: 9.043

2.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

3.  Efficient storage of high throughput DNA sequencing data using reference-based compression.

Authors:  Markus Hsi-Yang Fritz; Rasko Leinonen; Guy Cochrane; Ewan Birney
Journal:  Genome Res       Date:  2011-01-18       Impact factor: 9.043

4.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

Authors:  Heng Li
Journal:  Bioinformatics       Date:  2011-09-08       Impact factor: 6.937

5.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

Review 6.  The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Authors:  Peter J A Cock; Christopher J Fields; Naohisa Goto; Michael L Heuer; Peter M Rice
Journal:  Nucleic Acids Res       Date:  2009-12-16       Impact factor: 16.971

7.  A comprehensive analysis of high school genetics standards: are states keeping pace with modern genetics?

Authors:  M J Dougherty; C Pleasants; L Solow; A Wong; H Zhang
Journal:  CBE Life Sci Educ       Date:  2011       Impact factor: 3.325

8.  SNPedia: a wiki supporting personal genome annotation, interpretation and analysis.

Authors:  Michael Cariaso; Greg Lennon
Journal:  Nucleic Acids Res       Date:  2011-12-02       Impact factor: 16.971

9.  The variant call format and VCFtools.

Authors:  Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

10.  Veterans' attitudes regarding a database for genomic research.

Authors:  David Kaufman; Juli Murphy; Lori Erby; Kathy Hudson; Joan Scott
Journal:  Genet Med       Date:  2009-05       Impact factor: 8.822

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  4 in total

1.  In Different Voices: The Views of People with Disabilities about Return of Results from Precision Medicine Research.

Authors:  Maya Sabatello; Yuan Zhang; Ying Chen; Paul S Appelbaum
Journal:  Public Health Genomics       Date:  2020-04-15       Impact factor: 2.000

2.  DNA-based screening and personal health: a points to consider statement for individuals and health-care providers from the American College of Medical Genetics and Genomics (ACMG).

Authors:  Lora J H Bean; Maren T Scheuner; Michael F Murray; Leslie G Biesecker; Robert C Green; Kristin G Monaghan; Glenn E Palomaki; Richard R Sharp; Tracy L Trotter; Michael S Watson; Cynthia M Powell
Journal:  Genet Med       Date:  2021-03-31       Impact factor: 8.822

3.  Evaluating co-created patient-facing materials to increase understanding of genetic test results.

Authors:  Andrew A Dwyer; Margaret G Au; Neil Smith; Lacey Plummer; Margaret F Lippincott; Ravikumar Balasubramanian; Stephanie B Seminara
Journal:  J Genet Couns       Date:  2020-10-24       Impact factor: 2.537

4.  Frequency of ClinVar Pathogenic Variants in Chronic Kidney Disease Patients Surveyed for Return of Research Results at a Cleveland Public Hospital.

Authors:  Dana C Crawford; John Lin; Jessica N Cooke Bailey; Tyler Kinzy; John R Sedor; John F O'Toole; William S Bush
Journal:  Pac Symp Biocomput       Date:  2020
  4 in total

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