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= Affymetrix Exome Arrays =
= Affymetrix Exome Arrays =
== Coding Variants: Design Criteria ==
Probe sequences were a priori excluded if there was an adjacent polymorphism within 5bp of the target variant or if the cumulative genome-frequency count of each 16-mer in the probe exceeded 300.
The array was wet-lab validated against HapMap 270 and ~1000 Genomes Sample Collections.
{| cellpadding="2" cellspacing="1" border="0" summary="Summarizes the Number of SNPs in Each Category tat were attempted and those that passed wet lab validation. Note that Categories Overlap."
|+ '''Affymetrix Assay Design Summary'''
|-
! bgcolor="lightblue" scope="col" | Categories
! bgcolor="lightblue" scope="col" align="right"| Candidates
! bgcolor="lightblue" scope="col" align="center" | # wet lab validated <br> & working on Axiom
! bgcolor="lightblue" scope="col" | Comments
|-
! scope="row" align="left" | Non-synomynous Coding SNPs<br> /splice & stop
| align="right" |259,976<br> /19,672
| align="right" | 247,546<br> /17,066
| Includes 16K additional non-synonymous coding variants from <br> the Axiom Genomic Database. .
|-
! bgcolor="lightgray" scope="row" align="left" | GWAS
| bgcolor="lightgray" scope="row" align="right" | 5,542
| bgcolor="lightgray" scope="row" align="right" | 5,053
| bgcolor="lightgray" scope="row" |
|-
! scope="row" align="left" | Grid
| align="right" | 5,719
| align="right" | 5,478
|
|-
! bgcolor="lightgray" scope="row" align="left" | Synonymous cSNPs
| bgcolor="lightgray" scope="row" align="right" | 5,000
| bgcolor="lightgray" scope="row" align="right" | 4,367
| bgcolor="lightgray" scope="row" align="right" |
|-
! scope="row" align="left" | AIMs (Eur/African Ancestry)
| align="right" | 3,388
| align="right" | 3,283
|
|-
! bgcolor="lightgray" scope="row" align="left" | AIMs (Native American Ancestry)
| bgcolor="lightgray" scope="row" align="right" | 1,000
| bgcolor="lightgray" scope="row" align="right" | 962
| bgcolor="lightgray" scope="row" align="right" |
|-
! scope="row" align="left" | AIMs (Other)
| align="right" | 271
| align="right" | 271
| Includes supplemental AIMs from the Latin American Cancer <br> Epidemiology (LACE) Consortium.
|-
! bgcolor="lightgray" scope="row" align="left" | HLA
| bgcolor="lightgray" scope="row" align="right" | 2,536
| bgcolor="lightgray" scope="row" align="right"| 2,262
| bgcolor="lightgray" scope="row" align="right" |
|-
! scope="row" align="left" | ESP
| align="right" | 1,003
| align="right" | 952
|
|-
! bgcolor="lightgray" scope="row" align="left" | Fingerprint
| bgcolor="lightgray" scope="row" align="right" | 285
| bgcolor="lightgray" scope="row" align="right" | 268
| bgcolor="lightgray" scope="row" align="right" |
|-
! scope="row" align="left" | miRNA
| align="right" | 285
| align="right" | 250
|
|-
! bgcolor="lightgray" scope="row" align="left" | Mitochondrial DNA
| bgcolor="lightgray" scope="row" align="right"| 246
| bgcolor="lightgray" scope="row" align="right"| 207
| bgcolor="lightgray" scope="row" align="right" |
|-
! scope="row" align="left" | Chromosome Y
| align="right" | 232
| align="right" | 161
|
|-
! bgcolor="lightgray" scope="row" align="left" | Indels
| bgcolor="lightgray" scope="row" align="right" | 56,095
| bgcolor="lightgray" scope="row" align="right" | 35,137
| bgcolor="lightgray" scope="row" | Includes biallelic indels from the draft Phase 1 1000 Genomes Project <br> and previously validated indels in the Axiom Genomic Database; <br> indel size ranges from 1-138bp.
|-
! scope="row" |
| align="right" |
| align="right" |
|
|-
! bgcolor="lightblue" scope="row" border = "1"| Total Number Target Variants
| bgcolor="lightblue" align="right" | 369,656
| bgcolor="lightblue" align="right" | 318,983
| bgcolor="lightblue" |
|}
