Language

English

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

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.

Keywords

Humans, High-Throughput Nucleotide Sequencing, Bone Marrow Transplantation, Clinical Laboratory Services, Genotype, Laboratories, Next-generation sequencing (NGS), Clinical testing, Sex concordance, SNP genotyping

Published Open-Access

yes

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