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Martin K, Iyengar S, Kalyan A, Lan C, Simon AL, Stosic M, Kobara K, Ravi H, Truong T, Ryan A, Demko ZP, Benn P. Clinical experience with a single-nucleotide polymorphism-based non-invasive prenatal test for five clinically significant microdeletions. Clin Genet 2017; 93:293-300. [PMID: 28696552 DOI: 10.1111/cge.13098] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/30/2017] [Indexed: 01/06/2023]
Abstract
Single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT) can currently predict a subset of submicroscopic abnormalities associated with severe clinical manifestations. We retrospectively analyzed the performance of SNP-based NIPT in 80 449 referrals for 22q11.2 deletion syndrome and 42 326 referrals for 1p36, cri-du-chat, Prader-Willi, and Angelman microdeletion syndromes over a 1-year period, and compared the original screening protocol with a revision that reflexively sequenced high-risk calls at a higher depth of read. The prevalence of these microdeletion syndromes was also estimated in the referral population. The positive predictive value of the original test was 15.7% for 22q11.2 deletion syndrome, and 5.2% for the other 4 disorders combined. With the revised protocol, these values increased to 44.2% for 22q11.2 and 31.7% for the others. The 0.33% false-positive rate (FPR) for 22q11.2 deletion syndrome decreased to 0.07% with the revised protocol. Similarly, the FPR for the other 4 disorders combined decreased from 0.56% to 0.07%. Minimal prevalences were estimated to be 1 in 1255 for 22q11.2 deletion syndrome and 1 in 1464 for 1p36, cri-du-chat, and Angelman syndromes combined. Our results show that these microdeletions are relatively common in the referral population, and that the performance of SNP-based NIPT is improved with high-depth resequencing.
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Affiliation(s)
- K Martin
- Natera, Inc., San Carlos, California
| | - S Iyengar
- Natera, Inc., San Carlos, California
| | - A Kalyan
- Natera, Inc., San Carlos, California
| | - C Lan
- Natera, Inc., San Carlos, California
| | - A L Simon
- Natera, Inc., San Carlos, California
| | - M Stosic
- Natera, Inc., San Carlos, California
| | - K Kobara
- Natera, Inc., San Carlos, California
| | - H Ravi
- Natera, Inc., San Carlos, California
| | - T Truong
- Natera, Inc., San Carlos, California
| | - A Ryan
- Natera, Inc., San Carlos, California
| | - Z P Demko
- Natera, Inc., San Carlos, California
| | - P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut
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