Massively parallel next-generation sequencing technology is an essential tool that supports a wide range of biological research from whole-genome sequencing (WGS) to single-cell analysis and spatial transcriptomics. The University of Pittsburgh has multiple cores that provide sequencing services, each with its own concentration and skill set. The Center for Advanced Genomics is an umbrella website designed to help investigators determine which member core best supports their project needs. Member cores include the following:
- Health Sciences Sequencing Core at UPMC Children’s Hospital of Pittsburgh
- Low-input RNA-seq, spatial biology, ChIP-Seq or ATAC-Seq and high throughput sequencing
- High Throughput Genomics Core
- WGS or whole-exome sequencing (WES), high-input high-throughput RNA-Seq, Axiom arrays, College of American Pathologists/Clinical Laboratory Improvement Amendments (CAP/CLIA)-certified clinical testing and high-throughput sequencing
- Single Cell Core
- Multiple types of single-cell analyses
To initiate a project through the Center for Advanced Genomics, or if you have general inquiries, fill out a project inquiry form. Staff from the appropriate genomic core facility will respond.
In the next three editions, the Research Resource Nexus will highlight each core, showcasing their complementary and cooperative work. This month highlights the High Throughput Genomics Core.
High Throughput Genomics Core (HTGC)
The High Throughput Genomics Core (HTGC) operates the highest throughput sequencers from Illumina to offer CAP/CLIA-certified processing from biospecimens to results for WGS or WES and RNA sequencing.
HTGC is also a Thermo Fisher Scientific center of excellence for the PharmacoScan pharmacogenetics microarray and can process any array compatible with the Gene Titan instrument. Research and clinical specimens proceed through the same workflow under clinical-grade quality control and assurance.
Accurate and efficient high-throughput processing is at the heart of HTGC operations.
- Revvity Chemagic 360 instruments perform automated DNA/RNA extractions from blood, saliva, cell pellets and freshly frozen or Formalin-Fixed Paraffin-Embedded tissues.
- Using the Clarity Laboratory Information Management System, barcoded tubes rigorously and accurately track sample progress and tube locations.
- Automated Hamilton Vantage liquid handlers conduct library preparation, normalization and pooling before loading pooled libraries onto either the NovaSeq6000 or NovaSeq X Plus.
- Operates a MiSeqDX for lower-throughput clinically validated testing or sequencing for research projects requiring up to 25 million reads.
HTGC uses the efficiencies of automation and high-throughput instrumentation by batching smaller projects together with larger ones and pooling libraries of the same type across projects to maximize the output of sequencing flow cells.
HTGC also operates a Gene Titan system capable of running any 24- or 96-place Axiom genotyping array. Genotyping arrays investigating a known set of informative single nucleotide variants are a cost-effective alternative to sequencing for genome-wide association studies. The Axiom platform offers greater cost-effectiveness than many other platforms with parallel processing of 24 or 96 samples. Off-the-shelf and custom-designed options are available through Thermo Fisher Scientific.
Contact the HTGC with questions about how their services can meet your project needs. Users must submit the online project initiation form before submitting samples.
HTGC is in the Hoechstetter building, 5560 Centre Avenue, at the corner of Centre and Negley Avenues. Samples can be dropped off at that location or delivered through MedSpeed.
HTGC Project Spotlights
Udai Kammula uses HTGC for rapid clinical-grade RNA-Seq in his clinical trial testing the efficacy of a transcriptomic biomarker developed in his laboratory. The uveal melanoma immunogenomic score (UMIS) is a number derived from the relative expression levels of 2,400 transcripts measured in a biopsy of metastatic uveal melanoma. UMIS estimates the likelihood that Tumor-Infiltrating Lymphocyte (TIL) immunotherapy will be successful—offering the potential to relieve patients with unresponsive tumors from needless surgery and delays in alternate treatment. HTGC staff promptly process biopsies for this extensive multisite study using UMIS analysis methods, ensuring a quick turnaround essential for clinical operations.
Phil Empey relies on the HTGC for several investigations using the PharmacoScan genotyping array. MyPGx, a clinical trial, examines whether patients’ knowledge of their pharmacogenetic profiles optimizes medicinal decisions. HTGC performs the PharmacoScan assay on participants’ DNA under CAP/CLIA compliant workflows, with results either immediately integrated into their electronic health records (EHR) or held for one year. Upon return of results, a trained pharmacist reviews the findings via telehealth. This study aims to guide future preemptive pharmacogenetic screening. Empey also leads Pitt+Me Discovery, a biobanking project run in partnership with Pitt’s Clinical and Translational Science Institute, which houses 60,000 DNA samples at HTGC that are available for additional testing and investigation. Interested faculty members should contact the CTSI for access.
Gwen Sowa and Nam Vo are leading the Low Back Pain Research Study (LB3P), which utilized multiple core labs in the exploration of chronic low back pain. The HTGC's automated high throughput services for DNA extraction, library preparation, and WGS, were applied to 1007 patients and 200 controls. Sowa and Vo appreciated working with a local service provider, allowing their research team to hand-deliver samples and easily retrieve leftover DNA for long-term storage, avoiding shipping stress. HTGC support continued through publication, with delivery of additional data quality metrics not originally requested and extensive assistance with method write up. Initial analysis combines data generated by HTGC and the Mass Spectrometry Core to identify SNVs related to proteomic findings. The full multi-omic dataset will be publicly accessible for further research to alleviate chronic low back pain.