USTAR Center for Genetic Discovery

Overview

The USTAR Center for Genetic Discovery service recharge center helps investigate the genetic basis for human disease by providing whole exome and whole genome sequence analyses for research and clinical projects.  We specialize in variant calling and disease-gene discovery utilizing tools developed by the USTAR Center for Genetic Discovery, including VAAST, pVAAST, PHEVOR, Lumpy, WHAM, IOBIO, and others.

 

For general inquiries, price quotes, and timeline estimates, please contact Mary Anne Karren at makarren@genetics.utah.edu

Services

  • Alignment and variant calling for NGS datasets, including whole genome, whole exome, and panel sequences
  • Joint genotyping of separate data sets and controls
  • Disease gene discovery in cohorts and families using VAAST, pVAAST, PHEVOR, GEMINI, and IOBIO
  • Reference-free variant calling and investigation of de novo variants using RUFUS
  • Structural variant calling and prioritization using Lumpy and WHAM

For general inquiries, price quotes, and timeline estimates, please contact Mary Anne Karren at makarren@genetics.utah.edu

 

Rates

Variant calling 

Variant calling rates include consult time with our bioinformatics team to determine your analysis needs, receipt of data from sequencing vendor, storage and access to your data on our equipment at CHPC for 90 days after analyses are complete, and help with transfer to a final storage solution after project completion.  Our variant calling pipeline uses a GATK-based variant calling software, and includes WHAM for structural variant calling, as well as standard QC metrics (FastQC, samtools stats, samtools flagstat, bcftools stats, goleft).  You will receive polished, lossless BAM files, gVCF files, and finalized VCF files.  University of Utah investigators will access their data via GnomEx or directly on CHPC servers.  Data sharing method for external projects is determined on an individual basis.

Internal variant calling rates:

Variant calling rate (per sequence)
 # sequences 1-100 101-500 >500
WGS (60X) $52.0 $46.8 $42.1
WGS (30X) $48.0 $43.2 $38.9
WES $26.0 $20.8 $16.6
Panel $19.5 $15.6 $12.5

 

For external academic and commercial rates, please contact Mary Anne Karren makarren@genetics.utah.edu.

 

Post-VCF research analyses 

Our team of research analysts are available to help you with a variety of discovery analyses downstream of variant calling at the rate of $8,877 per month (minimum project is 0.25 months).  Our analysts benefit from collaboration with a dynamic team of researchers, clinicians, and software developers studying a broad range of inherited disorders including lung and heart disease, inflammatory and immune conditions, metabolic disease, and neurological conditions.  Analyses to be performed and total analyst time needed for your project will be determined on an individual basis after consultation with our team.

 

Joint genotyping

We can jointly genotype data across separate projects/datasets where variant calling has already been done.  The charge for this service is $0.51 per genome sequence with a minimum charge of $127.

 

Project management

Our team can help you transfer data to/from collaborators, and host and store your data sets on our equipment at CHPC.  The charge for this service is $0.64 per genome sequence with a minimum charge of $159 per dataset.

Referencing us

 

Please acknowledge our contribution to your research by including this statement in all publications:

 

(Service type) was performed at the USTAR Center for Genetic Discovery Service Recharge Center, part of the Health Sciences Center Cores at University of Utah.

Contact

 

We are located in the Eccles Institute of Human Genetics at the University of Utah School of Medicine.  For general inquiries, price quotes, and timeline estimates, please contact Mary Anne Karren at makarren@genetics.utah.edu

 

 

Team:

Mary Anne Karren, PhD

Director

801-581-7805

makarren@genetics.utah.edu

                         Barry Moore

         Director of Research and Science

             bmoore@genetics.utah.edu

Shawn Rynearson

Software Developer

Carson Holt, PhD

Software Developer

Jason Singer, PhD

Senior Research Analyst

Javier Hernandez, PhD

Postdoctoral Research Associate

Matt Velinder, PhD

Postdoctoral Research Associate

Bushra Gorsi, PhD

Postdoctoral Research Associate

Andrew Farrell, PhD

Postdoctoral Research Associate

Thomas Nicholas, PhD

Senior Research Analyst