Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping

Zheng, Yuting; Kong, Lingrong; Xu, Hui; Lu, Yong‐Jie; Zhao, Xuechao; Yang, Yi; Yu, Guoliang; Li, Pidong; Liang, Fan; Jin, Hongshuai; Kong, Xiangdong

doi:10.1002/pd.5607

Cited by 22 publications

(20 citation statements)

References 17 publications

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“…Nanochannel-based single molecule optical mapping allows to resolve structural genome variation on a megabasescale [Lam et al, 2012]. In contrast to paired-end and matepair sequencing, this approach allows to bridge repeat-rich regions such as segmental duplications, the Duchenne muscular dystrophy gene, and D4Z4 arrays in patients with facioscapulohumeral muscular dystrophy 1 [Kloosterman et al, 2011;Barseghyan et al, 2017;Zhang et al, 2019;Zheng et al, 2020]. Structural variations detected by single molecule optical mapping are in good accordance with those detected by other state-of-the-art methods [Chaisson et al, 2019;Neveling et al, 2020].…”

Section: Detection and Incidence Of Both Class I And Class Ii Rtsmentioning

confidence: 54%

Prevalence and Phenotypic Impact of Robertsonian Translocations

Poot

Hochstenbach

2021

Mol Syndromol

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Robertsonian translocations (RTs) result from fusion of 2 acrocentric chromosomes (e.g., 13, 14, 15, 21, 22) and consequential losses of segments of the p arms containing 47S rDNA clusters and transcription factor binding sites. Depending on the position of the breakpoints, the size of these losses vary considerably between types of RTs. The prevalence of RTs in the general population is estimated to be around 1 per 800 individuals, making RTs the most common chromosomal rearrangement in healthy individuals. Based on their prevalence, RTs are classified as “common,” rob(13;14) and rob(14;21), or “rare” (the 8 remaining nonhomologous combinations). Carriers of RTs are at an increased risk for offspring with chromosomal imbalances or with uniparental disomy. RTs are generally regarded as phenotypically neutral, although, due to RTs formation, 2 of the 10 ribosomal rDNA gene clusters, several long noncoding RNAs, and in the case of RTs involving chromosome 21, several mRNA encoding genes are lost. Nevertheless, recent evidence indicates that RTs may have a significant phenotypic impact. In particular, rob(13;14) carriers have a significantly elevated risk for breast cancer. While RTs are easily spotted by routine karyotyping, they may go unnoticed if only array-CGH and NextGen sequencing methods are applied. This review first discusses possible molecular mechanisms underlying the particularly high rates of RT formation and their incidence in the general population, and second, likely causes for the elevated cancer risk of some RTs will be examined.

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Section: Detection and Incidence Of Both Class I And Class Ii Rtsmentioning

confidence: 54%

Prevalence and Phenotypic Impact of Robertsonian Translocations

Poot

Hochstenbach

2021

Mol Syndromol

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“…In reproductive medicine and prenatal diagnosis, clinically significant structural variations can be detected in a single analysis by OGM. One study showed that Bianano optical mapping (BOM) can determine the number of D4Z4 repeats and exclude interference of the 10q26.3 homologous region, and in combination with karyomapping, can be used for rapid and accurate prenatal diagnosis of FSHD1 (Zheng et al, 2020). The single-molecule optical mapping (SMOM) has potential clinical application as a rapid tool to screen patients with balanced reciprocal translocations (BRTs) for underlying genetic causes of infertility and other diseases (Wang H. et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Analysis of Genomic Copy Number Variation in Miscarriages During Early and Middle Pregnancy

Huang

Zhang

et al. 2021

Front. Genet.

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The purpose of this study was to explore the copy number variations (CNVs) associated with miscarriage during early and middle pregnancy and provide useful genetic guidance for pregnancy and prenatal diagnosis. A total of 505 fetal specimens were collected and CNV sequencing (CNV-seq) analysis was performed to determine the types and clinical significance of CNVs, and relevant medical records were collected. The chromosomal abnormality rate was 54.3% (274/505), among which the numerical chromosomal abnormality rate was 40.0% (202/505) and structural chromosomal abnormality rate was 14.3% (72/505). Chromosomal monosomy mainly occurred on sex chromosomes, and chromosomal trisomy mainly occurred on chromosomes 16, 22, 21, 15, 13, and 9. The incidence of numerical chromosomal abnormalities in ≥35 year-old age pregnant women was significantly higher than <35 year-old age group. The highest incidence of pathogenic CNV (pCNV) was found in fetuses at ≤6 weeks of pregnancy (5.26%), and the incidence of variants of unknown significance (VOUS) CNVs decreased gradually with the increase of gestational age. The rate of chromosomal abnormalities of fetuses in early pregnancy (59.5%) was higher than that of fetuses in middle pregnancy (27.2%) (p < 0.001). There were 168 genes in VOUS + pCNV regions. 41 functions and 12 pathways (p < 0.05) were enriched of these genes by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Some meaningful genetic etiology information such as genes and pathways has been obtained, it may provide useful genetic guidance for pregnancy and prenatal diagnosis.

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“…16,18 Similarly, optical mapping, a long-read genome fragment analysis technology, has been used prenatally to characterize a known familial disease variant for facioscapulohumeral muscular dystrophy, an autosomal dominant disease that can be caused by a contraction of the D4Z4 repeat elements at chromosome 4q35. 77 Optical mapping served as an easier workflow in estimating the D4Z4 repeat number compared to the canonical, labour-intensive genotyping approach by pulsed-field gel electrophoresis and Southern blot analysis. Using the Oxford Nanopore platform, Miller et al investigated individuals with unresolved postnatal genetic disorders by targeted long-read sequencing.…”

Section: Other Emerging Omics Technologiesmentioning

confidence: 99%

“…As discussed earlier, long‐insert WGS had been successfully applied to prenatal cases previously known to carry cryptic complex rearrangements 16,18 . Similarly, optical mapping, a long‐read genome fragment analysis technology, has been used prenatally to characterize a known familial disease variant for facioscapulohumeral muscular dystrophy, an autosomal dominant disease that can be caused by a contraction of the D4Z4 repeat elements at chromosome 4q35 77 . Optical mapping served as an easier workflow in estimating the D4Z4 repeat number compared to the canonical, labour‐intensive genotyping approach by pulsed‐field gel electrophoresis and Southern blot analysis.…”

Section: Other Emerging Omics Technologiesmentioning

confidence: 99%

Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing

Liu

Vossaert

2022

Prenatal Diagnosis

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DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA‐sequencing, already used postnatally, can provide valuable complementary data to DNA‐based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long‐read and Hi‐C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome‐wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.

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Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping

Cited by 22 publications

References 17 publications

Prevalence and Phenotypic Impact of Robertsonian Translocations

Prevalence and Phenotypic Impact of Robertsonian Translocations

Analysis of Genomic Copy Number Variation in Miscarriages During Early and Middle Pregnancy

Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing

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