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Genetic sex validation for sample tracking in next-generation sequencing clinical testing.
Hu, Jianhong; Korchina, Viktoriya; Zouk, Hana; Harden, Maegan V; Murdock, David; Macbeth, Alyssa; Harrison, Steven M; Lennon, Niall; Kovar, Christie; Balasubramanian, Adithya; Zhang, Lan; Chandanavelli, Gauthami; Pasham, Divya; Rowley, Robb; Wiley, Ken; Smith, Maureen E; Gordon, Adam; Jarvik, Gail P; Sleiman, Patrick; Kelly, Melissa A; Bland, Harris T; Murugan, Mullai; Venner, Eric; Boerwinkle, Eric; Prows, Cynthia; Mahanta, Lisa; Rehm, Heidi L; Gibbs, Richard A; Muzny, Donna M.
Afiliação
  • Hu J; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Korchina V; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Zouk H; Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA.
  • Harden MV; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
  • Murdock D; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Macbeth A; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Harrison SM; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
  • Lennon N; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Kovar C; Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA.
  • Balasubramanian A; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Zhang L; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Chandanavelli G; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Pasham D; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Rowley R; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Wiley K; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Smith ME; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Gordon A; Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA.
  • Jarvik GP; Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA.
  • Sleiman P; Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
  • Kelly MA; Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
  • Bland HT; Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA, USA.
  • Murugan M; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
  • Venner E; Genomic Medicine Institute, Geisinger, Danville, PA, USA.
  • Boerwinkle E; Vanderbilt University Medical Center, Nashville, TN, USA.
  • Prows C; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Mahanta L; Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
  • Rehm HL; Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA.
  • Muzny DM; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
BMC Res Notes ; 17(1): 62, 2024 Mar 03.
Article em En | MEDLINE | ID: mdl-38433186
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 (49.09%), samples from transgender participants (3.64%) and stem cell or bone marrow transplant patients (7.27%) along with undetermined sample mix-ups (40%) for which sample swaps occurred prior to arrival at genome centers, however the exact cause of the events at the sampling sites resulting in the mix-ups were not able to be determined.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Sequenciamento de Nucleotídeos em Larga Escala / Serviços de Laboratório Clínico Limite: Humans Idioma: En Ano de publicação: 2024 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Sequenciamento de Nucleotídeos em Larga Escala / Serviços de Laboratório Clínico Limite: Humans Idioma: En Ano de publicação: 2024 Tipo de documento: Article