The 13th EUROPEAN CYTOGENOMICS CONFERENCE, organized by the European Cytogeneticists Association, was hosted online from 3 to 5 July 2021.
BioDiscovery recently presented a scientific poster at the 13th European Cytogenomics Conference. This conference was hosted virtually and further program information can be found here.
3.P47 Designing a Modern Cytogenetic Array and the Benefits of Using a SNP Array Backbone for Cytogenetic Testing
Alessio Venier, Shalini Verma, Raja Keshavan, Dan Saul, Soheil Shams
Cytogenetics Labs want to increase performance and value in their testing pipelines but need guidance on
selecting the best platform for their needs. With decreasing costs, whole genome sequencing (WGS) is gaining interest as a platform for copy number variant (CNV) detection but high-density SNP array is currently the most commonly used platform for cytogenetic testing. SNP arrays have an advantage with the ability to robustly detect allelic aberrations, such as regions of homozygosity (ROH), which is coverage dependent for WGS. We generated a tiered set of genes and regions that are clinically important by surveying prominent cytogenetic laboratories across the globe and cataloging current information for clinical resources, such as ClinGen, OMIM, and DDG2P. For the comparative analysis, we contrasted the probe content of several commonly used arrays for cytogenetic testing to assess the ability to resolve aberrations in these critical areas. The arrays used in
the comparison include the popular CytoScan HD offered by Thermo Fisher/Affymetrix, as well as the Global Screening Array (GSA) and the Global Diversity Array (GDA) from Illumina, which offer low-cost options. As each technology uses different types of “probes” we established a uniform measure to compare the different technologies. The statistical analysis includes a comparison of the inclusion of high minor allele frequency SNPs for the detection of ROH events, probe coverage of the functionally important areas of the genes (canonical exons of genes), and probe distribution genome-wide over these tiered genes and regions. Here we present the results assessing how the arrays compare to each other and to WGS in terms of both coverage and cost. In addition, we looked at the benefit of having SNV and CNV data generated by the same array for the same sample to determine UPD status.
For a complete copy of this poster please contact BioDiscovery at firstname.lastname@example.org.
To learn more about NxClinical software for the Global Screening Array (GSA) and the Global Diversity Array (GDA) from Illumina please visit our product page.