Title
Computational identification of candidate loci for recessively inherited mutation using high-throughput SNP arrays.
Abstract
Single nucleic polymorphisms (SNPs) are one of the most abundant genetic variations in the human genome. Recently, several platforms for high-throughput SNP analysis have become available, capable of measuring thousands of SNPs across the genome. Tools for analysing and visualizing these large genetic data sets in biologically relevant manner are rare. This hinders effective use of the SNP-array data in research on complex diseases, such as cancer.We describe a computational framework to analyse and visualize SNP-array data, and link the results in relevant databases. Our major objective is to develop methods for identifying DNA regions that likely harbour recessive mutations. Thus, the algorithms are designed to have high sensitivity and the identified regions are ranked using a scoring algorithm. We have also developed annotation tools that automatically query gene IDs, exon counts, microarray probe IDs, etc. In our case study, we apply the methods for identifying candidate regions for recessively inherited colorectal cancer predisposition and suggest directions for wet-lab experiments.R-package implementation is available at http://www.ltdk.helsinki.fi/sysbio/csb/downloads/CohortComparator/
Year
DOI
Venue
2007
10.1093/bioinformatics/btm263
Bioinformatics
Keywords
Field
DocType
human genome,snp-array data,abundant genetic variation,supplementary data,biologically relevant manner,candidate locus,colorectal cancer predisposition,high-throughput snp array,large genetic data set,microarray probe ids,computational identification,query gene ids,fi supplementary information,genetics,polymorphism,genetic variation,colorectal cancer,high throughput
Genome,Annotation,SNP array,Computer science,Single-nucleotide polymorphism,Bioinformatics,Human genome,Genetics,Locus (genetics),SNP,Mutation
Journal
Volume
Issue
ISSN
23
15
1367-4811
Citations 
PageRank 
References 
0
0.34
7
Authors
6
Name
Order
Citations
PageRank
Marko Laakso1645.66
Sari Tuupanen200.34
Auli Karhu300.34
Rainer Lehtonen483.34
Lauri A Aaltonen500.34
sampsa hautaniemi633748.60