Genomics Core

The Genomics Core (GC) at Indiana University School of Medicine (IUSM) provides state-of-the-art genomics services to investigators at IU Simon Comprehensive Cancer Center (IUSCCC), including next generation sequencing, single-cell analytics, microarray and high-throughput genotyping. With decades of experience and strong track record in supporting cancer research, significant subsidization from IUSM and IUSCCC, and strong ties with the Center for Computational Biology and Bioinformatics (CCBB), the GC strives to provide IUSCCC members high-quality genomic services with fast-turnaround times at affordable prices. This is done through the following Specific Aims:

Specific Aim 1: Provide state-of-the-art genomics services to IUSCC investigators. The GC provides three types of genomic services, including NGS, microarray and high-throughput genotyping. More than  90 percent of the service requests are for NGS. As a full NGS service core, the GC provides most of standard genomic services, including DNA sequencing (whole genome/exome sequencing, panel sequencing, such as Ampliseq cancer panel), RNA sequencing (mRNA-seq, total RNA-seq, exon capture for degraded RNA samples, ultralow input RNA-seq, single-cell RNA-seq and microRNA-seq), ChIP-seq, CLIP-seq, ATAC-seq, metagenomics (both 16S and shotgun sequencing), targeted bisulfite sequencing, and many others. Service scopes include preparation of sequencing libraries, QC of the client-generated NGS libraries, and sequencing run on Illumina or Ion Proton NGS systems.

Specific Aim 2: Evaluate and implement cutting-edge genomics technologies for supporting cancer research. The GC constantly evaluates new cutting-edge genomics technologies for genomic research, based on the input of the advisory committee and surveys among cancer center members. In the past two years, we have acquired several key technologies, including five Illumina sequencers (two NovaSeq 6000, one HiSeq 4000, one NextSeq 500 and one MiSeqDx), and 10X Genomics Chromium system for single cell genomics. These newly-acquired instruments are heavily used by IUSCCC members. In addition, we spend significant efforts in testing protocols that benefit cancer research, such as RNA-seq from FFPE and LMD (laser capture micro-dissection) samples, ATAC-seq protocol for epigenetic study, CRISPR screening, and single-cell analytics.

Specific Aim 3: Facilitate the development of novel experimental methods initiated by IUSCC members. In addition to providing standard services using established protocols, the GC plays key roles in designing novel experimental protocols in advancing cancer research. Such efforts are usually in response to specific needs from IUSCC investigators and involves both GC wet-lab scientists and CCBB/CBC computational biologists. For instance, the GC pairs with IUSCCC members and other IU investigators in technology development such as high-throughput reporter assays, high throughput CRISPR screening, and virus insertion site detection.

Specific Aim 4: Develop and organize training activities on genomics technologies, experimental assays, analysis methods. Besides providing high-quality genomics services to the users, one of the major missions of the GC is to provide education for IUSM and IUSCCC investigators on the state-of-the-art genomics technologies. Such activities include inviting vendors of key technology companies for presenting research seminars to IU investigators and IUSCCC members; offering short module courses introducing major applications using genomics  technologies  and  analysis  methods;  and  providing  training  opportunities  for college and high-school students in advancing biomedical research.

For more information, visit the core's Website.