Publication Date
3-3-2024
Journal
BMC Research Notes
DOI
10.1186/s13104-024-06723-w
PMID
38433186
PMCID
PMC10910835
PubMedCentral® Posted Date
3-3-2024
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
Keywords
Humans, High-Throughput Nucleotide Sequencing, Bone Marrow Transplantation, Clinical Laboratory Services, Genotype, Laboratories, Next-generation sequencing (NGS), Clinical testing, Sex concordance, SNP genotyping
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.
Included in
Biological Phenomena, Cell Phenomena, and Immunity Commons, Biomedical Informatics Commons, Genetics and Genomics Commons, Medical Genetics Commons, Medical Molecular Biology Commons, Medical Specialties Commons
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