96 research outputs found
Bioinformatic approaches to facilitate canine disease genetics and genomics
No full textSince the annotation of the dog genome in 2005, dogs have emerged as excellent models of human disease. Many disease associations of variant alleles in homologous genes have been discovered in dogs, providing new therapeutic candidates to the corresponding human diseases as well as establishing preclinical large animal models. Significant progress in genetic studies has happened after moving from microarrays to next generation sequencing or combining the two approaches. This transition has required the development and application of novel bioinformatic approaches to facilitate genetics and genomics. This thesis established a variety of bioinformatic approaches and tools to facilitate canine genomics and disease gene discovery.
In study I, the successful development and application of the bioinformatic pipelines resulted in the identification of causal variants of three new disease genes, SLC37A2, SCARF2 and FAM20C, of relevance to Caffey disease, van den Ende Gupta syndrome (VDEGS) and Raine syndrome in human, respectively.
In study II, novel genomic content was discovered through de novo assembly of genomic reads of Border Collies, which didn’t map to the current canine genome reference. This study revealed sequences that filled the existing gaps in the reference genome and identified gene models that were missing from the reference. Overall, this study reveals novel genomic content to facilitate the improvement of upcoming canine genome reference for disease variant allele discovery in candidate
genes.
In study III, a novel bioinformatic tool, webGQT, was successfully developed and piloted to handle and filter large amounts of next generation sequencing (NGS) data. This tool is purported to non-bioinformatics users to mine genetic information from millions to billions of variants among thousands of genomes. This tool has been successfully utilized in various disease genetics projects.
In summary, new bioinformatic approaches have been successfully developed and applied in this thesis to facilitate both the transition of the field to the NGS era and disease gene discovery and genomics in dogs. These findings in this thesis have implications to veterinary research, diagnostics and human medicine with novel candidate genes in three rare disorders.ei saavutettav
A pipeline for data analysis of canine exome-sequencing data
No full textSingle nucleotide polymorphisms (SNPs), short INDELS and large structural variations have become a common source of genetic variations for several rare and common disorders.
Whole-exome sequencing is a powerful application for identifying this large number of complex disease associated genetic variants in exons that contribute to the clinical diagnosis of the diseases.
In this project, we focused on the genetic analyses of the canine disease heritage as a model for human genetic diseases.
Illumina HiSeq 2000 was used for sequencing ten canine exome samples.
Since, exome sequencing is a novel approach in canine genomics and there is not any existing literature on this methodology, the primary aim of this thesis is to develop a thorough and efficient analysis pipeline for paired-end sequencing data to reveal possible kinds of genetic polymorphisms.
This developed exome-sequencing pipeline, incorporates several existing bioinformatics tools to perform several computational steps in the analysis of the data.
These steps range from quality check of raw data to alignment, variant calling and annotation of the variants.
The results from the pipeline gives a comprehensive set of information to the medical geneticists for further downstream analysis in discovering causative mutations in different projects
A CNGB1 Frameshift Mutation in Papillon and Phalene Dogs with Progressive Retinal Atrophy
No full textPeer reviewe
Pedigree of PRA affected Papillons and Phalènes.
No full text<p>Pedigree indicates the affected dogs that were used in the study. Samples from six affected dogs were available for genotyping. Disease segregation is consistent with autosomal recessive mode of inheritance as all affected dogs are born from healthy parents and both sexes are affected. Obligate carrier parents of affected dogs are marked in the pedigree. Obligate carriers genotyped as heterozygous for <i>CNGB1</i> mutation are marked with a yellow background.</p
Genome wide association and linkage analyses.
No full text<p><b>A</b>) A Manhattan plot of genome-wide case-control association analysis performed using 6 cases and 14 controls indicate the most highly associated region in CFA2. <b>B</b>) The PRA associated region on chromosome 2 spans from 61.4 Mb to 63.3 Mb based on association, linkage and joint analyses. <b>C</b>) Genotypes at the PRA associated region on CFA2. All cases share a 1.9 Mb homozygous block, and within this block SNPs BICF2S23238410, BICF2P309315 and BICF2P75954 show complete recessive segregation with the disease. <b>D</b>) Chromatograms of the c.2685delA (arrow), c.2687_2688insTAGCTA (shadowed) mutations in <i>CNGB1</i> gene in an affected (2) and normal (1) dog. The <i>CNGB1</i> gene is located between the two segregating SNPs (BICF2P309315, BICF2P75954).</p
CNGB1 protein alignments.
No full text<p><b>A)</b> CNGB1 amino acid alignment of the normal and affected dogs. The p.Tyr889Serfs*5 mutation in the affected dog results in a loss of a significant part of the C-terminus of the protein and probable NMD of the <i>CNGB1</i> mRNA <b>B</b>) CNGB1 sequence alignment between different vertebrates. The mutation is located in a highly conserved region across species. The arrows mark the first mutated amino acid caused by the frameshift and the premature stop codon.</p
Intronic variant in POU1F1 associated with canine pituitary dwarfism
No full textThe anterior pituitary gland secretes several endocrine hormones, essential for growth, reproduction and other basic physiological functions. Abnormal development or function of the pituitary gland leads to isolated or combined pituitary hormone deficiency (CPHD). At least 30 genes have been associated with human CPHD, including many transcription factors, such as POU1F1. CPHD occurs spontaneously also in mice and dogs. Two affected breeds have been reported in dogs: German Shepherds with a splice defect in the LHX3 gene and Karelian Bear Dogs (KBD) with an unknown genetic cause. We obtained samples from five KBDs presenting dwarfism and abnormal coats. A combined analysis of genome-wide association and next-generation sequencing mapped the disease to a region in chromosome 31 and identified a homozygous intronic variant in the fourth exon of the POU1F1 gene in the affected dogs. The identified variant, c.605-3C>A, resided in the splice region and was predicted to affect splicing. The variant's screening in three new prospective cases, related breeds, and similar to 8000 dogs from 207 breeds indicated complete segregation in KBDs with a carrier frequency of 8%, and high breed-specificity as carriers were found at a low frequency only in Lapponian Herders, a related breed. Our study establishes a novel canine model for CPHD with a candidate POU1F1 defect.Peer reviewe
Improving Copy Number Variant Detection from Sequencing Data with a Combination of Programs and a Predictive Model
No full textTable_1_webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering.xlsx
No full textSummaryGenotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions.ResultswebGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups.AvailabilitywebGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt.</p
Missense variant in LOXHD1 is associated with canine nonsyndromic hearing loss
No full textHearing loss is a common sensory deficit in both humans and dogs. In canines, the genetic basis is largely unknown, as genetic variants have only been identified for a syndromic form of hearing impairment. We observed a congenital or early-onset sensorineural hearing loss in a Rottweiler litter. Assuming an autosomal recessive inheritance, we used a combined approach of homozygosity mapping and genome sequencing to dissect the genetic background of the disorder. We identified a fully segregating missense variant in LOXHD1, a gene that is known to be essential for cochlear hair cell function and associated with nonsyndromic hearing loss in humans and mice. The canine LOXHD1 variant was specific to the Rottweiler breed in our study cohorts of pure-bred dogs. However, it also was present in some mixed-breed dogs, of which the majority showed Rottweiler ancestry. Low allele frequencies in these populations, 2.6% and 0.04%, indicate a rare variant. To summarize, our study describes the first genetic variant for canine nonsyndromic hearing loss, which is clinically and genetically similar to human LOXHD1-related hearing disorder, and therefore, provides a new large animal model for hearing loss. Equally important, the affected breed will benefit from a genetic test to eradicate this LOXHD1-related hearing disorder from the population.Peer reviewe
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