Dataset Information

Clinical application of single-molecule optical mapping to a multigeneration FSHD1 pedigree.

ABSTRACT:

Introduction

Facioscapulohumeral muscular dystrophy 1 (FSHD1) is a relatively common autosomal dominant adult muscular dystrophy with variable disease penetrance. The disease is caused by shortening of a D4Z4 repeat array located near the telomere of chromosome 4 at 4q35. This causes activation of a dormant gene DUX4, permitting aberrant DUX4 expression which is toxic to muscles. Molecular diagnosis of FSHD1 by Southern blot hybridization or FISH combing is difficult and time consuming, requiring specialist laboratories. As an alternative, we apply a novel approach for the diagnosis of FSHD1 utilizing single-molecule optical mapping (SMOM).

Methods

Long DNA molecules with BssS1 enzyme marking were subjected to SMOM on the Bionano Genomics platform to determine the number of D4Z4 repeats. Southern blot and molecular combing were used to confirm the FSHD1 haplotypes.

Results

In a study of a five-generation FSHD1 pedigree, SMOM correctly diagnosed the disease and normal haplotypes, identifying the founder 4qA disease allele as having 4 D4Z4 repeat units. Southern blot and molecular combing analysis confirmed the SMOM results for the 4qA disease and 4qB nondisease alleles.

Conclusion

Based on our findings, we propose that SMOM is a reliable and accurate technique suitable for the molecular diagnosis of FSHD1.

SUBMITTER: Zhang Q

PROVIDER: S-EPMC6418370 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Clinical application of single-molecule optical mapping to a multigeneration FSHD1 pedigree.

Zhang Qian Q Xu Xueqin X Ding Lirong L Li Huanzheng H Xu Chengyang C Gong Yuyan Y Liu Ying Y Mu Ting T Leigh Don D Cram David S DS Tang Shaohua S

Molecular genetics & genomic medicine 20190121 3

<h4>Introduction</h4>Facioscapulohumeral muscular dystrophy 1 (FSHD1) is a relatively common autosomal dominant adult muscular dystrophy with variable disease penetrance. The disease is caused by shortening of a D4Z4 repeat array located near the telomere of chromosome 4 at 4q35. This causes activation of a dormant gene DUX4, permitting aberrant DUX4 expression which is toxic to muscles. Molecular diagnosis of FSHD1 by Southern blot hybridization or FISH combing is difficult and time consuming, ...[more]

PMID: 30666819

Similar Datasets

Project description:UnlabelledNext-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio-generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism's biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes.ImportanceStudying whole-genome sequences has become an important aspect of biological research. The advent of next-generation sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBio-generated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome analyses to facilitate functional studies into an organism's biology.

Dataset Information

Clinical application of single-molecule optical mapping to a multigeneration FSHD1 pedigree.

Introduction

Methods

Results

Conclusion

Publications

Clinical application of single-molecule optical mapping to a multigeneration FSHD1 pedigree.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets