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SNP Analysis of Canine Progressive Retinal Atrophy in Italian Greyhounds

This study investigates the genetic underpinnings of Progressive Retinal Atrophy (PRA) in Italian Greyhounds, focusing on 8 affected and 2 unaffected individuals. Utilizing SNP genotyping, we examine allele-specific PCR methods to address common errors such as no call and allele miscall. The analysis identifies disease loci near homozygous SNPs, indicating an autosomal recessive pattern and potential loss of genomic functionality. We develop a program for seed formation, expansion, and merging of consistent and inconsistent SNP blocks, contributing insights into the genetic complexities of PRA.

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SNP Analysis of Canine Progressive Retinal Atrophy in Italian Greyhounds

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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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