KinSNP Software for homozygosity mapping of disease genes using SNP microarrays El-Ad David Amir 1, Ofer Bartal 1, Yoni Sheinin 2, Ruti Parvari 2 and Vered Chalifa-Caspi 3 1 Dept. of Computer Science 2 Dept. of Virology and Developmental Genetics 3 National Institute of Biotechnology in the Negev Ben-Gurion University of the Negev, Be’er Sheva, Israel Introduction Genotyping individuals from consanguineous (inbred) families affected with a homozygous recessive genetic disease offers a unique advantage for positional cloning of rare diseases. Homozygosity mapping is a powerful technique for identification of potential sites of the causing mutations. KinSNP is a new software tool for homozygosity mapping in consanguineous families using SNP arrays. KinSNP searches for stretches of SNPs (“blocks”) which are homozygous to the same allele in all ascertained sick individuals. Candidate disease regions are then prioritized and reported, along with genotypes of healthy controls. Here we demonstrate using the software to help identify the location of a mutated gene causing insensitivity to pain (IP), SCN9A, in a large Bedouin family. A Consanguineous Family: The Founder Effect F mutation!! A mutation which occurred in a founder (F) may be inherited to his descendants. The original segment surrounding the mutation may be gradually shortened due to recombination events. Upon consanguineous marriage between two carriers of the mutated chromosome segment, offspring homozygous to that segment may be born. If the mutation causes a recessive disease, these offspring will be sick. KinSNP Interface KinSNP workflow The “Set Analysis settings” dialog Tweak parameters according to family distance between individuals; allows for a certain amount of genotyping errors Analysis Results An Excel file summarizes the found homozygous blocks, including their position and length in both physical and genetic units. Blocks may be sorted according to their length or according to KinSNP calculated score (see below). Block names are hyperlinks to chromosome-specific excel files containing colored genotype information. Score Calculation SCN9A For interactive visualization of KinSNP results, a simplified version of Affymetrix’ open source Integrated Genome Browser (IGB) has been integrated with the program. Homozygous blocks and colored genotypes may be displayed along with genes, other genomic annotations, as well as other experimental results such as previous KinSNP analyses, copy number variation and gene expression data. Blocks summary View of Chromosome 2: After zooming and scrolling: Detailed view Genotypes of all SNPs in both sick and control individuals are shown according to their position along the chromosome. Heterozygote SNPs are colored in green, and homozygotes in red (AA) or blue (BB). Low confidence calls, based on user-specified confidence cutoff, are displayed with lighter colors. Homozygous blocks in analyzed sick individuals are surrounded by black vertical lines. Integrated Genome Browser Definitions: N –number of SNPs in the block O –probability of one SNP to be homozygous for a shared allele over all analyzed chips C –genetic length, in cMs, of block S 1 = O N S 2 = logN∙C KinSNP offers two possible scores. Both scores estimate the significance of a block being homozygous. S 1 is an exact probabilistic calculation (Woods et al., JMG 2004;41:e101), S 2 is a heuristic estimate. Homozygous block Choose individuals (chips) for analysis

Join us For a hands-on experience of KinSNP May 22nd, Weizmann Institute (Google “kinsnp hands-on”)