MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

Hou, Hongwei; Zhao, Fangqing; Zhou, Lanlan; Zhu, Erle; Teng, Huajing; Li, Xiaokun; Bao, Qiyu; Wu, Jinyu; Sun, Zhen

doi:10.1093/nar/gkq302

Cited by 45 publications

(27 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Then, we identified SNPs using the SOAPsnp program, realigned the reads by BWA, and determined the deletions or insertions (InDels) with the GATK software [11]. After annotation of the identified InDels and SNPs using the Exome-assistant program (http://122.228.158106/exomeassistant), candidate SNPs, InDels and the short read alignments were viewed by Magic Viewer [12] To determine pathogenicity, four algorithms, PolyPhen, SIFT, Mutationtaster and PMut were used to evaluated nonsynonymous variant. Sequencing data were deposited in to NIH Short Read Archive (SRP033329).…”

Section: Methodsmentioning

confidence: 99%

Identification of a novel DMD duplication identified by a combination of MLPA and targeted exome sequencing

Wang

Jin

et al. 2017

Mol Cytogenet

View full text Add to dashboard Cite

BackgroundDuchenne muscular dystrophy (DMD) is an X-linked recessive muscle-wasting disease caused by a mutation in the DMD gene. The aim of this study was to identify a de novo mutation of the DMD gene in the family of a 9-month-old Chinese male patient, as well as to describe the phenotypic characteristics of this patient.ResultsThe patient was suspected to suffer from DMD according to physical examination, biochemical analyses, and electromyogram. We identified a duplication of exons 4–42 in DMD gene with targeted exome sequencing and multiplex ligation-dependent probe amplification (MLPA). In addition, the patient’s mother was a carrier of the same mutation.ConclusionsWe identified a de novo duplication of exons 4–42 in a patient with early stage DMD. The discovery of this mutation may provide insights into future investigations.

show abstract

Section: Methodsmentioning

confidence: 99%

Identification of a novel DMD duplication identified by a combination of MLPA and targeted exome sequencing

Wang

Jin

et al. 2017

Mol Cytogenet

View full text Add to dashboard Cite

show abstract

“…The identified SNPs and InDels were annotated using the Exome-assistant program (). MagicViewer was used to view the short read alignment, and confirm the candidate SNPs and InDels (15). Non-synonymous variants were evaluated using the four algorithms, PolyPhen (), Sorting Intolerant From Tolerant [SIFT; ()], Protein Analysis Through Evolutionary Relationships (PANTHER; ) and Pathogenic Mutation Prediction (Pmut; ) to determine pathogenicity (16).…”

Section: Methodsmentioning

confidence: 99%

Identification of a missense mutation of COL3A1 in a Chinese family with atypical Ehlers-Danlos syndrome using targeted next-generation sequencing

Zhang¹,

Han²,

Zhou³

et al. 2016

Molecular Medicine Reports

View full text Add to dashboard Cite

Aortopathy represents an important cause of mortality in industrialized countries, with a number of genes identified as predispose factors. It can be difficult to identify the genetic lesions underlying this disorder, particularly when the phenotype is atypical. The present study performed targeted next-generation sequencing of 428 genes associated with cardiovascular diseases in a family with aortopathy, the proband of which presented with abdominal aortic aneurysm rupture only, with tissue fragility noted in surgery. After targeted capture, sequencing and bioinformatics analysis, a missense mutation, p.A1259T, was identified in the collagen type III α1 (COL3A1) gene and co-segregated with the disease in the family. Crystal structure modeling revealed abnormal hydrogen bonds generated by the mutation, which likely affected the spatial structure of the procollagen C-propeptide. Mutations in the procollagen C-propeptide are rare and genotype-phenotype correlation may explain the atypical manifestations of affected individuals. The results of the present study suggested that targeted gene capture combined with next-generation sequencing can serve as a useful technique in the genetic diagnosis of aortopathy, particularly in the content of an atypical phenotype.

show abstract

“…The reads were aligned for single-nucleotide polymorphism (SNP) calling and subsequent analysis (Supplementary Table S2 online). 12,13 Nonsynonymous/splice acceptor and donor site/insertions or deletions (NS/SS/InDel) variants in the dbSNP v130 (http:// www.ncbi.nlm.nih.gov/projects/SNP/), HapMap samples, and 1000 Genome (http://www.ncbi.nlm.nih.gov/Ftp/) were removed. Synonymous changes were filtered using SIFT software (http://sift.jcvi.org).…”

Section: Methodsmentioning

confidence: 99%

Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing

Shen

Shi

et al. 2012

Genetics in Medicine

View full text Add to dashboard Cite

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

Cited by 45 publications

References 15 publications

Identification of a novel DMD duplication identified by a combination of MLPA and targeted exome sequencing

Identification of a novel DMD duplication identified by a combination of MLPA and targeted exome sequencing

Identification of a missense mutation of COL3A1 in a Chinese family with atypical Ehlers-Danlos syndrome using targeted next-generation sequencing

Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing

Contact Info

Product

Resources

About