Genetic sex validation for sample tracking in next-generation sequencing clinical testing
-
期刊论文
-
出版模式:
开放获取
-
发表日期:
2024年3月3日
- 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,
- Debra J. Abrams,
- Samuel E. Adunyah,
- Ladia H. Albertson-Junkans,
- Berta Almoguera,
- Paul S. Appelbaum,
- Samuel Aronson,
- Sharon Aufox,
- Lawrence J. Babb,
- Hana Bangash,
- Melissa A. Basford,
- Meckenzie Behr,
- Barbara Benoit,
- Elizabeth J. Bhoj,
- Sarah T. Bland,
- Kenneth M. Borthwick,
- Erwin P. Bottinger,
- Deborah J. Bowen,
- Mark Bowser,
- Murray Brilliant,
- Adam H. Buchanan,
- Andrew Cagan,
- Pedro J. Caraballo,
- David J. Carey,
- David S. Carrell,
- Victor M. Castro,
- Rex L. Chisholm,
- Wendy Chung,
- Christopher G. Chute,
- Brittany B. City,
- Ellen Wright Clayton,
- Beth L. Cobb,
- John J. Connolly,
- Paul K. Crane,
- Katherine D. Crew,
- David R. Crosslin,
- Renata P. da Silva,
- Jyoti G. Dayal,
- Mariza De Andrade,
- Josh C. Denny,
- Ozan Dikilitas,
- Alanna J. DiVietro,
- Kevin R. Dufendach,
- Todd L. Edwards,
- Christine Eng,
- David Fasel,
- Alex Fedotov,
- Stephanie M. Fullerton,
- Birgit Funke,
- Stacey Gabriel,
- Vivian S. Gainer,
- Ali Gharavi,
- Joe T. Glessner,
- Jessica M. Goehringer,
- Adam S. Gordon,
- Chet Graham,
- Heather S. Hain,
- Hakon Hakonarson,
- John Harley,
- Margaret Harr,
- Andrea L. Hartzler,
- Scott Hebbring,
- Jacklyn N. Hellwege,
- Nora B. Henrikson,
- Christin Hoell,
- Ingrid Holm,
- George Hripcsak,
- Alexander L. Hsieh,
- Elizabeth D. Hynes,
- Darren K. Johnson,
- Laney K. Jones,
- Yoonjung Y. Joo,
- Sheethal Jose,
- Navya Shilpa Josyula,
- Anne E. Justice,
- Elizabeth W. Karlson,
- Kenneth M. Kaufman,
- Jacob M. Keaton,
- Eimear E. Kenny,
- Dustin L. Key,
- Atlas Khan,
- H. Lester Kirchner,
- Krzysztof Kiryluk,
- Terrie Kitchner,
- Barbara J. Klanderman,
- David C. Kochan,
- Emily Kudalkar,
- Benjamin R. Kuhn,
- Iftikhar J. Kullo,
- Philip Lammers,
- Eric B. Larson,
- Matthew S. Lebo,
- Ming Ta Michael Lee,
- Kathleen A. Leppig,
- Chiao-Feng Lin,
- Jodell E. Linder,
- Noralane M. Lindor,
- Todd Lingren,
- Cong Liu,
- Yuan Luo,
- John Lynch,
- Bradley A. Malin,
- Brandy M. Mapes,
- Maddalena Marasa,
- Keith Marsolo,
- Elizabeth McNally,
- Frank D. Mentch,
- Erin M. Miller,
- Hila Milo Rasouly,
- Shawn N. Murphy,
- Melanie F. Myers,
- Bahram Namjou,
- Addie I. Nesbitt,
- Jordan Nestor,
- Yizhao Ni,
- Janet E. Olson,
- Aniwaa Owusu Obeng,
- Jennifer A. Pacheco,
- Joel E. Pacyna,
- Thomas N. Person,
- Josh F. Peterson,
- Lynn Petukhova,
- Cassandra Pisieczko,
- Siddharth Pratap,
- Megan J. Puckelwartz,
- Alanna K. Rahm,
- James D. Ralston,
- Arvind Ramaprasan,
- Luke V. Rasmussen,
- Laura J. Rasmussen-Torvik,
- Dan M. Roden,
- Elisabeth A. Rosenthal,
- Maya S. Safarova,
- Avni Santani,
- Juliann M. Savatt,
- Daniel J. Schaid,
- Steven Scherer,
- Baergen I. Schultz,
- Aaron Scrol,
- Soumitra Sengupta,
- Gabriel Q. Shaibi,
- Ning Shang,
- Himanshu Sharma,
- Richard R. Sharp,
- Yufeng Shen,
- Rajbir Singh,
- Jordan W. Smoller,
- Duane T. Smoot,
- Ian B. Stanaway,
- Justin Starren,
- Timoethia M. Stone,
- Amy C. Sturm,
- Agnes S. Sundaresan,
- Peter Tarczy-Hornoch,
- Casey Overby Taylor,
- Lifeng Tian,
- Sara L. Van Driest,
- Matthew Varugheese,
- Lyam Vazquez,
- David L. Veenstra,
- Digna R. Velez Edwards,
- Miguel Verbitsky,
- Kimberly Walker,
- Nephi Walton,
- Theresa Walunas,
- Firas H. Wehbe,
- Wei-Qi Wei,
- Scott T. Weiss,
- Quinn S. Wells,
- Chunhua Weng,
- Marc S. Williams,
- Janet Williams,
- Leora Witkowski,
- Laura Allison B. Woods,
- Julia Wynn,
- Yanfei Zhang,
- Jodell Jackson,
- Cynthia Prows,
- Lisa Mahanta,
- Heidi L. Rehm,
- Richard A. Gibbs,
- Donna M. Muzny
摘要
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.
ResultsPrecise 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.