Title | Genetic sex validation for sample tracking in next-generation sequencing clinical testing. |
Publication Type | Journal Article |
Year of Publication | 2024 |
Authors | Hu, J, Korchina, V, Zouk, H, Harden, MV, Murdock, D, 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 Authors | eMERGE III consortium |
Journal | BMC Res Notes |
Volume | 17 |
Issue | 1 |
Pagination | 62 |
Date Published | 2024 Mar 03 |
ISSN | 1756-0500 |
Keywords | Bone 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. |
DOI | 10.1186/s13104-024-06723-w |
Alternate Journal | BMC Res Notes |
PubMed ID | 38433186 |
PubMed Central ID | PMC10910835 |
Grant List | U01HG8684 / 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 U01HG8676 / HG / NHGRI NIH HHS / United States |
Genetic sex validation for sample tracking in next-generation sequencing clinical testing.
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