Genetic Sex Validation for Sample Tracking in Clinical Testing.

TitleGenetic Sex Validation for Sample Tracking in Clinical Testing.
Publication TypeJournal Article
Year of Publication2023
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
JournalRes Sq
Date Published2023 Sep 11
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, samples from transgender participants and stem cell or bone marrow transplant patients along with undetermined sample mix-ups.

DOI10.21203/rs.3.rs-3304685/v1
Alternate JournalRes Sq
PubMed ID37790445
PubMed Central IDPMC10543510
Grant ListU01 HG008676 / HG / NHGRI NIH HHS / United States
U01 HG008657 / HG / NHGRI NIH HHS / United States
U01 HG008672 / HG / NHGRI NIH HHS / United States
U01 HG008684 / HG / NHGRI NIH HHS / United States
U01 HG008679 / HG / NHGRI NIH HHS / United States
U01 HG008666 / HG / NHGRI NIH HHS / United States
U54 MD007593 / MD / NIMHD NIH HHS / United States
U01 HG008680 / HG / NHGRI NIH HHS / United States
U01 HG008673 / HG / NHGRI NIH HHS / United States
U01 HG008685 / HG / NHGRI NIH HHS / United States
U01 HG006379 / HG / NHGRI NIH HHS / United States
U01 HG008664 / HG / NHGRI NIH HHS / United States
U01 HG008701 / HG / NHGRI NIH HHS / United States