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Canine SNP Analysis

Matthew Kusner. Canine SNP Analysis. Background. Samples Studying Progressive Retinal Atrophy (PRA) 8 affected & 2 unaffected Italian Greyhounds SNP Genotyping and Errors Allele-specific PCR No call vs. allele miscall. Background. SNP data File conversion Ordered by genomic position

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Canine SNP Analysis

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  1. Matthew Kusner Canine SNP Analysis

  2. Background • Samples • Studying Progressive Retinal Atrophy (PRA) • 8 affected & 2 unaffected Italian Greyhounds • SNP Genotyping and Errors • Allele-specific PCR • No call vs. allele miscall

  3. Background • SNP data • File conversion • Ordered by genomic position • Genotype “codes” • 0 = AA • 1 = AB • 2 = BB • -1 = unknown

  4. Background • Disease Characteristics • Autosomal Recessive • Increased likelihood of some loss of genomic functionality • Disease loci near homozygous SNPs • Duplicate gene copies • Larger region = possibly more genes involved

  5. Program • Nomenclature • For a given SNP: • Consistent – All affected dogs homozygous for one allele (A or B). • Inconsistent – All affected dogs consist of a combination of both alleles (A and B). • Informative – All affected and unaffected dogs consist of a combination of both alleles. • Uninformative – All affected and unaffected dogs homozygous for one allele.

  6. Program • Seed Formation • Run through data • Form blocks of >= 5 consecutive consistent SNPs. These are the seeds. • Expansion • Forward (based on genomic position) seed expansion if one of the cases apply: • Next SNP is consistent • Next SNP is inconsistent, yet an under-representation of inconsistent SNPs in block • Next SNP is inconsistent based on one alleleandan under-representation of such SNPs. We'll call these “changed” SNPs.

  7. Program • Backward (based on genomic position) seed expansion is the same. • If block collision occurs, blocks combined. • Merge • Blocks merged (equivalent to “combining” blocks as above) if both cases apply: • An under-representation of inconsistent SNPs in merged block. • An under-representation of changed SNPs in merged block.

  8. Program • Sort • Blocks sorted first by size (based on earlier reasoning) then by Consistent/Informative product (for blocks of the same size). Blocks are then outputted.

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