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• W4239657238 abstract "American Journal of Medical Genetics Part AVolume 170, Issue 3 p. 556-557 the AJMG SEQUENCE: Decoding News and Trends for the Medical Genetics Community by Deborah LevensonFree Access Noninvasive prenatal testing can detect gene deletions, duplications Use of cell-free fetal DNA for NIPT promising but not yet ready for clinical use First published: 17 February 2016 https://doi.org/10.1002/ajmg.a.37581Citations: 1AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Noninvasive prenatal testing (NIPT) that relies on cell-free fetal DNA circulating in maternal blood to detect extra chromosomes can also find smaller deletions and duplications in genes, but is not ready for the clinic, according to recent research. These tests are now widely used to prenatally screen for trisomies 13, 18, and 21. Using NIPT to screen for single-gene disorders has been challenging because most of the DNA in the maternal plasma is derived from the mother. Writing in Proceedings of the National Academy of Sciences (PNAS), researchers at the University of California at San Diego (UCSD) who used NIPT to detect subchromosomal variations say the technique may need a higher percentage of fetal DNA or a higher depth of coverage than conventional aneuploidy testing and has a high false-positive rate (Yin et al., 2015). The researchers tested their shotgun sequencing method on 1,476 pregnant women with fetal abnormalities previously detected by ultrasound and invasive testing with array comparative genomic hybridization (CGH). At a sequencing depth of 35 million reads, NIPT initially detected only 71.9% percent of the deletions and duplications that were detected by CGH. When the team increased sequencing depth to 10 million reads and identified only those abnormalities larger than 1 megabase (Mb), the detection rate rose to 94.5%, showing that a deeper sequencing depth may be necessary, researchers say. “In pregnancy, [single-gene disorders] such as cystic fibrosis or sickle cell anemia have to be detected in amniotic fluid right now. Our ultimate goal is to diagnose all genetic defects of the fetus with maternal blood as soon as possible,” says senior author Kang Zhang, MD, PhD, Chief of Ophthalmic Genetics and Founding Director of the Institute for Genomic Medicine at UCSD. False Positives Reported Using NIPT in these women returned a false-positive rate of 3.8% with a sequencing depth of 3.5 million reads, one that Dr. Zhang calls “a little too high.” Of those false-positive results, 67.2% predicted small variations less than 5 Mb in size. In addition to variation size, genetic abnormalities in maternal blood may also play a role in false positives. Validation by CGH testing of samples with false-positive results revealed that a majority (63.6%) contained deletions and duplications in maternal DNA. “We need to improve accuracy by making sure [detected] defects are from the fetus, not the mother,” says Dr. Zhang. Timing is an important factor in the test's accuracy. Gestational age ranged from 12 to 37 weeks, with an average age of 24 weeks, “much later than NIPT would ideally be applied,” note researchers. Most gynecologists want NIPT results confirmed by diagnostic testing by week 16 of pregnancy. Advances in noninvasive prenatal testing may make it a viable screening method for a wider array of single-gene disorders. © Romaset/Shutterstock.com But about one-third of pregnant women in weeks 12 to 16 did not have sufficient amounts of fetal DNA for the test to detect, according to researchers. Levels of fetal DNA in maternal blood rise as pregnancy progresses. The researchers have called for more study of their test earlier in the first trimester of pregnancy. Ethical Issues Raised In their paper, the authors emphasize the need for appropriate genetic counseling for patients who undergo NIPT to explain findings that could include variants of unknown significance. The ethical issues involved with NIPT as a screen for single-gene disorders are the same as those for all other prenatal screening tests, says Joe Leigh Simpson, MD, Senior Vice President at the March of Dimes Foundation in White Plains, New York. They include the prospect of terminating the pregnancy based on test results and proper informed consent that includes discussion of possible findings indicating risk of an untreatable childhood disease or one that likely would not strike until adulthood. The test might even detect variations that could cause cancer or other diseases in the mother, he notes. With time, however, NIPT will become a viable prenatal screening method for a wider array of single-gene disorders, Dr. Simpson predicts. “When this test works, it will be unconscionable not to offer the test to patients,” he adds. Reference Yin AH, Peng CF, Zhao X, Caughey BA, Yang JX, Liu J, Huang WW, Liu C, Luo DH, Liu HL, Chen YY, Wu J, Hou R, Zhang M, Ai M, Zheng L, Xue RQ, Mai MQ, Guo FF, Qi YM, Wang DM, Krawczyk M, Zhang D, Wang YN, Huang QF, Karin M, Zhang K. 2015. Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA. Proc Natl Acad Sci USA 112(47): 14670– 14675. Citing Literature Volume170, Issue3March 2016Pages 556-557 ReferencesRelatedInformation" @default.
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• W4239657238 title "Noninvasive prenatal testing can detect gene deletions, duplications" @default.
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