Seeing the whole picture – integrated view of CNVs, AOH, and sequence variants for Improved results

Alessio Venier1, Andrea O’Hara1, Soheil Shams1

1 BioDiscovery, Inc. 715 North Douglas Street, El Segundo, CA, 90245

Given the separate technologies used to detect CNVs, AOH, and Sequence Variants (SNP Microarrays for CNVs and AOH, and NGS for Sequence Variants), this data commonly has been reviewed in isolated silos. This segregation has also been exaggerated by the separate expertise in Cytogenomics and Molecular Genetics. However, as the fields are now coming together, the importance of an integrated view of the data has become even more apparent. Here we present a new system that can integrate data from any array as well as NGS platforms to create a single genomic view of structural changes in a sample. The data is presented in a view familiar to cytogenomicists with aberrations displayed across an ideogram with supporting evidence for each call (e.g. probes from arrays and reads from NGS). Historical data and outside database knowledge is integrated into this view allowing the analyst access to all information needed to make assessments of the results. We will demonstrate the utility of this system using a few samples with compound heterozygous aberrations that are detected using different technologies. This includes a case with a microdeletion detected by custom exon array and SNV detected with a custom targeted NGS panel. Another case includes a variant in a large region of homozygosity.


Dr. Soheil Shams is the founder and President of BioDiscovery, Inc. a privately held bioinformatics company based in El Segundo, California established in 1997. He received his Masters and Ph.D. degrees from University of Southern California in 1986 and 1992 respectively in the field of Computer Engineering. He has been a pioneer in the field of microarray image and data processing having invented many of the basic approaches to array analysis resulting in numerous issued US patents. Under the direction of Dr. Shams, BioDiscovery has played a pioneering role in development of software tools for conducting array based research and more recently in clinical application of arrays in cytogenetic and molecular genetic diagnostics as well as Next Generation

Sequencing (NGS) data analysis. Prior to founding BioDiscovery, he was a Sr. Member of Staff at Hughes Research Laboratories (HRL) in Malibu and taught undergraduate and graduate classes in Artificial Intelligence, Machine Perception, and Data Mining at UCLA. His research interests span a wide range with concentration on pattern recognition technologies and parallel processing architectures. He has worked with many of the pioneering scientist in microarray research and has authored over 50 technical publications and book chapters.

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