Genomics Core

The GC provides three types of genomic services:

• NGS
• Single cell analytics
• Spatial transcriptomics

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
• Long-read sequencing
• And many others

Service scopes include preparation of sequencing libraries, QC of the client-generated NGS libraries, and sequencing run on Illumina platform.

The GC constantly evaluates new cutting-edge genomics technologies for genomic research, based on the input of the advisory committee and surveys among IU Simon Comprehensive Cancer Center members.

In the past two years, we have acquired several key technologies, and currently have three Illumina sequencers (two NovaSeq X Plus and one NextSeq 2000), two Oxford Nanopore sequencers for long-read sequencing, three 10x Genomics Chromium system for single cell genomics, and two 10x Genomics spatial analysis systems (CytAssist and Xenium). These newly-acquired instruments are heavily used by IU Simon Comprehensive Cancer Center members.

In addition, we spend significant effort 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
• Single-cell analytics
• Spatial transcriptomics

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 cancer center investigators and involve both GC wet-lab scientists and CCBB/CBC computational biologists.

For instance, the GC pairs with IU Simon Comprehensive Cancer Center members and other IU investigators in technology development such as high-throughput reporter assays, high throughput CRISPR screening, and virus insertion site detection.

Besides providing high-quality genomics services to the users, one of the major missions of the GC is to provide education for IU School of Medicine and IU Simon Comprehensive Cancer Center investigators on the state-of-the-art genomics technologies.

Such activities include:

• Inviting vendors of key technology companies to present research seminars to IU investigators and cancer center members
• Offering short module courses introducing major applications using genomics technologies and analysis methods
• Providing training opportunities for college and high-school students in advancing biomedical research