Penn Medicine

Services

The focus of the CPD's initial efforts has been toward developing two cancer gene sequencing panels: a custom hematologic malignancy panel and a solid tumor panel. The primary targets will include leukemias, lymphomas and solid tumors, beginning with brain, melanoma, and lung tumors. The goal is to identify genomic alterations that allow clinicians to design and implement optimal treatment plans.

Personalized genomic testing at the CPD is performed with:

  • MiSeq and HiSeq sequencers (Illumina)
  • Ion Torrent Personal Genome Machine (Life Technologies)
  • Cytoscan Array (Affymetrix) technologies

Gene Panels

The CPD offers mutation analysis of the following Gene Sets:

Hematologic Malignancy Sequencing Panel

Sequence analysis of 68 genes*

ABL1 CEBPA** GATA2 MAP2K1 NPM1 RUNX1 TP53
ASXL1 CSF1R GNAS MAPK1 NRAS SETBP1 TPMT
ATM CSF3R HNRNPK MIR142 PDGFRA SF1 U2AF1
BCOR DDX3X IDH1 MPL PHF6 SF3A1 U2AF2
BCORL1 DNMT3A IDH2 MYC POT1 SF3B1 WT1
BIRC3 ETV6 IL7R MYCN PRPF40B SMC1A XPO1
BRAF EZH2 JAK2 MYD88 PTEN SRSF2 ZMYM3
CALR FAM5C KIT NF1 PTPN11 STAG2 ZRSR2
CBL FBXW7 KLHL6 NOTCH1 RAD21 TBL1XR1  
CDKN2A FLT3 KRAS NOTCH2 RIT1 TET2  

Solid Tumor Sequencing Panel

Sequence analysis of 47 genes*

ABL1 AKT1 ALK APC ATM BRAF CDH1
CSF1R CTNNB1 EGFR ERBB2 ERBB4 FBXW7 FGFR1
FGFR2 FGFR3 FLT3 GNA11 GNAQ GNAS HNF1A
HRAS IDH1 JAK2 JAK3 KDR KIT KRAS
MET MLH1 MPL NOTCH1 NPM1 NRAS PDGFRA
PIK3CA PTEN PTPN11 RB1 RET SMAD4 SMARCB1
SMO SRC STK11 TP53 VHL    

Services Overview

The Center for Personalized Diagnostics offers the highest volume of genome testing in the region. In clinical cases, disease-associated mutations have been reported in 75% of patient tests revealing results with therapeutic significance.

The CPD turnaround time for the vast majority of its reports is 10-14 days. (Note: the capacity of sequencing instruments requires a 3-day minimum, while auxiliary testing to confirm rare mutations may require up to 21 days.)

The genomic sequencing reports are specifically geared toward actionable knowledge for clinicians. The reports focus on normal or abnormal gene information and provide interpretation, comments, and references for disease-associated mutations or variants of uncertain significance.

As one of a few institutions worldwide, Penn Medicine's CPD offers a unique and custom-developed sequencing panel, built using the latest literature, that specifically addresses hematologic malignancies.

The CPD continues to benefit from the clinical and translational expertise at Penn as an integrated component of a major academic medical center. One of the results of this thorough and sustained integration is the CPD's precision diagnostics method, which allows for higher sensitivity leading to fewer false negative results. This bioinformatics method was custom-developed at the CPD by testing commercial tools with artificial data sets that demonstrated missed mutations. The CPD's unique computer programs and validation methods can address those inadequacies and can detect mutations that evade many standard analysis pipelines.

Services Under Development

To maintain a position at the leading edge of implementing genomic technologies in a clinical environment, the Center for Personalized Diagnostics is actively engaged in new test development. This includes collaborations for developing SNP array protocols for FFPE specimens, single cell genomic analyses, analysis of cell-free tumor DNA and both exome and whole genome sequencing of a variety of tumor types.

If you are a physician looking for information on how to order tests, please visit the "For Physicians page".

*The design of each panel was based on the literature at the time of development, either the full length of a gene or the mutational hot spots of a gene are targeted. For a complete listing of genomic coordinates covered in this panel please contact the laboratory.

**CEBPA will be analyzed only when a diagnosis of AML is provided.

Questions & Information:

Call 800-PENN-LAB