This guide will help you find local resources that are available to Pitt investigators for designing experiments, sequencing samples, analyzing data, and storing data for research involving Next Generation Sequencing (NGS). Faculty and staff are available at each facility to assist you with identifying the technology application best suited to answering your research question and to assist with moving the project to the next step in the process, including referrals to other facilities. 

• Quick Reference Card for the experienced user who knows what he or she needs. This table provides a list of resources with links to the related facility web sites.


• Initial Consultation to help you identify where to start and direct you to the appropriate resources based on your project goals. Deborah Hollingshead; hollings@pitt.edu; (412) 648-1284


• Review the Concise Resource Summary below.

Concise Resource Summary

Study Design and Technical Project Design Consultation

• Initial Consultation: Get started.
  • > Deborah Hollingshead; hollings@pitt.edu; (412) 648-1284
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• Biostatistics, Epidemiology, and Research Design Core: Statistical and study design assistance accessed through CTSI facilitators. Ten hours of free assistance per project. Begin with study design and power analysis before starting a project and prior to bioinformatics analysis. You may also consult with a CTSI biostatistician after bioinformatics analysis for help with statistical interpretation of bioinformatics output.
  • > Contact CTSI facilitators: https://ctsi.pitt.edu/about-us/research-facilitator-contacts/
  • > https://ctsi.pitt.edu/research-services/core-services/biostatistics-epid...

Sequencing

• ​Health Sciences Sequencing Core at Children’s Hospital of Pittsburgh: Low to medium throughput Illumina Sequencing using NextSeq 500 & 2000 and MiSeq for small to medium sized projects. Services include sample and library preparation and DNA and RNA sequencing.
  • > William A MacDonald, PhD; w.a.macdonald@pitt.edu; (412) 692-3555
  • > http://www.nextgen.pitt.edu
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• UPMC Genome Center: High throughput DNA and RNA sequencing using Illumina’s NovaSeq 6000 series. Services include sample processing and library preparation for blood, saliva, and tissue samples, whole genome and exome sequencing, and RNA sequencing. Bioinformatics processing of raw data is provided through DNAnexus and Edico (alignment and variant calling), and variant annotation is provided through Wuxi NextCode. Clinical grade whole genome sequencing through the CLIA-certified Genome Center is also available.
  • > genome_center@upmc.edu
  • > https://upmcgenomecenter.com/
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• Center for Medicine and the Microbiome: Microbiome sequencing using Illumina MiSeq. Services include sample preparation, sequencing, bioinformatics, and statistical analysis.
  • > Contact: http://www.microbiome.pitt.edu/submit-a-request
  • > http://www.microbiome.pitt.edu

Bioinformatics Analysis

• Genomics Analysis Core: Data analysis services for RNASeq, WXS, WGS, ChIPSeq; this facility will use the CRC for computing resources and temporary data storage. For long term storage needs, please consult the GAC or CRC.  Custom analysis is performed based on investigator and project’s objectives. 
  • > Uma Chandran, PhD; Chandran@pitt.edu; (412) 648-9326
  • > http://www.genomicsanalysis.pitt.edu
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• Molecular Biology Information Service of the Health Sciences Library System: Access to software and software training is available for investigators who want to analyze their own data from RNAseq, variant analysis, and other RNA and DNA sequencing experiments.
  • > Ansuman Chattopadhyay, PhD; hslsmolb@pitt.edu
  • > https://hsls.pitt.edu/molbio


• Center for Medicine and the Microbiome: Bioinformatics and statistical analysis for microbiome dervied data.
  • > Contact: http://www.microbiome.pitt.edu/submit-a-request
  • > http://www.microbiome.pitt.edu

High Performance Computing

• Center for Research Computing: Software, Computing, and Data Storage. Consultation to improve bioinformatics workflows and assistance with adopting software for new types of data is available. Use of computing is free and is limited to two million service units per year (e.g., 2 million core hours of computing time). Data storage up to 5 TB is free when the computing resources of this facility are utilized. Users uncertain of their needs should consult with CRC personnel before contacting the Pittsburgh Supercomputing Center.
  • > Fangping Mu, PhD; fangping@pitt.edu; (412) 624-5041
  • > http://www.crc.pitt.edu
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• Pittsburgh Supercomputing Center: Software, Computing, and Data Storage. Consultation to improve bioinformatics workflows and assistance with adopting software for new types of data is available. Use of computing is free, but access requires the investigator to submit a formal application and compete nationally for usage hours. Use of this facility should be considered when the computing need exceeds two million core hours of computing time per year.
  • > http://www.psc.edu
  • > Contact by phone: 412-268-4960
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