Proof-of-principle rapid noninvasive prenatal diagnosis of autosomal recessive founder mutations
David A. Zeevi, … , Arndt Rolfs, Ari Zimran
David A. Zeevi, … , Arndt Rolfs, Ari Zimran
Published August 31, 2015
Citation Information: J Clin Invest. 2015;125(10):3757-3765. https://doi.org/10.1172/JCI79322.
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Clinical Medicine Genetics

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, Protalix Biotherapeutics Inc., and Centogene AG.

Authors

David A. Zeevi, Gheona Altarescu, Ariella Weinberg-Shukron, Fouad Zahdeh, Tama Dinur, Gaya Chicco, Yair Herskovitz, Paul Renbaum, Deborah Elstein, Ephrat Levy-Lahad, Arndt Rolfs, Ari Zimran

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Figure 3

Noninvasive fetal allele identification based on familial and/or the N370S founder haplotype.

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Noninvasive fetal allele identification based on familial and/or the N37...
Illustrations depict the immediate GBA-proximal locus and SNPs that were deep sequenced for the construction and typing of fetal alleles (as indicated in the “Haplotype legend”). (A) In family 1, the paternal WT allele was diagnosed by inference from the family-based N370S-linked haplotype (red squares). The consensus N370S haplotype could not be used to phase the paternal allele in the fetus due to paternal homozygosity in the founder haplotype region. (B) On the other hand, the maternal N370S allele in family 1 was readily identified (in multiple sites) via the consensus haplotype, and this result was corroborated by equivalent matches to the family-based maternal N370S haplotype. (C) For the family 2 maternal allele, the fetal N370S haplotype could only be matched to a single polymorphic site in the family-based haplotype (red square). This site and 2 other fetal SNPs were definitively matched to the N370S mutation by comparison to the founder N370S haplotype. Therefore, in this case, it would not have been possible to reliably diagnose the maternal allele in the fetus without the N370S founder sequence.