A pipeline for data analysis of canine exome-sequencing data
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School of Science |
Master's thesis
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Date
2013
Department
Major/Subject
Informaatiotekniikka
Mcode
T-61
Degree programme
Language
en
Pages
63
Series
Abstract
Single 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.Description
Supervisor
Lähdesmäki, HarriThesis advisor
Lohi, HannesKeywords
canine exome-sequencing, pipeline, NGS