Clinical performance of non‐invasive prenatal testing (NIPT) using targeted cell‐free DNA analysis in maternal plasma with microarrays or next generation sequencing (NGS) is consistent across multiple controlled clinical studies

Abstract

ObjectiveTo evaluate the clinical performance of non‐invasive prenatal testing for trisomy 21, 18, and 13 using targeted cell‐free DNA (cfDNA) analysis.MethodsTargeted cfDNA analysis using DANSR™ and FORTE™ with microarray quantitation was used to evaluate the risk of trisomy 21, 18, and 13 in blinded samples from 799 singleton, twin, natural, and IVF pregnancies. Subjects either had fetal chromosome evaluation by karyotype, FISH, QF‐PCR, or karyotype for newborns with suspected aneuploidy at birth. The results of targeted cfDNA analysis were compared to clinical genetic testing outcomes to assess clinical performance.ResultsTargeted cfDNA analysis with microarray quantification identified 107/108 trisomy 21 cases (99.1%), 29/30 trisomy 18 cases (96.7%), and 12/12 trisomy 13 cases (100%). The specificity was 100% for all three trisomies. Combining this data with all published clinical performance studies using DANSR/FORTE methodology for greater than 23 000 pregnancies, the sensitivity of targeted cfDNA analysis was calculated to be greater than 99% for trisomy 21, 97% for trisomy 18, and 94% for trisomy 13. Specificity for each trisomy was greater than 99.9%.ConclusionTargeted cfDNA analysis demonstrates consistently high sensitivity and extremely low false positive rates for common autosomal trisomies in pregnancy across quantitation platforms. © 2015 Ariosa Diagnostics Inc. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

Noninvasive prenatal screening for fetal aneuploidy, 2016 update: a position statement of the American College of Medical Genetics and Genomics

“…Analytical validity has been established for the variety of screening methods discussed in this article. 10,[16][17][18][19] • Clinical validity refers to how well NIPS performs and focuses on detection rate (DR), the proportion of those who screen positive and will have the clinical condition (clinical sensitivity), and the proportion who will not (clinical specificity (SPEC)). These test metrics are independent of the prevalence of the condition being screened.…”

“…Validation studies make the point that DR and SPEC depend on many variables (e.g., depth of read), 10,[60][61][62][63] which can change the false-positive and false-negative rate when NIPS is used for prenatal detection of CNVs. Pretest and posttest counseling is further confounded by variable expressivity and penetrance of the conditions being screened, size of the deletion being screened, specific genes within the critical region of the locus interrogated, and the number of genes within the critical region being screened.…”

“…9 Microarray technology can also be used to quantify DNA. 10 Bioinformatics that enable these methodologies is complex and proprietary. Since the introduction of NIPS in 2011, health-care providers and patients have experienced marketing pressures, rapidly evolving professional practice guidelines, and confusion regarding the appropriate role of Noninvasive prenatal screening using cell-free DNA (NIPS) has been rapidly integrated into prenatal care since the initial American College of Medical Genetics and Genomics (ACMG) statement in 2013.…”

Establishment of a human trisomy 18 induced pluripotent stem cell line from amniotic fluid cells

“…This trisomy usually manifests as abnormal development of multiple tissues and organs during prenatal ultrasound screening and is subsequently confirmed by karyotype analysis of cultured amniotic fluid cells (AFC). As a result of recent developments in and clinical use of next-generation sequencing (NGS)-based noninvasive prenatal diagnosis (NIPD) technologies, an unprecedentedly large number of fetuses with 18T have been screened, and 18T has been identified as a leading cause of miscarriages (3)(4)(5).…”

Noninvasive Prenatal Screening of Fetal Aneuploidy without Massively Parallel Sequencing

“…The actual fetal fraction is dependent on factors such as ges-tational age, maternal weight, and extraction method (10,11 ). In particular, these tests rely on whole-genome or targeted sequencing (12,13 ) to reveal the overrepresentation of chromosome 21 (in terms of Down syndrome) in comparison to the euploid reference genome (14 ); however, 1 group has introduced a microarraybased approach employing a similar counting method (15 ). The small increase in read counts from chromosome 21 is detectable owing to the unprecedented coverage and depth of the next-generation sequencing (NGS) platform.…”