학술논문
Genetic sex validation for sample tracking in next-generation sequencing clinical testing
Document Type
Report
Author
Hu, Jianhong; Korchina, Viktoriya; Zouk, Hana; Harden, Maegan V.; Murdock, David; Macbeth, Alyssa; Harrison, Steven M.; Lennon, Niall; Kovar, Christie; Balasubramanian, Adithya; Zhang, Lan; Chandanavelli, Gauthami; Pasham, Divya; Rowley, Robb; Wiley, Ken; Smith, Maureen E.; Gordon, Adam; Jarvik, Gail P.; Sleiman, Patrick; Kelly, Melissa A.; Bland, Harris T.; Murugan, Mullai; Venner, Eric; Boerwinkle, Eric; Abrams, Debra J.; Adunyah, Samuel E.; Albertson-Junkans, Ladia H.; Almoguera, Berta; Appelbaum, Paul S.; Aronson, Samuel; Aufox, Sharon; Babb, Lawrence J.; Bangash, Hana; Basford, Melissa A.; Behr, Meckenzie; Benoit, Barbara; Bhoj, Elizabeth J.; Bland, Sarah T.; Borthwick, Kenneth M.; Bottinger, Erwin P.; Bowen, Deborah J.; Bowser, Mark; Brilliant, Murray; Buchanan, Adam H.; Cagan, Andrew; Caraballo, Pedro J.; Carey, David J.; Carrell, David S.; Castro, Victor M.; Chisholm, Rex L.; Chung, Wendy; Chute, Christopher G.; City, Brittany B.; Clayton, Ellen Wright; Cobb, Beth L.; Connolly, John J.; Crane, Paul K.; Crew, Katherine D.; Crosslin, David R.; da Silva, Renata P.; Dayal, Jyoti G.; De Andrade, Mariza; Denny, Josh C.; Dikilitas, Ozan; DiVietro, Alanna J.; Dufendach, Kevin R.; Edwards, Todd L.; Eng, Christine; Fasel, David; Fedotov, Alex; Fullerton, Stephanie M.; Funke, Birgit; Gabriel, Stacey; Gainer, Vivian S.; Gharavi, Ali; Glessner, Joe T.; Goehringer, Jessica M.; Gordon, Adam S.; Graham, Chet; Hain, Heather S.; Hakonarson, Hakon; Harley, John; Harr, Margaret; Hartzler, Andrea L.; Hebbring, Scott; Hellwege, Jacklyn N.; Henrikson, Nora B.; Hoell, Christin; Holm, Ingrid; Hripcsak, George; Hsieh, Alexander L.; Hynes, Elizabeth D.; Johnson, Darren K.; Jones, Laney K.; Joo, Yoonjung Y.; Jose, Sheethal; Josyula, Navya Shilpa; Justice, Anne E.; Karlson, Elizabeth W.; Kaufman, Kenneth M.; Keaton, Jacob M.; Kenny, Eimear E.; Key, Dustin L.; Khan, Atlas; Kirchner, H. Lester; Kiryluk, Krzysztof; Kitchner, Terrie; Klanderman, Barbara J.; Kochan, David C.; Kudalkar, Emily; Kuhn, Benjamin R.; Kullo, Iftikhar J.; Lammers, Philip; Larson, Eric B.; Lebo, Matthew S.; Lee, Ming Ta Michael; Leppig, Kathleen A.; Lin, Chiao-Feng; Linder, Jodell E.; Lindor, Noralane M.; Lingren, Todd; Liu, Cong; Luo, Yuan; Lynch, John; Malin, Bradley A.; Mapes, Brandy M.; Marasa, Maddalena; Marsolo, Keith; McNally, Elizabeth; Mentch, Frank D.; Miller, Erin M.; Rasouly, Hila Milo; Murphy, Shawn N.; Myers, Melanie F.; Namjou, Bahram; Nesbitt, Addie I.; Nestor, Jordan; Ni, Yizhao; Olson, Janet E.; Obeng, Aniwaa Owusu; Pacheco, Jennifer A.; Pacyna, Joel E.; Person, Thomas N.; Peterson, Josh F.; Petukhova, Lynn; Pisieczko, Cassandra; Pratap, Siddharth; Puckelwartz, Megan J.; Rahm, Alanna K.; Ralston, James D.; Ramaprasan, Arvind; Rasmussen, Luke V.; Rasmussen-Torvik, Laura J.; Roden, Dan M.; Rosenthal, Elisabeth A.; Safarova, Maya S.; Santani, Avni; Savatt, Juliann M.; Schaid, Daniel J.; Scherer, Steven; Schultz, Baergen I.; Scrol, Aaron; Sengupta, Soumitra; Shaibi, Gabriel Q.; Shang, Ning; Sharma, Himanshu; Sharp, Richard R.; Shen, Yufeng; Singh, Rajbir; Smoller, Jordan W.; Smoot, Duane T.; Stanaway, Ian B.; Starren, Justin; Stone, Timoethia M.; Sturm, Amy C.; Sundaresan, Agnes S.; Tarczy-Hornoch, Peter; Taylor, Casey Overby; Tian, Lifeng; Van Driest, Sara L.; Varugheese, Matthew; Vazquez, Lyam; Veenstra, David L.; Velez Edwards, Digna R.; Verbitsky, Miguel; Walker, Kimberly; Walton, Nephi; Walunas, Theresa; Wehbe, Firas H.; Wei, Wei-Qi; Weiss, Scott T.; Wells, Quinn S.; Weng, Chunhua; Williams, Marc S.; Williams, Janet; Witkowski, Leora; Woods, Laura Allison B.; Wynn, Julia; Zhang, Yanfei; Jackson, Jodell
Source
BMC Research Notes. March 3, 2024, Vol. 17 Issue 1
Subject
Language
English
ISSN
1756-0500
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: Next-generation sequencing (NGS), Clinical testing, Sex concordance, SNP genotyping
Author(s): Jianhong Hu[sup.1] , Viktoriya Korchina[sup.1] , Hana Zouk[sup.3,4] , Maegan V. Harden[sup.5] , David Murdock[sup.1,2] , Alyssa Macbeth[sup.5] , Steven M. Harrison[sup.3,5] , Niall Lennon[sup.5] , Christie Kovar[sup.1] , [...]
Author(s): Jianhong Hu[sup.1] , Viktoriya Korchina[sup.1] , Hana Zouk[sup.3,4] , Maegan V. Harden[sup.5] , David Murdock[sup.1,2] , Alyssa Macbeth[sup.5] , Steven M. Harrison[sup.3,5] , Niall Lennon[sup.5] , Christie Kovar[sup.1] , [...]