CHOP High-throughput Sequencing and Analytical Core

Within the PennCHOP Microbiome Program is the CHOP Microbiome Center, the program’s sequencing and analytical resource. The Center supports the planning of microbiome projects, DNA purification, library preparation, high-throughput sequencing, and bioinformatic analysis of the output.

While the Microbiome Center has resumed operations after closure due to the pandemic, we are experiencing a backlog of projects. We might not be able to start your project immediately but are happy to accept new projects and conduct consults.

If you are interested in working with our center, please fill out our customer request form.

If you have any questions about the application process, please contact us at: [email protected].

CHOP High-throughput Sequencing Core

The CHOP High-throughput Sequencing Core provides expertise in next-generation sequencing of microbiome samples. Services include sample aliquoting, DNA extraction, quantitative PCR, library preparation, and sequencing. All protocols and workflows are optimized for individual sample types.

Infrastructure for deep sequencing includes an Illumina HiSeq 2500 instrument, MiSeq instruments, and Oxford Nanopore technology. The sequencing facility is housed in the Colket Translational Research Building at CHOP with the wet lab in the adjoining Abramson Research Center, which includes dedicated pre- and post-PCR spaces. The labs are well equipped with the latest instruments including two automated liquid-handling robots for high-throughput processing. The Sequencing Core is staffed by a laboratory manager and three research technicians.

Analytical Core

The Analytical Core provides expertise in large-scale bioinformatics analysis of microbiome datasets. Core services start with a thorough quality check and review of sequencing results. This includes removal of host genomic sequences and other DNA added during the sequencing protocol. Automated pipelines assess the bacterial, fungal, and viral taxa found in each sample. Alignments to genes of known function are summarized, and the data are queried against a curated collection of full genomes for microbes of interest. The primary mission of the Analytical Core is to follow up basic bioinformatics analysis with targeted bioinformatics and statistical approaches that are unique to each study..

The Analytical Core is located at the Roberts Center for Pediatric Research. High capacity network lines connect the Analytical Core to the Sequencing Core, and to the CHOP supercomputing facility in Allentown, Pennsylvania. The Core is staffed by three full-time programmer/analysts and supported by a network of consulting statisticians.