In the past several months there have been lots of noteworthy new papers citing the use of Ingenuity® Variant Analysis™ for interpretation and filtering. We round up just a few of them here to offer a sense of the types of studies for which Ingenuity Variant Analysis makes a difference.
A Case of HDR syndrome and Ichthyosis: Dual diagnosis by whole genome sequencing of novel mutations in GATA3 and STS genes
First author: Gregory Goodwin
In this paper, published in January 2016 in The Journal of Clinical Endocrinology & Metabolism, scientists from the Children’s Hospital of Boston report the genomic diagnosis of a young boy whose symptoms could not be understood through existing tests. They used Ingenuity Variant Analysis to filter and interpret the whole-genome data generated by Illumina sequencing, identifying 31 variants potentially associated with the child’s syndrome.
A novel missense mutation of TNNI2 in a Chinese family cause distal arthrogryposis type 1
First author: Bo Wang
Scientists from the Shanghai Jiao Tong University School of Medicine published in the American Journal of Medical Genetics results of their study of a three-generation Chinese family with several members who have distal arthrogryposis syndromes. The team performed exome sequencing of two affected and one unaffected family members, and evaluated SNPs and indels with Ingenuity Variant Analysis. They identified a novel pathogenic mutation in a gene that encodes some of the troponin complex, which is important for muscle contraction.
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders
First authors: Pauline van Schouwenburg and Emma Davenport
In this Clinical Immunology article, scientists from the UK and US collaborated to study patients with common variable immunodeficiency disorders. They sequenced the full genomes of 34 patients and incorporated transcriptome analysis, using Ingenuity Variant Analysis to identify variants (both known and novel) associated with these disorders.
Exome Sequencing Identifies Pathogenic and Modifier Mutations in a Child With Sporadic Dilated Cardiomyopathy
First author: Pamela Long
In the Journal of the American Heart Association, scientists from the Mayo Clinic and University of Arizona Medical Center describe a whole-exome sequencing study of a family trio with a child diagnosed with idiopathic dilated cardiomyopathy. The scientists used Ingenuity Variant Analysis to analyze variants called from the exomes. They found a novel missense mutation in TNNT2 and other mutations in XIRP2, genes related to heart physiology.
Whole-Exome Sequencing in the Differential Diagnosis of Primary Adrenal Insufficiency in Children
First author: Li Chan
Scientists from Queen Mary University of London published this Frontiers in Endocrinology paper about using exome analysis to determine the genetic basis for disease among 43 patients diagnosed with familial glucocorticoid deficiency. For 40% of patients, exome sequencing alone provided a near-immediate genetic diagnosis. Ingenuity Variant Analysis was used to screen for causal variants.
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HGMD®, the Human Gene Mutation Database is used by scientists around the world to find information on reported genetic mutations. The papers below use the database to advance our understanding of disease, DNA dynamics, and more.
Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes
First author: Albino Bacolla
Scientists in the US and UK published results in Nucleic Acids Research of a detailed analysis of single-base substitutions and indels in the human genome. Their findings show that certain base positions are more susceptible to mutagenesis than others. They used HGMD Professional to find mutations in specific genomic regions for analysis; the paper includes charts showing mutation patterns, germline SNPs, and more from HGMD data.
High prevalence of CDH23 mutations in patients with congenital high-frequency sporadic or recessively inherited hearing loss
First author: Kunio Mizutari
This Orphanet Journal of Rare Diseases paper from scientists in Japan sequenced 72 patients with unexplained hearing loss, finding several CDH23 mutations, some of which were novel. Mutations in the gene have been linked to Usher syndrome and other forms of hereditary hearing loss. The scientists used HGMD to find all known CDH23 mutations within nearly 70 coding regions.
Mutation analyses and prenatal diagnosis in families of X-linked severe combined immunodeficiency caused by IL2Rγ gene novel mutation
First author: Q.L. Bai
In Genetics and Molecular Research, scientists report the utility of mutation analysis of the interleukin-2 receptor gamma gene to assess carrier status and perform prenatal diagnosis for X-linked severe combined immunodeficiency. They studied two high-risk families, along with 100 controls, to evaluate the approach. Sequence variation was determined using HGMD Professional and an X-SCID database, and a new mutation was discovered in the project.
Impact of glucocerebrosidase mutations on motor and nonmotor complications in Parkinson’s disease
First author: Tomoko Oeda
Researchers from three hospitals in Japan published this Neurobiology of Aging report that may help stratify Parkinson’s disease patients by prognosis. They sequenced mutations in the GBA gene in 215 patients, finding that those who had mutations associated with Gaucher disease suffered dementia and psychosis much earlier than those who didn’t. The team found previously reported GBA mutations using HGMD Professional.
Comprehensive Genetic Characterization of a Spanish Brugada Syndrome Cohort
First author: Elisabet Selga
In this PLoS One publication, scientists from a number of institutions in Spain examined genetic variation among patients with Brugada syndrome, a rare genetic cardiac arrhythmia. They sequenced 14 genes in 55 patients, identifying 61 variants and finding the subset that appear pathogenic. Variants were filtered against a number of databases, including HGMD.
Learn more about HGMD.
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Many great papers citing CLC Genomics Workbench have come out just in the last few months. To give you an overview of how our software can be used in different types of research, we've selected a handful of papers to be presented here.
Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome
First author: Runsheng Li
This Nature Scientific Reports paper from scientists at Hong Kong Baptist University and Illumina describes an effort to analyze the C. elegans genome using synthetic long reads, recovering some missing sequence with the new assembly. Researchers used CLC Genomics Workbench to map reads to a reference genome and to analyze differences between the two assemblies.
Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvumisolates directly from stool samples
First authors: Stephen Hadfield, Justin Pachebat, Martin Swain
In this BMC Genomics publication, scientists from Singleton Hospital and Aberystwyth University in the UK report a new method for sequencing the whole genome of Cryptosporidium species from human stool samples. This approach is significantly faster and less resource-intensive than current methods to sequence this organism. CLC Genomics Workbench was used to perform bioinformatics analysis and de novo contig assembly.
Are Shiga toxin negative Escherichia coli O157:H7 enteropathogenic or enterohaemorrhagic Escherichia coli? A comprehensive molecular analysis using whole genome sequencing
First author: Mithila Ferdous
Scientists from the University of Groningen and other organizations report in the Journal of Clinical Microbiology a project designed to analyze virulence in E. coli isolates, both with and without the gene encoding Shiga toxin. They used CLC Genomics Workbench to perform de novo assembly of the sequence data.
Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma
First author: Joakim Crona
In PLoS One, researchers from Uppsala University and the University of Duisburg-Essen evaluated CLC Genomics Workbench and other bioinformatics tools to assess their reliability for potential use in a clinical setting. They report findings on sensitivity, specificity, read alignment, and more, reporting that these methods were at least as good as Sanger sequencing with earlier analysis tools.
Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches
First author: Rhonda Foley
Researchers from CSIRO Agriculture Flagship and the University of Western Australia report in BMC Plant Biology the genomic and transcriptomic analysis of conglutin proteins in lupin seeds during varying stages of development. These proteins are particularly interesting for their nutritional and pharmaceutical benefits. The authors used CLC Genomics Workbench to identify and align conglutin sequences from RNA-seq data.
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