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Method Detail
Submitter Method Handle: EXOME_CHIP
Submitter Method ID: COMMUNITY_COLLABORATION
Submitted method description:
This methods description summarizes more detailed information provided
on a web page and slide deck:
http://genome.sph.umich.edu/wiki/Exome_Chip_Design
http://genome.sph.umich.edu/w/images/3/32/2011.09_-_Exome_Chip.pdf
The SNPs submitted under the EXOME_CHIP handle consist primarily of
a collection of 274,320 non-synonymous coding SNPs assembled from
preliminary analyses of unpublished sequencing data from 16 different
exome and whole genome sequencing studies, as of September, 2011.
To these are added 23,457 largely non-coding SNPs which may help in
checking genotypes, sample tracking and association analysis integrity.
The 16 contributing studies are informally identified in the web page as:
NHLBI Exome Sequencing Project, Autism, GO-T2D, 1000 Genomes
Project, Sweden Schizophrenia Study, SardiNIA, Sanger / CoLaus,
Cancer Genome Atlas, T2D Genes, Cancer Cohort Study, Pfizer-MGH-
Broad, Lipid Extremes, Int'l HIV Controllers Study, SAEC DILI (merged
with Autism tranches), I2B2 - Major Depression, BMI Extremes. Sample
sizes and contact persons for the individual studies are also given on the
web page. It is estimated that the chip design is based on sequencing
results from approximately 9000 individuals of primarily European
ancestry, 2000 individuals of primarily African ancestry and about 500
individuals each of primarily Hispanic and Asian ancestries.
The inclusion criteria for nonsynonymous coding variants are that each
variant must have been seen >= 3 times and in >= 2 call sets. For stop
codon and splice site variants this is relaxed to allow variants seen >= 2
times and in >= 2 call sets. The allele frequency criterion is further
relaxed for ancestries supported by fewer individuals. The current
submission covers all SNPs from the 'ProposedContent' directories in
the anonymous ftp site: ftp://share.sph.umich.edu/exomeChip. Not all
of these variants will be included on either of the commercial genotyping
products being developed from this collection, but they are included for
completeness. The numbers of SNPs from each class listed below count
non-redundant sites after allocating each SNP to just one of the design
categories. They are systematically smaller than the numbers of sites
shown on the web page and in the slides. In particular, a large fraction
of sites in the 'ESP Requests' class coincide with sites already selected
as nonsynonymous coding variants.
A total of 297,777 SNPs are submitted here. These break down by
selection category as follows:
254,730 nonsyn NonSynonymous coding
12,505 splice Splice Variants
7,085 stopgl Stop Gain or Stop Loss
274,320 Total protein altering variants
4918 synctl Random Synonymous included as "controls"
5687 common Grid of Common Variants
5171 .GWAS. GWAS Tag SNPs
2350 HLAsnp Human Leukocyte Antigen locus tags
3324 AimAfr Ancestry Inf markers for African ancestry
994 AimAmr Ancestry Inf markers for Native American ancestry
277 micRNA Micro RNA target sites
196 finger Fingerprint SNPs
137 ESP.rq Exome Sequencing Project Requests
187 chr.Y. Chromosome Y
216 mitoch Mitochondrial
23,457 Total included for other criteria

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
EXOME_CHIP Assay proposed_content 136