The Human Genome is composed of 3 billion nucleotides carrying hereditary information which determines an individual’s genetic potential. There is about 0.1% - 0.2% genomic DNA sequence difference between races and individuals, due mainly to single nucleotide polymorphisms (SNPs). Many of the SNPs can generate different inherited biochemical characteristics. For example, the ABO blood group site markers, leukocyte HLA site markers and individual disparities in drug metabolism. Knowledge of the DNA sequence differences and single nucleotide polymorphisms and their significance has begun to revolutionize diagnosis, treatment, prognosis and prevention in man.
The new Affymetrix Genome-Wide Human SNP Array 6.0 for example contains more than 906,600 SNPs and more than 946,000 probes for the detection of copy number variation. SNPs on the array are present on 200 to 1,100 base pairs (bp) Nsp I or Sty I digested fragments in the human genome, and are amplified using the Genome-Wide Human SNP Nsp/Sty Assay Kit. This assay now combines the Nsp and Sty fractions previously assayed on two separate arrays. The Human SNP Array 6.0 were screened in more than 500 discrete samples, including 270 HapMap samples and separate diversity samples. Approximately 482,000 SNPs are derived from the previous-generation Mapping 500K and SNP 5.0 Arrays. The remaining 424,000 SNPs include tag SNP markers derived from the International HapMap Project, better representation of SNPs on chromosomes X and Y, mitochondrial SNPs, SNPs in recombination hotspots and new SNPs added to the dbSNP database after completion of the Mapping 500K Array.
The array also contains 202,000 probes targeting 5,677 known regions of copy number variation from the Toronto Database of Genomic Variants. These regions resolve into 3,182 distinct, nonoverlapping segments, each interrogated with an average of 61 probes. In addition to the interrogation of these regions of known copy number polymorphism, more than 744,000 probes were chosen, evenly spaced along the genome, to enable the detection of novel copy number variation. The median inter-marker distance taken over all 1.8 million SNP and copy number markers combined is less than 700 bases.
◆ Other genetic differences, such as copy number variations, can be measured in addition to SNPs
◆ Sample preparation can be completed by one primer amplification
◆ Only 500 ng of genomic DNA is required
◆ Information of 500,000 SNP sites can be obtained by each one primer amplification
◆ Specific design of the microarray guarantees a reproducibility of 99.9%
◆ Association studies
◆ Linkage disequilibrium
◆ Loss of heterozygosity
◆ Copy number variants
◆ Population genetics
◆ Cancer genetics
No. of SNPs
GeneChip Genome-Wide Human SNP Array 6.0 Service