High Throughput Genomics Core

About Us:

The High Throughput Genomics Core (HTGC) is a CAP/CLIA-certified state of the art genomics facility located in the center of Shadyside in Pittsburgh, PA. The facility houses a high-throughput, clinical-grade, 9,000 ft2 next generation sequencing (NGS) laboratory with an integrated bioinformatics cloud infrastructure. The HTGC staff includes two laboratory directors, laboratory staff, bioinformaticians, and IT support personnel.

 

The HTGC provides numerous laboratory and data analysis services to local research, commercial, and clinical interests. Our flexible, modular approach to project management allows samples to enter and leave the workflow at any stage, so investigators requisition only the services they require. Some clients complete highly customized portions of an experiment at their own or other facilities while realizing significant cost savings by completing sequencing and analysis at the HTGC. The HTGC works closely with UPMC in addition to other University of Pittsburgh’s genetics “core” laboratories to facilitate inter-lab sample transfer and batching to maximize efficiency and minimize cost for these projects. Other clients utilize our end-to-end workflow beginning with nucleic acid extraction and ending with comprehensive bioinformatics analysis or clinical reporting, including customizations available throughout the process. In other cases, we generate clinical-grade data for downstream analysis and treatment decision-making by collaborators.

 

Our Services

We can perform any combination of the following:

1. DNA/RNA Extraction

2. Quantity, Concentration, and Quality Checks (extracted DNA/RNA, prepared libaries)

3. RNA and DNA Library Preparation (mRNA, Total-RNA, Whole Genome, and Whole Exome libraries)

4. Next Generation Sequencing Services

5. Pharmacogenomics*

6. Axiom Microarray Services

 

Bioinformatics and Data Analysis

We provide a range of custom and standard bioinformatics analyses including but not limited to:

1. Whole Exome or Genome Germline and Somatic/Tumor Variant Calling

2. Whole Genome Copy Number Variant and Tumor Purity

3. RNAseq Feature Counts with/without Variant Calling

4. RNAseq Differential Gene Expression

5. 10x Genomics Cellranger Primary Analysis

 

Raw or formatted sequencing data files (bcl, fastq, BAM, VCF and CEL ) files for use in external analysis are also available for relevant test types.

 

Equipment list:

• 3 – Vantage liquid handlers by Hamilton

• 1 – Chemagic 360 24-head automated nucleic acid extraction instrument by Perkin Elmer

• 1 – Chemagic 360 96-head automated nucleic acid extraction instrument by Perkin Elmer

• 1 – Synergy by BioTek

• 1 – Qubit by Invitrogen

• 3 – Fragment Analyzer by Agilent

• 1 – LightCyclers by Roche

• 1 – Tecan Infinite 200 Pro by Tecan

• 1 – NovaSeq X Plus by Illumina

• 1 – Novaseq 6000 by Illumina

• 1 – MiSeqDX by Illumina

• 1 – Biomek FXP liquid handler by Beckman Coulter

• 1 – GeneTitan by ThermoFisher

• Various small lab equipment