Noninvasive Prenatal Testing of Methylmalonic Acidemia cblC Type Using the cSMART Assay for MMACHC Gene Mutations.

Zhuo Li,Lianshu Han,Xin Chen,Lingqian Wu,Weigang Lv,Yanling Teng,Weijuan Wu,Huimin Zhu,Lili Liang,Desheng Liang

doi:10.3389/fgene.2021.750719

Abstract

Noninvasive prenatal testing (NIPT) for monogenic disorders has been developed in recent years; however, there are still significant technical and analytical challenges for clinical use. The clinical feasibility of NIPT for methylmalonic acidemia cblC type (cblC type MMA) was investigated using our circulating single-molecule amplification and re-sequencing technology (cSMART). Trios molecular diagnosis was performed in 29 cblC type MMA-affected children and their parents by traditional Sanger sequencing. In the second pregnancy, invasive prenatal diagnosis (IPD) of the pathogenic MMACHC gene was used to determine fetal genotypes, and NIPT was performed using a novel MMACHC gene–specific cSMART assay. Maternal–fetal genotypes were deduced based on the mutation ratio in maternal plasma DNA. Concordance of fetal genotypes between IPD and NIPT, and the sensitivity and specificity of NIPT were determined. After removing two cases with a low P value or reads, the concordance ratio for NIPT and IPD was 100.00% (27/27), and the sensitivity and specificity were 100.00% (54.07–100.00%) and 100.00% (83.89–100.00%), respectively. This study demonstrates that NIPT using the cSMART assay for cblC type MMA was accurate in detecting fetal genotypes. cSMART has a potential clinical application as a prenatal diagnosis and screening tool for carrier and low-risk genotypes of cblC type MMA and other monogenic diseases.

Highlights

Methylmalonic acidemia (MMA) is an autosomal recessive metabolic genetic disorder
29 probands were identified as cblC type MMA-affected, with pathogenic variants of the MMACHC gene, and the variants derived from their parents were validated by Sanger sequencing (Supplementary Table 3)
Noninvasive prenatal testing (NIPT) and invasive prenatal diagnosis (IPD) were performed, and the concordance rate achieved was 100.00% (27/27) after removing two quality control (QC)-failed cases, indicating high sensitivity and specificity of the circulating single-molecule amplification and re-sequencing technology (cSMART) assay compared with IPD

Summary

Introduction

Methylmalonic acidemia (MMA) is an autosomal recessive metabolic genetic disorder. Cobalamin C type MMA (cblC type MMA, MIM #277,400) is the most common form of MMA in China. Patients with cblC type MMA exhibit a wide spectrum of clinical manifestations and usually exhibit multisystem abnormalities with varying degrees of severity (Weisfeld-Adams et al, 2013; Fischer et al, 2014). More than 100 pathogenic mutations have been identified in patients with cblC type MMA disease (Hu et al, 2018; Wang et al, 2019). In the Chinese population, the five most common MMACHC mutations were c.609G > A (p.Trp203Ter), c.658_660delAAG (p.Lys220del), c.80A > G (p.Gln27Arg), c.482G > A (p.Arg161Gln), and c.394C > T (p.Arg132Ter), and they account for more than 75% of all pathogenic variants (Liu et al, 2010; Hu et al, 2018; Wang et al, 2019)

Methods

Results

Discussion

Conclusion