Advantages of Affymetrix CytoScan HD arrays, provides solution for high resolution molecular cytogenetic analysis with its 2,690,000 marker content (750,000 polymorphic (SNP) and 1,900,000 non-polymorphic (CNV) markers). Affymetrix CytoScan HD arrays are unique for cytogenetic studies because of its extensive coverage.

Advantages of Affymetrix CytoScan HD arrays can be listed as shorter hands-on time(2,5 days), small amounts of gDNA(250ng), higher definition outcomes(20kb-100kb) according to old fashioned cytogenetic techniques like, Molecular karyotyping and FISH.
By Affymetrix CytoScan HD arrays whole genome copy number variations can be detected. All the information related to deletions over 20kb-100kb and amplifications can be identified by user-friendly Affymetrix softwares. Thus enables exon level microdeletion analysis.

Information about size, exact location in the genome, copy number variations, information about the marker that was detected by, which gene region it is located, variations about its region, FISH probes and etc. can be accessed by softwares which are correlated with databases such as NCBI, UCSC, Ensembl, Toronto, and OMIM.

Affymetrix CytoScan HD arrays provides markers for the entire cancer related genes identified so far, RefSeq genes, X chromosome genes and 97% of OMIM genes. These makes Affymetrix CytoScan HD arrays unique for genotyping and copy number variation analysis.

Having SNP(single nucleotide polymorphism) and CNV(copy number variation) markers together in a single array enables determination of LOH(loss of heterozygosity) and UPD(uni-parental disomies).