Agilent Serial Number Lookup

[Ezilda Newnam]

Thestructural variation copy number (SV) probes include 202,000 probes targeting 5,677 known CNV regionsfrom the Toronto Database of Genomic Variants. The additional 744,000 probes are evenly spaced throughout the genome.

Non-SNP subtracks are colored in alternating shades ofgreen andorangeto highlight track boundaries. SNP subtracksare colored blue with SNP probes coloreddark blue and CGH probescoloredlight blue.

TheGlobal Diversity Array-8 v1.0 BeadChip includes coverage of the ACMG 59-geneclinical research variants and multi-ethnic, genome-wide content. The GDA is the commercial versionof the array chosen by the All of Us ResearchProgram and is designed to capture a wider range of the world's populationsthan traditionalmicroarrays.

With the Infinium MethylationEPIC BeadChip Kit, researchers can interrogate over 850,000methylation sites quantitatively across the genome at single-nucleotide resolution. Multiplesamples, including FFPE, can be analyzed in parallel to deliver high-throughput power whileminimizing the cost per sample. These tracks show positions being measured on the Illumina 450k and850k (EPIC) microarray tracks. More information about the arrays can be found on theInfinium MethylationEPIC Kit website.Illumina CytoSNP 850K Probe ArrayThe Infinium CytoSNP-850K v1.2 BeadChip provides comprehensive coverage ofcytogenetically relevant genes on a proven platform, helping researchers find valuable informationthat may be missed by other technologies. It contains approximately 850,000 empirically selectedsingle nucleotide polymorphisms (SNPs) spanning the entire genome with enriched coverage for 3,262genes of known cytogenetics relevance in both constitutional and cancer applications. Items in thistrack are colored according to their strand orientation. Blue indicatesalignment to the negative strand, and red indicates alignment to thepositive strand.

Position, strand, and polymorphism data were obtained from Affymetrix and supplemented with links to corresponding dbSNP rsIDs based on a positionallookup 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 wasnot present in dbSNP at the Affymetrix array position. Reference allele information was retrieved from the UCSC database based on dbSNP positionand 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.

Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables the study of genome-wide DNA copy number changes at a high resolution. The CGH probes on Agilent aCGH microarrays are 60-mer oligonucleotides synthesized in situ using Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH microarrays have been selected using algorithms developed specifically for the CGH application, assuring optimal performance of these probes in detecting DNA copy number changes.

Non-SNP subtracks are colored in alternating shades of green and orange to highlight track boundaries. SNP subtracks are colored blue with SNP probes colored dark blue and CGH probes colored light blue. The track consists of the following subtracks:

The raw data can be explored interactively with theTable Browser or theData Integrator.For automated analysis, the data may be queried from ourREST APIor downloaded from our Downloads site. Please refer to ourmailing list archives for questions, or ourData Access FAQ for more information.

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