1 / 8

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

audra
Télécharger la présentation

Canine SNP Analysis

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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.

More Related