Description
This track displays the SNPs used in genotyping platforms.
Affymetrix Genome-Wide Human SNP Array 6.0 and SV
The SNP Array 6.0 includes more than 906,600 single nucleotide polymorphisms (SNPs)
and more than 946,000 probes for the detection of copy number variation.
The SNPs include the 482,000 SNPs from the 5.0 Array (unbiased selection).
In addition, 424,000 new SNPs were chosen in the following areas:
- Tag SNPs
- SNPs from chromosomes X and Y
- Mitochondrial SNPs
- New SNPs added to dbSNP
- SNPs in recombination hotspots
The structural variation copy number (SV) probes include 202,000 probes
targeting 5,677 known CNV regions
from the Toronto Database of Genomic Variants. The additional 744,000 probes
are evenly spaced throughout the genome.
Affymetrix Genome-Wide Human SNP Array 5.0
The SNP Array 5.0 is a single microarray featuring all single nucleotide
polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as
well as 420,000 additional non-polymorphic probes that can measure other
genetic differences, such as copy number variation.
Affymetrix 500K (250K Nsp and 250K Sty)
This annotation displays the SNPs available for genotyping with the
GeneChip Human Mapping 500K Array Set from Affymetrix. It is comprised of
two arrays: Nsp and Sty, which contain approximately 262,000 and 238,000 SNPs,
respectively.
Illumina HumanHap650Y
This annotation displays the SNPs available for genotyping with Illumina's
HumanHap650Y Genotyping BeadChip. The HumanHap650Y contains over 650,000 markers,
extending the HumanHap550 by adding 100,000 additional Yoruba-specific tag
SNPs. On average, there is 1 SNP every 5.3 kb, 6.2 kb and 5.4 kb across
the genome in the CEU, CHB+JPT and YRI populations, respectively.
The HumanHap650Y was derived from release 21 of the
International HapMap Project.
Illumina HumanHap550
This annotation displays the SNPs available for genotyping with Illumina's
HumanHap550 Genotyping BeadChip. The HumanHap550 contains over 550,000 markers,
the majority of which are tag SNPs
derived from release 20 of the
International HapMap Project. In addition,
approximately 7800 non-synonymous SNPs, a higher density of tag SNPs in
the MHC region, over 150 mitochondrial SNPs and over 4000
SNPs from regions with copy number polymorphism were included.
In the CEU population, an r-squared threshold of 0.8 was used
for common SNPs in genes, within 10 kb of genes or in evolutionarily
conserved regions. For all other regions, an r-squared threshold of 0.7 was used.
On average, there is 1 SNP every 5.5 kb, 6.5 kb and 6.2 kb across the genome in
the CEU, CHB+JPT and YRI populations, respectively.
Illumina HumanHap300
This annotation displays the SNPs available for genotyping with Illumina's
HumanHap300 Genotyping BeadChip. The HumanHap300 contains over 317,000 tagSNP markers
derived from Phase I of the
International HapMap Project. In addition,
approximately 7300 non-synonymous SNPs and a higher density of tag SNPs in
the MHC region were included. On average, there is 1 SNP every 9 kb across
the genome and median spacing is 5 kb.
Illumina Human1M-Duo
This annotation displays the SNPs available for genotyping with Illumina's
Human1M-Duo Genotyping BeadChip. The Human1M-Duo contains more than 1,100,000 tagSNP markers
and a set of ~60,000 additional CNV-targeted markers.
The median spacing is 1.5kb (mean - 2.4 kb).
Illumina HumanOmni1-Quad v1
The HumanOmni1-Quad BeadChip consists of 1,140,419 markers in a 4-sample
format. The whole-genome content provides high
genomic coverage rates of 93%, 92%, and 76% at r2 > 0.8 for the CEU,
CHB+JPT, and YRI populations, respectively. High density markers with a
median spacing of 1.2 kb ensure the highest level of resolution for CNV
and breakpoint identification.
The content has been derived from the 1,000 Genomes Project,
all three HapMap phases, and recently published studies, including
new coding variants identified by the 1000 Genomes Project and
markers chosen in high-value regions of the genome: ABO blood
typing SNPs, cSNPs, disease-associated SNPs, eSNPs, SNPs in mRNA splice
sites, ADME genes, AIMs, HLA complexes, indels, introns, MHC regions,
miRNA binding sites, mitochondrial DNA, PAR, promoter regions, and
Y-chromosome.
Illumina Human660W-Quad v1
The Human660W-Quad BeadChip consists of 657,366 markers in a 4-sample
format. The Human660W-Quad BeadChip provides 87%, 85%, and 56% coverage
of CEU, CHB+JPT, and YRI populations at r2 > 0.8. For
CNV and cytogenetic analysis, the dense backbone content is combined
with an additional ~100,000 markers that target observed common CNVs.
HumanCytoSNP-12 v2.1
The 301,232 markers on the HumanCytoSNP-12 represents a complete 12-sample panel of
genome-wide SNPs for a uniform backbone and additional markers targeting all regions of
known cytogenetic importance. Backbone markers provide genome-wide marker spacing of 10kb.
This is supplemented with dense coverage (at 6 kb spacing average) of ~250 genomic regions
commonly studied in cytogenetics labs and targeted coverage in ~400 additional genes,
subtelomeric regions, pericentromeric regions, and sex chromosomes.
An efficiency-optimized tagging strategy provides a panel for GWAS
(70% coverage in CEU at r2 > 0.8) in the highest throughput and most cost-effective
whole-genome DNA Analysis BeadChip.
References
More information on the Affymetrix arrays is available at these sites:
More information on the Illumina arrays is available at these sites:
Methods
Position, strand, and polymorphism data were obtained from Affymetrix and
supplemented with links to corresponding dbSNP rsIDs based on a positional
lookup into
dbSNP. The Affy 6.0 Array is based on dbSNP build 127; the Affy 5.0 Array
is based on dbSNP build 126. The Affy 500K Array is based on dbSNP build 125
and was translated from hg17 by UCSC using rsID lookup.
In fewer than 2% of the cases, a dbSNP rsID was
not present in dbSNP at the Affymetrix array position.
Reference allele information was retrieved from the UCSC database based on dbSNP position
and strand data.
Illumina data were supplied as rsIDs and position based on dbSNP build 126.
Strand, polymorphism and reference allele information was retrieved from the UCSC database
based on rsID and position.
The Illumina arrays are comprised of probes for 4 of the possible single-base substitutions:
A/C, A/G, C/T and G/T. A/T and C/G probes will be available in future arrays.
For Illumina Human1M-Duo, the position, strand, polymorphism and reference allele information was
retrieved from the snp129 table of UCSC database if the marker ID can be found in dbSNP 129,
otherwise the information is retrieved from the data provided by Illumina.
For Illumina HumanOmni1-Quad, Human660W-Quad, and HumanCytoSNP-12,
the position, strand, polymorphism and reference allele information was
retrieved from the snp130 table of UCSC database if the marker ID can be found in dbSNP 130,
otherwise the information is retrieved from the data provided by Illumina.
Credits
Thanks to Venu Valmeekam from Affymetrix, Luana Galver and Jennifer L. Stone from Illumina for
providing these data.