Genetic sex validation for sample tracking in next-generation sequencing clinical testing.

TitleGenetic sex validation for sample tracking in next-generation sequencing clinical testing.
Publication TypeJournal Article
Year of Publication2024
AuthorsHu, J, Korchina, V, Zouk, H, Harden, MV, Murdock, DR, Macbeth, A, Harrison, SM, Lennon, N, Kovar, C, Balasubramanian, A, Zhang, L, Chandanavelli, G, Pasham, D, Rowley, R, Wiley, K, Smith, ME, Gordon, A, Jarvik, GP, Sleiman, P, Kelly, MA, Bland, HT, Murugan, M, Venner, E, Boerwinkle, E, Prows, C, Mahanta, L, Rehm, HL, Gibbs, RA, Muzny, DM
Corporate AuthorseMERGE III consortium
JournalBMC Res Notes
Volume17
Issue1
Pagination62
Date Published2024 Mar 03
ISSN1756-0500
KeywordsBone Marrow Transplantation, Clinical Laboratory Services, Genotype, High-Throughput Nucleotide Sequencing, Humans, Laboratories
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.

DOI10.1186/s13104-024-06723-w
Alternate JournalBMC Res Notes
PubMed ID38433186
PubMed Central IDPMC10910835
Grant ListU01HG8684 / HG / NHGRI NIH HHS / United States
U01HG8685 / HG / NHGRI NIH HHS / United States
U01HG8657 / HG / NHGRI NIH HHS / United States
U01HG8679 / HG / NHGRI NIH HHS / United States
U01HG8666 / HG / NHGRI NIH HHS / United States
U01HG8673 / HG / NHGRI NIH HHS / United States
U01 HG008685 / HG / NHGRI NIH HHS / United States
U01HG8664 / HG / NHGRI NIH HHS / United States
U01HG8701 / HG / NHGRI NIH HHS / United States
U01 HG008680 / HG / NHGRI NIH HHS / United States
U01HG8676 / HG / NHGRI NIH HHS / United States

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