Center for Personalized Diagnostics Current Gene Panels and Research

Gene Panels

The CPD offers mutation analysis of the following Gene sets:

PennSeq™ Hematologic Malignancies Panel

Sequence analysis of 116 genes

• 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

The PennSeq assay enriches for many genomic regions and then is computationally filtered to report variants from a curated set of genes. Incidental variants may be discovered during routine review of the genomic data that fall outside of the curated set of genes. Any Disease-Associated or other potentially significant variant discovered incidentally will be included in the clinical report with a comment and appropriate interpretive text, as needed. By requesting this testing and accepting this report for clinical purpose, implied consent is given that information on incidentally identified genomic variants may be received.

PennSeq™ Solid Tumor Panel

Sequence analysis of 183 genes 

• Accepted Specimens: Formalin-fixed, paraffin-embedded (FFPE) tissue; fresh tissue in PreservCyt
• Minimum Requirements: 10% neoplastic 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; Targeted copy number gains
• 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

The PennSeq assay enriches for many genomic regions and then is computationally filtered to report variants from a curated set of genes. Incidental variants may be discovered during routine review of the genomic data that fall outside of the curated set of genes. Any Disease-Associated or other potentially significant variant discovered incidentally will be included in the clinical report with a comment and appropriate interpretive text, as needed. By requesting this testing and accepting this report for clinical purpose, implied consent is given that information on incidentally identified genomic variants may be received.

Fusion Transcript Panel

RNA sequencing analysis of 56 genes for rearrangements

• 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

• 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

Targeted Expedited Molecular Profiling (TEMP)

DNA sequence analysis of single nucleotide variant (SNV) and insertion/deletion (indel) hotspots in 45 genes. RNA sequence analysis of 13 fusion drivers and 2 oncogenic isoforms.

• Accepted specimens: Formalin-fixed paraffin-embedded (FFPE) tissue, cytology samples, FNA rinses, pleural effusion/fluid, and fresh tissue
• Minimum requirements: 10% neoplastic tissue
• Covers: DNA hotspots and selected fusions and oncogenic isoforms in the genes listed above
• Detects: SNVs, small indels, targeted fusions and oncogenic isoforms with known breakpoints and non-targeted fusions with unknown breakpoints
• Limitations: Only detects known hotspot SNV and indel variants and known fusions/oncogenic isoforms; lower limit of reportability of 2.5% variant allele fraction (VAF) for SNVs, 2.0% VAF for indels; no methylation; no copy number changes