VUMC IMGSCT Core (Immunogenomics, Microbial Genetics and Single Cell Technologies)

Overview of Services

VUMC Immunogenomics, Microbial Genetics and Single Cell Technologies (IMGSCT) core provides high throughput high resolution immunogenomics sequencing, including HLA typing, KIR typing, and ERAP typing. Additionally, the core will provide single-cell studies focused on TCR sequencing and RNA transcriptomics, microbial genetics assays and digital droplet PCR assays.

The Core provides support for:

• High throughput high resolution immunogenomics sequencing

1. a) High resolution (4 digit) HLA typing: HLA-A, B, C, DR, DP, DQ
2. b) KIR typing
3. c) ERAP typing

• Single-cell TCR sequencing and RNA transcriptomics

1. This includes Smart-seq2 library preparation
2. Analysis of sequence data
3. Access to our Visual Genome Analysis Studio (VGAS) designed by our group which allows presentation of data, sequence alignment and epitope mapping (Ref: Leary, Shay & Cooper, Don & Chopra, Abha & Watson, Mark. (2013). IIID VGAS - A Visual Genome Analysis Studio incorporating high performance next generation sequence analysis)

• Bulk TCR sequencing from RNA
• Digital droplet PCR assays
• Microbial genetics assays
  1. Nucleic acid isolation: RNA or DNA
  2. Library preparation for (sequencing referred to VANTAGE)
     1. Whole Transcriptome profiling
     2. Metatranscriptomic profiling
  3. Viral and bacterial genome sequencing

The facility has pre and post PCR laboratories (rooms U3304 and U3308) that contains two Biomek Robotic liquid handling systems for automated, high throughput assays . Liquid handlers are used wherever possible in order to minimize manual handling of samples. IMGSCT core also has a Mantis which is a microfluidic liquid handling device, useful when working with very small volume reactions. The Mantis enables us to reduce reagent cost which in turn help us having competitive pricing for single cell assays.

The IMGCT Core also has Droplet Digital instrument, PCR and, Realtime PCR instruments.

Droplet Digital™ PCR (ddPCR™) is an elegant technology that enables accurate and absolute quantification of target nucleic acid molecules. By partitioning a PCR reaction into thousands of nanoliter-sized droplets followed by amplification and subsequent interrogation of each droplet, ddPCR assays allow increased quantitative resolution, enhanced detection of difficult-to-amplify targets, better reproducibility, and simplified data analysis.

Description of services

1. High throughput high resolution immunogenomics sequencing
2. a) High resolution (4 digit) HLA typing: HLA-A, B, C, DR, DP, DQ
3. b) KIR allele typing
4. c) ERAP typing
5. d) KIR typing

We ship samples to the Institute for Immunology and Infectious Diseases (IIID) in Perth, Australia for our collaborators to process. Our core was built and designed to mirror this high throughput laboratory that was partly designed by members in our group. They have automated systems, with large throughput work flow and standard operating procedures that facilitate the generation of large volume work-loads from all over the world in an expedited manner. IIID is accredited by the National Association of Testing Authorities, Australia and American Society for Histocompatibility and Immunogenetics(ASHI) for compliance to the ISO/IEC 17025 standard for laboratory testing and HLA typing respectively(http://www.iiid.com.au). Final analyzed results are sent to Investigators through IMGSCT core.

1. Single-cell TCR sequencing and RNA transcriptomics

Using the smart seq 2 technology we generate cDNA from sorted single cells, amplifying TCR from barcoded cDNA from each cell and sequenced on Illumina Mi Seq platform (IIID)

Single cell whole libraries are made from sorted single cells individually barcoded (IMGCT) and sequencing is done at VANTAGE core on Novaseq

Bulk TCR sequencing of bulk T cell populations(lysates or RNA), Viral and Bacterial genome  sequencing is also performed at IIID, and analyzed data will be sent to the Investigators through IMGCT core.

Data analysis is via VGAS, with a 3-month access provided to users to analyze data with option of extension as needed

Leadership

Simon Mallal, Core Scientific Director

Elizabeth Phillips, Core Scientific Co-Director
Suman Das, Core Deputy Director
Rama Gangula, Core Operations Manager 
Meghan Shilts, Core Deputy Operations Manager

For general questions or assistance, please contact our support team at IMGCTCore@vanderbilt.edu.

Location and hours of operation

Links and Resources

1. VUMC Office of Research - iLab User Guides & FAQs