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- Title
Genetic sex validation for sample tracking in next-generation sequencing clinical testing.
- Authors
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.
- 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.
- Subjects
NUCLEOTIDE sequencing; BONE marrow; BONE marrow cells; SAMPLING errors; QUALITY control; SINGLE nucleotide polymorphisms
- Publication
BMC Research Notes, 2024, Vol 17, Issue 1, p1
- ISSN
1756-0500
- Publication type
Article
- DOI
10.1186/s13104-024-06723-w