Identifying rare, medically-relevant genetic variation in a diverse population: opportunities and pitfalls Article Swipe
Kevin M. Bowling
,
Michelle L. Thompson
,
Stacy W. Gray
,
James M.J. Lawlor
,
Kelly L. Williams
,
Kelly M. East
,
Whitley V. Kelley
,
Irene Moss
,
Devin Absher
,
E. Christopher Partridge
,
Anna Hurst
,
Jeffrey C. Edberg
,
Gregory S. Barsh
,
Bruce R. Korf
,
Gregory M. Cooper
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1101/2020.05.28.122457
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1101/2020.05.28.122457
Purpose To evaluate the effectiveness and specificity of population-based genomic screening in Alabama. Methods The Alabama Genomic Health Initiative (AGHI) has enrolled and evaluated 5,369 participants for the presence of pathogenic/likely pathogenic (P/LP) variants using the Illumina Global Screening Array (GSA), with validation of all P/LP variants via Sanger sequencing in a CLIA-certified laboratory before return of results. Results Among 131 variants identified by the GSA that were evaluated by Sanger sequencing, 67 (51%) were false positives (FP). For 39 of the 67 FP variants, a benign/likely benign variant was present at or near the targeted P/LP variant. Importantly, African-Americans were significantly enriched for FP variants, likely due to a higher rate of non-targeted alternative alleles close to array-targeted P/LP variants. Conclusion In AGHI, we have implemented an array-based process to screen for highly penetrant genetic variants in actionable disease genes. We demonstrate the need for clinical validation of array-identified variants in direct-to-consumer or population testing, especially for diverse populations.
Related Topics
Concepts
Sanger sequencing
False positive paradox
Genetics
Computational biology
Population
Biology
Allele frequency
Allele
Gene
Medicine
DNA sequencing
Computer science
Environmental health
Machine learning
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2020.05.28.122457
- https://www.biorxiv.org/content/biorxiv/early/2020/06/02/2020.05.28.122457.full.pdf
- OA Status
- green
- References
- 30
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3031360147
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3031360147Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2020.05.28.122457Digital Object Identifier
- Title
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Identifying rare, medically-relevant genetic variation in a diverse population: opportunities and pitfallsWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2020Year of publication
- Publication date
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2020-06-02Full publication date if available
- Authors
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Kevin M. Bowling, Michelle L. Thompson, Stacy W. Gray, James M.J. Lawlor, Kelly L. Williams, Kelly M. East, Whitley V. Kelley, Irene Moss, Devin Absher, E. Christopher Partridge, Anna Hurst, Jeffrey C. Edberg, Gregory S. Barsh, Bruce R. Korf, Gregory M. CooperList of authors in order
- Landing page
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https://doi.org/10.1101/2020.05.28.122457Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2020/06/02/2020.05.28.122457.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2020/06/02/2020.05.28.122457.full.pdfDirect OA link when available
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Sanger sequencing, False positive paradox, Genetics, Computational biology, Population, Biology, Allele frequency, Allele, Gene, Medicine, DNA sequencing, Computer science, Environmental health, Machine learningTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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30Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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