Proof-of-principle rapid noninvasive prenatal diagnosis of autosomal recessive founder mutations

Abstract

BACKGROUND.Noninvasive prenatal testing can be used to accurately detect chromosomal aneuploidies in circulating fetal DNA; however, the necessity of parental haplotype construction is a primary drawback to noninvasive prenatal diagnosis (NIPD) of monogenic disease. Family-specific haplotype assembly is essential for accurate diagnosis of minuscule amounts of circulating cell-free fetal DNA; however, current haplotyping techniques are too time-consuming and laborious to be carried out within the limited time constraints of prenatal testing, hampering practical application of NIPD in the clinic. Here, we have addressed this pitfall and devised a universal strategy for rapid NIPD of a prevalent mutation in the Ashkenazi Jewish (AJ) population. METHODS.Pregnant AJ couples, carrying mutation(s) in GBA, which encodes acid β-glucosidase, were recruited at the SZMC Gaucher Clinic. Targeted next-generation sequencing of GBA-flanking SNPs was performed on peripheral blood samples from each couple, relevant mutation carrier family members, and unrelated individuals who are homozygotes for an AJ founder mutation. Allele-specific haplotypes were constructed based on linkage, and a consensus Gaucher disease-associated founder mutation-flanking haplotype was fine mapped. Together, these haplotypes were used for NIPD. All test results were validated by conventional prenatal or postnatal diagnostic methods. RESULTS.Ten parental alleles in eight unrelated fetuses were diagnosed successfully based on the noninvasive method developed in this study. The consensus mutation-flanking haplotype aided diagnosis for 6 of 9 founder mutation alleles. CONCLUSIONS.The founder NIPD method developed and described here is rapid, economical, and readily adaptable for prenatal testing of prevalent autosomal recessive disease-causing mutations in an assortment of worldwide populations. FUNDING. SZMC,

Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

“…This haplotype-based approach has imposed two limitations to NIPT. First, it requires the elucidation of the maternal haplotype using a direct haplotyping approach (11)(12)(13), via pedigree analysis (8,14), or via founder haplotype analysis in selected populations (15). Second, this haplotype-based approach has limited the resolution in which the maternal inheritance of the fetus can be determined.…”

Non‐invasive prenatal testing for fetal inheritance of maternal β‐thalassaemia mutations using targeted sequencing and relative mutation dosage: a feasibility study

“…However, there have been few studies concerning detection of the maternal mutation. Recent work has demonstrated successful use of RHDO for detection of inheritance of maternal mutations . RHDO has been implemented successfully into some clinical laboratories, but generally remains prohibitively expensive .…”

“…Recent work has demonstrated successful use of RHDO for detection of inheritance of maternal mutations. [26][27][28][29][30] RHDO has been implemented successfully into some clinical laboratories, but generally remains prohibitively expensive. 26 Importantly, most of RHDO requires a proband for haplotyping, meaning the test would not be available to a couple during their first pregnancy.…”

Pilot study of a novel multi‐functional noninvasive prenatal test on fetus aneuploidy, copy number variation, and single‐gene disorder screening

“…In 2011, Peters et al () successfully identified a 4.2 M deletion on fetal chromosome 12 from cffDNA and proved that it is feasible to detect fetal sub‐chromosomal CNVs with the noninvasive method. Subsequently, between 2015 and 2017, a number of reports have demonstrated that fetal single‐gene disorders such as congenital adrenal hyperplasia, Duchenne muscular dystrophy, and type I Gaucher disease could also be identified via the noninvasive NGS approach (New et al, ; Xu et al, ; Zeevi et al, ).…”