Clinical Service Delivery of Noninvasive Prenatal Diagnosis by Relative Haplotype Dosage for Single-Gene Disorders

Abstract

A relative haplotype dosage (RHDO)–based method was developed and implemented into routine clinical practice for noninvasive prenatal diagnosis (NIPD) of multiple single-gene disorders: spinal muscular atrophy, Duchenne and Becker muscular dystrophies, and cystic fibrosis. This article describes the experiences of the first 152 pregnancies to have NIPD by RHDO as part of a routine clinical service. Provision of results within a clinically useful time frame (mean, 11 calendar days) was shown to be possible, with a very low failure rate (4%), none being due to a technical failure. Where follow-up confirmatory testing was performed for audit purposes, 100% concordance was seen with the NIPD result, and no discrepancies have been reported. The robust performance of the assay, together with high sensitivity and specificity, demonstrates that NIPD by RHDO is feasible for use in a clinical setting.

Non-Invasive Prenatal Diagnosis of Retinoblastoma Inheritance by Combined Targeted Sequencing Strategies

“…The fetal fraction is known to increase with maternal gestation [16,17]. In our recent publication evaluating our NIPD by RHDO service on over 150 pregnancies [7], less than 6% of tests required a second sample to be taken due to a low fetal fraction after 8 weeks' gestation. In order to achieve a reportable result, we find that a fetal fraction >4% is often required for both amplicon-and capture-based NIPD, although as Family A shows, it is possible to detect the presence of a paternal or de novo mutation when the fetal load is less than this.…”

“…For families where the father is known to carry an RB1 variant >10 bp, RHDO analysis is an option where the couple has had a previous child. We have already implemented RHDO for paternal inheritance in autosomal recessive disorders SMA and CF [7,12]. While haplotype analysis is not suitable for de novo variants, we report a proof-of-principle case where NIPD of a variant of~2 Mb was achieved through capture-based targeted sequencing and direct detection.…”

“…Non-invasive prenatal diagnosis (NIPD), which analyses cell-free fetal DNA within the mother's blood, offers all the potential advantages of a prenatal result while avoiding the issues associated with an invasive procedure. Unlike non-invasive prenatal testing (NIPT) screening, NIPD is considered a definitive diagnostic test, where confirmation by invasive means is not required [7]. Furthermore, NIPD testing is available from 8 weeks' gestation, earlier than both CVS and amniocentesis.…”

“…This method overcomes the difficulty in detecting maternal variants and, as it uses linkage-based approach, does not require test development for family-specific variants, some of which may be unsuitable for direct detection. These tests are now part of our routine clinical service in the UK, providing non-invasive prenatal diagnosis for pregnancies at risk of cystic fibrosis (CF), spinal muscular atrophy (SMA), Duchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD), with over 150 pregnancies tested since September 2016 [7].…”

Next Generation Sequencing after Invasive Prenatal Testing in Fetuses with Congenital Malformations: Prenatal or Neonatal Investigation

“…Since the advent of next generation sequencing and digital PCR, the potential of cell-free fetal DNA based testing for monogenic disorders has increased dramatically. There are a number of reports in the literature reporting routine use for pregnancies where there is a relevant family history of a specific disorder [ 24 , 25 , 26 , 27 ]. There is ongoing translational research into circulating fetal cells and circulating fetal trophoblast cells (CFTCs) for NIPD of monogenic disease [ 28 , 29 ].…”