Genetic Sex Validation for Sample Tracking in Clinical Testing-Reference-Cited by-同舟云学术

Genetic Sex Validation for Sample Tracking in Clinical Testing

Published:2023-09-11 Issue: Volume: Page:
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Author:

Hu Jianhong¹,Korchina Viktoriya¹,Zouk Hana²,Harden Maegan V.³,Murdock David¹,Macbeth Alyssa³,Harrison Steven M.²,Lennon Niall³,Kovar Christie¹,Balasubramanian Adithya¹,Zhang Lan¹,Chandanavelli Gauthami¹,Pasham Divya¹,Rowley Robb⁴,Wiley Ken⁴,Smith Maureen E.⁵,Gordon Adam⁵,Jarvik Gail P.⁶,Sleiman Patrick⁷,Kelly Melissa A⁸,Bland Harris T.⁹,Murugan Mullai¹,Venner Eric¹,Boerwinkle Eric¹,Prows Cynthia¹⁰,Mahanta Lisa²,Rehm Heidi L.³,Gibbs Richard A.¹,Muzny Donna M.¹

Affiliation:

1. Baylor College of Medicine, Human Genome Sequencing Center (HGSC)

2. Laboratory for Molecular Medicine (LMM), Mass General Brigham

3. Broad Institute of MIT and Harvard

4. National Human Genome Research Institute

5. Northwestern University Feinberg School of Medicine

6. University of Washington Medical Center

7. Children's Hospital of Philadelphia

8. Genomic Medicine Institute, Geisinger

9. Vanderbilt University Medical Center

10. Cincinnati Children's Hospital Medical Center

Abstract

Abstract Objective Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. Results Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients along with undetermined sample mix-ups.

Publisher

Research Square Platform LLC

Reference16 articles.

1. Next-generation sequencing to identify genetic causes of cardiomyopathies;Norton N;Curr Opin Cardiol,2012

2. Exome sequencing: dual role as a discovery and diagnostic tool;Ku CS;Ann Neurol,2012

3. Clinical whole-exome sequencing for the diagnosis of mendelian disorders;Yang Y;N Engl J Med,2013

4. A Review of Medical Errors in Laboratory Diagnostics and Where We Are Today;Hammerling JA;Lab Med,2012

5. Short tandem repeat analysis for human identity testing;Butler JM;Curr Protoc Hum Genet,2004