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Center for Applied Genomics (CHOP)

Directors: Hakonarson, Hakon., MD, PhD; Santani, Avni., PhD


Our Mission

The mission of the Center for Applied Genomics (CAG) is to develop new and better ways to diagnose and treat children affected by rare and complex medical disorders. The CAG is a specialized Center of Emphasis at the Children’s Hospital of Philadelphia with the primary goal of translating basic research findings to medical innovations.

We aim to discover genetic causes for the most prevalent diseases of childhood including ADHD, asthma, autism, diabetes, epilepsy, obesity, schizophrenia, pediatric cancer, and a range of rare diseases. Ultimately, our objective is to generate new diagnostic tests and to guide physicians to the most appropriate therapies.

The CAG is one of the world's largest genetics research programs, and the only center at a pediatric hospital to have large-scale access to state-of-the-art high-throughput genomics technology.

CAG Services:

The Center for Applied Genomics has an experienced team of researchers analyzing the immense amount of data generated from our high-throughput facility. We have expertise in carrying out large scale NGS, GWAS, CNV, and methylation studies.





  • NGS- HiSeq ( Material processing service )

    Our HiSeq v4 reagent kits generate up to 1 terabase (1Tb) of data per 6-day run (up to 500 Gb per flow cell), increasing daily throughput to 167 Gb per day. The new v4 reagents increase the number of clusters by 33% compared to the TruSeq SBS Kit v3, adding additional capacity for counting assays.

    Type of Run – Single Read (SR) or Paired End (PE)

    Applications Offered:

    Target Sequencing/Custom panels
    Exome Sequencing
    Whole Genome Sequencing

  • NGS-MiSeq ( Service )

    Our MiSeq reagent kits generate up to 25 million of data per day run. MiSeq is useful when you don't need a lot of reads for your project and turnaround time is paramount.

    Type of Run – Single Read (SR) or Paired End (PE)

    Applications Offered:

    Target Sequencing/Custom panels
    Exome Sequencing
    Whole Genome Sequencing


  • Annovar ( Algorithmic software suite )

    ANNOVAR is an efficient software tool to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).

  • GenGen ( Algorithmic software suite )

    GenGen is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.

  • ParseCNV Copy Number Variant Call Association Software ( Algorithmic software suite )

    ParseCNV CNV Call Association Software

  • PennCNV ( Algorithmic software component )

    PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.

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Last updated: 2019-10-08T13:00:03.350-04:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016