Health Alert:

See the latest Coronavirus Information including testing sites, visitation restrictions, appointments and scheduling, and more.

Penn Center for Personalized Diagnostics

Gene Panels

The CPD offers mutation analysis of the following Gene sets:

PennSeq™ Hematological Malignancies Panel

Sequence analysis of 116 genes

ABL1 ASXL1 ATM B2M BCL2 BCOR BCORL1
BIRC3 BRAF BRCA1 BRCA2 BRINP3 BRIP BTK
CALR CARD11 CBL CD79A CD79B CDKN2A CEBPA
CIITA CREBBP CSF1R CSF3R CXCR4 DDX3X DDX41
DICER1 DNMT3A EGR2 ERCC4 ETV6 EZH2 FANCA
FANCC FANCD2 FANCE FANCF FANCG FANCL FANCM
FBXW7 FLT3 GATA2 GNA13 GNAS HNRNPK ID3
IDH1 IDH2 IKZF1 IL7R JAK2 JAK3 KIT
KLF2 KLHL6 KRAS MAP2K1 PAK1 RIP142 MPL
MYC MYCN MYD88 NF1 NFKBIE NOTCH1 NOTCH2
NPM1 NRAS PALB2 PDGFRA PHF6 PLCG1 PLCG2
POT1 PRPF40B PTEN PTPN11 RAD21 RAD51 RAD51C
RHOA RIT RPS15 RRAGC RUNX1 SETBP1 SF1
SF3A1 SF3B1 SLX4 SMC1A SOCS1 SRSF2 STAG2
STAT3 STAT5B TBL1XR1 TCF3 TERT11 TET2 TNFAIP3
TNFSRF14 TP53 TPMT TRAF3 U2AF1 U2AF2 WT1
XPO1 XRCC2 ZMYM3 ZRSR2
  • Accepted Specimens: Blood; bone marrow; formalin-fixed, paraffin-embedded (FFPE) tissue; fresh tissue in PreservCyt
  • Minimum Requirements: 10% tumor nuclei for tissue; 100ng DNA (non-FFPE), 200ng DNA (FFPE)
  • Covers: Genes listed for the entire coding sequence +/- ~8bp flanking intronic sequence; two hotspots in the TERT promoter
  • Detects: Single nucleotide variants (SNVs); small indels; copy number gains in ABL1, PDGFRA, and MYC
  • Limitations: Lower limit of reportability 4% variant allele fraction (VAF) [1% for FLT3 ITDs only]. No deep intronic splice variants; no promoter variants outside of TERT; no structural rearrangements; no methylation; no copy number loss
  • 1 Includes hotspots in the promoter region

Solid Tumor Panel

Sequence analysis of 152 genes

ABL1 AKT1 AKT2 AKT3 ALK
APC AR ARAF ARID1A ARID2
ATM ATRX AURKA BAP1 BRAF
BRCA1 BRCA2 BRIP BTK CBP
CCND1 CCND2 CCND3 CCNE1 CDH1
CDK4 CDK6 CDKN2A CHEK2 CIC
CRKL CSF1R CTNNB1 DAXX DDR2
DNMT3A EGFR EIF1Ax EPHA3 ERBB2
ERBB3 ERBB4 ERCC2 ERG ESR1
ESR2 EZH2 FBXW7 FGF3 FGFR1
FGFR2 FGFR3 FGFR4 FLT3 FUBP1
GATA3 GNA11 GNAQ GNAS HRAS
H3F3A IDH1 IDH2 IGF1R JAK1
JAK2 JAK3 KDM5A KDM5C KDM6A
KDR KIT KMT2C KRAS MAP2K1
MAP2K2 MAP2K4 MAPK1 MAPK3 MAX
MCL1 MDM2 MDM4 MED12 MEN1
MET MITF MLH1 MRE11A MSH2
MSH6 MTOR MYC MYCN NBN
NF1 NF2 NTRK1 NTRK2 NTRK3
NKX2-1 NOTCH1 NOTCH2 NOTCH3 NRAS
EP300 PAK1 PALB2 PBRM1 PDGFRA
PIK3CA PIK3CB PIK3R1 PTCH1 PTEN
PTPN11 RAB35 RAC1 RAD50 RAD51
RAD51B RAD51C RAD51D RAF1 RB1
RET RHOA RNF43 SETD2 SF3B1
SLIT2 SMAD4 SMARCA4 SMO SPOP
SRC STAG2 STK11 SUFU SUZ12
SYK TET2 TGFBR2 TP53 TRAF7
TSC1 TSC2 TSHR U2AF1 VHL
WT1 XRCC2
  • Accepted Specimens: Formalin-fixed, paraffin-embedded (FFPE) tissue; fresh tissue in PreservCyt
  • Minimum Requirements: 10% neoplastic tissue
  • Covers: Entire coding sequence +/- ~10bp flanking intronic sequence of listed genes (see above)
  • Detects: Single nucleotide variants (SNVs); small indels; Copy Number Variants (CNVs); Tumor Mutational Burden (TMB)
  • Limitations: Lower limit of reportability 2% variant allele fraction (VAF); Indels unreliable > 30bp; no deep intronic splice variants; no promoter variants; no structural rearrangements; no methylation

Fusion Transcript Panel

RNA sequencing analysis of 55 genes for rearrangements

AKT1 ALK AXL BCOR BRAF
CALCA CAMTA1 CCNB3 CCND1 CIC
EGFR3 EPC1 ERBB2 ERG ESR1
EWSR1 FGFR1 FGFR2 FGFR3 FOXO1
FUS GLI1 HMGA2 JAZF1 KRT20
KRT7 MEAF6 MET4 MKL2 NCOA2
NRG1 NTRK1 NTRK2 NTRK3 PDGFB
PIK3CA PLAG1 PMS2 PPARG PTH
RAF1 RET ROS1 SLC5A5 SS18
STAT6 TAF15 TCF12 TERT TFE3
TFG THADA TMPRSS2 USP6 YWHAE
  • Accepted Specimens: Formalin-fixed, paraffin-embedded (FFPE) tissue; fresh tissue in PreservCyt
  • Minimum Requirements: 10% neoplastic tissue
  • Covers: Selected exon-intron boundaries
  • Detects: Aberrant transcripts involving the included exons; can detect novel fusion partners at known break-points
  • Limitations: Only detects fusions which include at least one of the targets at the included exons; no SNVs; no copy number changes; no small indels; no methylation
  • 3In addition to fusions involving EGFR, the assay detects aberrant isoforms EGFRvII and EGFRvIII.
  • 4 The assay detects aberrant spliceforms resulting from MET exon 14 skipping (MetΔex14).

Penn Precision Panel 2.0

Sequence analysis of 59 genes

ABL1 AKT1 ALK APC ATM
BRAF CDH1 CDKN2A CSF1R CTNNB1
DDR2 DNMT3A EGFR EIF1Ax ERBB2
ERBB4 ESR1 EZH2 FBXW7 FGFR1
FGFR2 FGFR3 FLT3 FOXL2 GNA11
GNAQ GNAS HNF1A HRAS IDH1
IDH2 JAK2 JAK3 KDR KIT
KRAS MAP2K1 MET MPL MSH6
NOTCH1 NPM1 NRAS PDGFRA PIK3CA
PTEN PTPN11 RB1 RET ROS1
STK11 SMAD4 SMARCB1 SMO SRC
TP53 TSC1 TSHR VHL
  • Accepted Specimens: Formalin-fixed, paraffin-embedded (FFPE) tissue; fresh tissue in PreservCyt; blood; bone marrow
  • Minimum Requirements: 10% neoplastic tissue
  • Covers: Hotspots and the entire coding sequence of TP53
  • Detects: Single nucleotide variants (SNVs); small indels
  • Limitations: Lower limit of reportability 4% variant allele fraction (VAF); indels unreliable >20bp; no deep intronic splice variants; no structural rearrangements; no copy number variants; no methylation
Share This Page: