optima suite is a device that includes arrays, reagents and easy to use data
analysis software. It is used for a cost effective and streamlined analysis of the
parental and product of conception (POC) samples. The traditional cytogenetic
technique such as karyotyping and FISH has certain limitations due to cell
culture failure and usually lack the appropriate sensitivity. Cytoscan optima
on the other hand, offers whole genome coverage for accurate detection of
chromosomal abnormalities with increased probe coverage targeting 396 relevant
regions for parental and miscarriage applications. This high resolution method provides
genotyping information for the detection of copy neutral loss/absence of
heterozygosity (LOH/AOH), which can be used to detect uniparental isodisomy
(UPD). Since 50% of miscarriages are caused due to chromosomal
software used here to analyze the results of the following test, is called
Chromosome analysis suite (ChAS). The
software is tailored according to Affymertix to fit the cytogenetic research
analysis. Due to its high resolution, it becomes easier to distinguish between aberrations
and artifacts. The observed advantages of the software are Quick streamlined
results, Summarized version of chromosomal aberrations across the whole genome,
Focused analysis at different levels of resolutions on specific regions of
significance, Can directly access the external databases such as NCBI, OMIM,
female infertility samples are processed using Cytoscan Optima and analyzed
using ChAS software.
other types of Cytoscan are as follows: Cytoscan 750k and Cytoscan HD.
750K array method enables one to detect high resolution copy number across
genome and provide allelic imbalance from SNPs. This technique makes use of
750,000 markers for copy number and about 200,000 genotype-able SNP for the
purpose of providing high resolution copy number and LOH detection. LOH rightly
stands for Loss of Heterozygosity. It can be defined as the phenomenon where,
at the chromosomal crossing event, it results in the loss of an entire gene.
HD is a highly sensitive and reliable detection method for about 25-50kb copy
number changes across the genome. The technique covers 2.6 million copy number
markers. This helps detect SNPs at about 99% genotype accuracy. ChAS is the
software used for analysis purpose.