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Featured Shared Resource: Molecular and Genomic Analysis Core

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August 2012 Issue

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Richard Head, MS

The Molecular and Genomic Analysis (MGA) Core is expanding genomic analysis services through coordination with the Department of Genetics' Genome Technology Access Center (GTAC.) 

Richard Head, MS, research associate professor of genetics, has been named core director of the Siteman Cancer Center MGA Core. Former directors Mark Watson, MD, PhD, who directed the Multiplexed Gene Analysis Core beginning in 2000, and Jacqueline Payton, MD, PhD, who joined the MGA core in 2009, were instrumental in building this important shared resource for SCC researchers. 

As the current director of the Genome Technology Access Center (GTAC), Head brings more than 20 years of experience in medical research, with nearly 15 years in the use of high-throughput genomic technologies (microarray, sequencing, etc). In addition to detailed technical knowledge, he brings considerable understanding of how to apply these genomic tools to the fields of drug discovery and clinical research. The core staff will coordinate with the Department of Genetics' GTAC in order to provide cancer center members with preferred access to a broader range of genomic analysis platforms, including high-throughput PCR-based assays; additional array-based technology platforms; novel multiplex platforms; and next-generation sequencing.

The GTAC currently houses multiple high-end next-generation sequencing machines, including the Illumina HiSeq 2000 and MiSeq that can be used in both research and clinical settings (CAP/CLIA). Laboratory and bioinformatic protocols have been developed for calling both constitutional and somatic mutations.

Tier1 bioinformatic services, through the generation of the variant call file (VCF), will be provided to members as part of the delivery of sequencing data. In addition, access to the Fluidigm BioMark system will enable members to perform rapid SNP genotyping studies, amplicon sequencing studies, digital PCR and high-throughput, real-time PCR (gene expression). Overall, members will be able to perform studies in a far more comprehensive genomic research environment.

Additional enhancements will be added to the web-based submission and tracking system that is nearing completion. These enhancements will allow investigators to track the progress of their samples from specimen in que, waiting for quality control, assay completion and archiving. Eventually, this will be tied in with the billing system as well as publication tracking.

During the past year, new equipment and services have been added to the MGA Core. An additional Fluidic 450 Station was purchased for a total of eight fluidic stations. Two new digital readout Hybridization Oven 645s are now available.
New services include:

  • Cytoscan_HD: The most comprehensive and relevant coverage of constitutional and cancer genes on a single array. This array has been incorporated in our core for clinical use by the Cytogenetics Core. It is a clinical and research array that includes more than 2.67 million copy number markers, of which 1.9 million are nonpolymorphic probes and 750,000 are SNP probes that genotype with 99 percent accuracy. This high-density SNP array enables digital readout Hybridization Oven 645 and enhanced low-level mosaicism detection. Cytoscan HD array offers confident breakpoint determination thoughout the whole genome and genotype-able SNPs for parent-of-origin studies.
  • miRNA array vs. 2: The GeneChip miRNA array is a powerful tool for studying the regulatory mechanisms mediated by miRNAs and their importance in cancer and other diseases. miRNA studies can also facilitate the discovery of biomarkers and disease signatures. The GeneChip miRNA 2.0 array is comprised of 15,632 mature microRNA sequences from miRBASE (version 15) and contains an additional 1,534 sequences of human snoRNA and scRNA from the Ensembl database and snoRNABASE as well as 153 organisms. Additionally, miRNA vs 3 contains 2,999 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences.
  • Cytoscan HD cytogenetics solution: Designed by cytogeneticists for cytogeneticists. This assay is for use with the Cytoscan HD array and has been simplified and streamlined. All reagents have been kitted with only two additional vendors required. It has been streamlined to a three-day rather than four-day workflow from genomic DNA to result.

These new technologies facilitate the discovery of biomarkers and disease signatures and allow genotyping of constitutional and cancer genes with 99 percent accuracy. Core services are customized and tailored to investigators’ projects, and core staff members work closely with investigators to design testing that is specific to their project goals and specimen types. These services are unique in that they are not available via other campus cores or commercial companies. The core can provide CLIA-quality performance for research prices.

The core staff welcomes contacts from all interested investigators. Please contact Mike Heinz at 314-286-1276. Alternatively, investigators are encouraged to visit the core website. (Please note that a new website is under construction and will be available soon.)