Academic Journal
Genetic sex validation for sample tracking in next-generation sequencing clinical testing
| Title: | Genetic sex validation for sample tracking in next-generation sequencing clinical testing |
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| Authors: | Jianhong Hu, Viktoriya Korchina, Hana Zouk, Maegan V. Harden, David Murdock, Alyssa Macbeth, Steven M. Harrison, Niall Lennon, Christie Kovar, Adithya Balasubramanian, Lan Zhang, Gauthami Chandanavelli, Divya Pasham, Robb Rowley, Ken Wiley, Maureen E. Smith, Adam Gordon, Gail P. Jarvik, Patrick Sleiman, Melissa A. Kelly, Harris T. Bland, Mullai Murugan, Eric Venner, Eric Boerwinkle, the eMERGE III consortium, Cynthia Prows, Lisa Mahanta, Heidi L. Rehm, Richard A. Gibbs, Donna M. Muzny |
| Source: | BMC Research Notes, Vol 17, Iss 1, Pp 1-8 (2024) |
| Publisher Information: | BMC, 2024. |
| Publication Year: | 2024 |
| Collection: | LCC:Medicine LCC:Biology (General) LCC:Science (General) |
| Subject Terms: | Next-generation sequencing (NGS), Clinical testing, Sex concordance, SNP genotyping, Medicine, Biology (General), QH301-705.5, Science (General), Q1-390 |
| More Details: | 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. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 1756-0500 |
| Relation: | https://doaj.org/toc/1756-0500 |
| DOI: | 10.1186/s13104-024-06723-w |
| Access URL: | https://doaj.org/article/3d38e5b62ab94770bb1d2b0b1ce48ef7 |
| Accession Number: | edsdoj.3d38e5b62ab94770bb1d2b0b1ce48ef7 |
| Database: | Directory of Open Access Journals |
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| ISSN: | 17560500 |
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| DOI: | 10.1186/s13104-024-06723-w |
| Published in: | BMC Research Notes |
| Language: | English |