1,555
edits
Changes
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= Illumina Exome Arrays =
= Illumina Exome Arrays =
== Coding Variants ==
== Coding Variants ==
Design criteria included a requirement for an assay design score >= 0.50, a primer that didn't overlap a nearby variant with minor allele count >100, a primer that didn't map with 0, 1 or 2 mismatches to other genomic locations. Assay design failures appeared to be largely independent of frequency.
Design criteria included a requirement for an assay design score >= 0.50, a primer that didn't overlap a nearby variant with minor allele count >100, a primer that didn't map with 0, 1 or 2 mismatches to other genomic locations. Assay design failures appeared to be largely independent of frequency.
In the Illumina platform, 243,094 of the original set of 275,165 coding variants (non-synonymous, stop and splice) passed assay design criteria. We expect that 80-90% of the variants that pass design criteria will ultimately be included in genotyping arrays.
In the Illumina platform, 243,094 of the original set of 275,165 coding variants (non-synonymous, stop and splice) passed assay design criteria. We expect that 80-90% of the variants that pass design criteria will ultimately be included in genotyping arrays.
== Assay Design Rates ==
{| border="1" align="center" cellpadding="1" cellspacing="1" summary="Summarizes the Number of SNPs in Each Category That Passed Assay Design. Note that Categories Overlap."
|+ Illumina Assay Design Summary
|-
! scope="col" | SNP Set
! scope="col" | Number of <br>Candidates
! scope="col" | Number of <br>Successful Designs
! scope="col" | Additional <br>Notes
|-
! scope="row" | Coding Content
| 275,165
| 243,094
| An additional set of 8,242 SNPs that were unique to the 1000 Genomes Project and populations under-represented in the design was added.
|-
! scope="row" | GWAS Tag SNPs
| 5,763
| 5,325
|
|-
! scope="row" | Grid of Common Variants
| 5,710
| 5,286
|
|-
! scope="row" | Randonly Selected Synonymous SNPs
| 5,000
| 4,651
| For 1,000 SNPs, assays were generated on both strands - to faciliate QC efforts and future development of methods for genotyping of rare variants.
|-
! scope="row" | AIM - African Ancestry
| 3,388
| 3,241
|
|-
! scope="row" | AIM - Native American Ancestry
| 1,000
| 998
|
|-
! scope="row" | HLA Tags
| 2,536
| 2,459
|
|-
! scope="row" | ESP Requests
| 1,003
| 843
|
|-
! scope="row" | Fingerprint SNPs
| 285
| 259
|
|-
! scope="row" | MicroRNA Target Sites
| 285
| 270
|
|-
! scope="row" | Mitochondrial Variants
| 246
| 246
|
|-
! scope="row" | Chromosome Y
| 188
| 128
|
|-
! scope="row" | Indels
| 181
| 181
|
|-
! scope="row" |
|
|
|
|}
