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Noninvasive prenatal test of single-gene disorders by linked-read direct haplotyping: application in various diseases

European Journal of Human Genetics volume 29, pages 463–470 (2021)Cite this article

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Abstract

Direct haplotyping enables noninvasive prenatal testing (NIPT) without analyzing proband, which is a promising strategy for pregnancies at risk of an inherited single-gene disorder. Here, we aimed to expand the scope of single-gene disorders that NIPT using linked-read direct haplotyping would be applicable to. Three families at risk of myotonic dystrophy type 1, lipoid congenital adrenal hyperplasia, and Fukuyama congenital muscular dystrophy were recruited. All cases exhibited distinct characteristics that are often encountered as hurdles (i.e., repeat expansion, identical variants in both parents, and novel variants with retrotransposon insertion) in the universal clinical application of NIPT. Direct haplotyping of parental genomes was performed by linked-read sequencing, combined with allele-specific PCR, if necessary. Target DMPK, STAR, and FKTN genes in the maternal plasma DNA were sequenced. Posterior risk calculations and an Anderson–Darling test were performed to deduce the maternal and paternal inheritance, respectively. In all cases, we could predict the inheritance of maternal mutant allele with > 99.9% confidence, while paternal mutant alleles were not predicted to be inherited. Our study indicates that direct haplotyping and posterior risk calculation can be applied with subtle modifications to NIPT for the detection of an expanded range of diseases.

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Fig. 1: Flow chart of the overall strategy for noninvasive prenatal diagnosis of single-gene disorders in this study.
Fig. 2: Pedigree of three families with DM1 (family A), Lipoid CAH (family B), and FCMD (family C).
Fig. 3: Distribution of the fraction of Hap I alleles according to the inheritance of either maternal Hap I or Hap II in three families with DM1 (A), Lipoid CAH (B), and FCMD (C).

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Acknowledgements

Funding

This study was supported by grant 03-2016-0050 from the Seoul National University Hospital (SNUH) Research Fund.

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Authors and Affiliations

  1. Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea

    Jee-Soo Lee, Man Jin Kim, Sung Im Cho, Sung Sup Park & Moon-Woo Seong

  2. Department of Statistics, Seoul National University, Seoul, Republic of Korea

    Kyung Bok Lee

  3. Genome Opinion Inc., 7, Yeonmujang 5ga-gil, Seongdong-gu, Seoul, Republic of Korea

    Han Song & ChoongHyun Sun

  4. Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea

    Young Kyung Lee

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  1. Jee-Soo Lee
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Correspondence to Moon-Woo Seong.

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Lee, JS., Lee, K.B., Song, H. et al. Noninvasive prenatal test of single-gene disorders by linked-read direct haplotyping: application in various diseases. Eur J Hum Genet 29, 463–470 (2021). https://doi.org/10.1038/s41431-020-00759-9

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