Cancer Panels
Comprehensive Cancer Gene Panels
The Division of Genomic Diagnostics at Children’s Hospital of Philadelphia has launched a series of hereditary and somatic cancer gene panels to facilitate a precision medicine approach to cancer diagnostics. Genetic alterations identified by these panels will facilitate diagnosis, determine prognosis, stratify patient risk, inform treatment decisions, and evaluate patients’ eligibility for clinical trials.
Comprehensive Solid Tumors Panel (Solid + Fusion)
Test Information
The CHOP Solid Tumor Panel utilizes next-generation sequencing technology to simultaneously analyze a panel of genes known to be associated with a variety of solid tumors including pediatric solid tumors. Most cancers result from accumulation of multiple genomic alterations that lead to dysfunction of cancer-associated genes. These genomic alterations are important diagnostic, prognostic, and therapeutic markers.
The CHOP Solid Tumor Panel test can provide important genomic information regarding tumor development and progression, which facilitates more accurate disease diagnosis, risk stratification, and therapeutic decision. Two hundred thirty-seven genes known to be associated with cancer predisposition are analyzed using Next Generation Sequence (NGS) technology.
All coding exons of the 237 genes and 5 base pairs of 5’ and 3’ flanking intronic sequences are analyzed. Certain known intronic mutations of these genes are also evaluated. Clinically actionable or potentially actionable variants detected by NGS are confirmed by Sanger sequencing or other methodologies when necessary. The genes included in this panel are listed below:
ABL1, ACVR1, AKT1, AKT2, AKT3, ALK,APC, AR, ARAF, ARID1A, ARID1B, ARID2, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXL, B2M, BAP1, BARD1, BCL2, BCL6, BCOR, BCORL1, BLM, BRAF, BRCA1, BCRA2, BRD4, BRIP1, CARD11, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD274, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CHEK1, CHEK2, CIC, CREBBP, CRKL, CRLF2, CSF1R, CTCF, CTNNB1, DAXX, DDR2, DNMT3A, DOT1L, EED, EGFR, EP300, EPHA3, EPHA5, EPHB1, ERBB2, ERBB3, ERBB4, ERG, ESR1, ETV6, EZH2, FAM46C, FANCA, FANCC, FBXW7, FGF19, FGF3, FGF4, FGFR1, FGFR2, FGFR3, FGFR4, FLCN, FLT1, FLT3, FLT4, FOXL2, FOXP1, FUBP1, GATA1, GATA2, GATA3, GNA11, GNAQ, GNAS, GRIN2A, GSK3B, H3F3A, HGF, HIST1H1C, HIST1H3B, HNF1A, HRAS, IDH1, IDH2, IGF1R, IKBKE, IKZF1, IL7R, INPP4B, IRF4, IRS2, JAK1, JAK2, JAK3, JMJD1C, JUN, KDM5A, KDM5C, KDM6A, KDR, KEAP1, KIT, KMT2A, KMT2C, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAPK1, MCL1, MDM2, MDM4, MED12, MEF2B, MEN1, MET, MITF, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYB, MYC, MYCN, MYD88, MYOD1, NF1, NF2, NFE2L2, NKX2-1, NOTCH1, NOTCH2, NPM1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PAX5, PBRM1, PDCD1, PDGFRA, PDGFRB, PHOX2B, PIK3CA, PIK3CG, PIK3R1, PIK3R2, PIM1, PPM1D, PPP2R1A, PRDM1, PRKAR1A, PTCH1, PTEN, PTPN11, RAD50, RAD51, RAF1, RARA, RB1, RET, RHOA, RICTOR, RNF43, ROS1, RPTOR, RUNX1, SDHA, SDHB, SDHC, SDHD, SETD2, SF3B1, SMAD2, SMAD4, SMARCA4, SMARCB1, SMO, SOCS1, SOX2, SPEN, SPOP, SRC, STAG2, STK11, SUFU, SUZ12, TERT, TET2, TGFBR2, TNFAIP3, TNFRSF14, TOP1, TP53, TP63, TSC1, TSC2, TSHR, U2AF1, VHL, WHSC1, WT1, AMER1, XPO1
One hundred and six fusion gene partners are analyzed for over 500 fusions and many more novel fusions using anchored multiplex PCR technology followed by NGS. The technology allows detecting novel fusions associated with genes in this panel. Fusions are confirmed by FISH or Real Time PCR when necessary. This panel does not detect fusions not included in this panel. The panel should not be used for detecting residual fusions at present time. Customized Real Time PCR for monitoring residual fusions are available in our laboratory. The fusion partner genes included in this panel are listed below:
ABL1, ABL2, AKT3, ALK, ARHGAP26, AXL, BCL2, BCL6, BCR, BRAF, BRD3, BRD4, CAMTA1, CBFB, CCNB3, CCND1, CIC, CRFL2, CSF1R, DUSP22, EGFR, EPC1, EPOR, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FGR, FOXO1, FUS, GLI1, GLIS2, HMGA2, IL2RB, INSR, JAK2, JAZF1, KMT2A, MALT1, MAML2, MAST1, MAST2, MEAF6, MECOM, MET, MKL1, MKL2, MSMB, MUSK, MTB, NCOA2, NOTCH1, NOTCH2, NRG1, NTRK1, NTRK2, NTRK3, NUMBL, NUP214, NUP98, NUT, PAX5, PDGFB, PDGFRA, PDGFRB, PICALM, PIK3CA, PKN1, PLAG1, PPARG, PRKCA, PRKCB, PTK2B, RAF1, RARA, RBM15, RELA, RET, ROS1, RSPO2, RSPO3, RUNX1, RUNX1T1, SS18, STAT6, TAF15, TAL1, TCF12, TCF3, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TSLP, TYK2, USP6, YWHAE
Copy number variations (CNVs) of these genes are evaluated by analyzing NGS data. These CNVs are confirmed by MLPA, Real Time PCR, or Array CGH Analysis (aCGH) when necessary. Certain genes or exons may not be evaluated for gross copy number variations, such as genes with no known gross deletion/duplication mutations, or genes or exons with pseudogenes or highly homologous sequences in the genome.
Methodology
Targeted Capture and anchored multiplex PCR (for fusions) followed by Massively Parallel Sequencing. MLPA, Real Time PCR, or aCGH may be used when needed.
Sample & Shipping Information
Fresh Tissue: Submit 150 mg (0.5-2.0 cm3) Fresh tissue in transport media. Deliver to the laboratory within 24 hours at room temperature.
Fresh Frozen Tissue: Submit 150 mg (0.5-2.0 cm3) Fresh tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
FFPE tumor slides or block: Submit 10 unstained 10 um FFPE slides containing adequate amounts of tumor to be analyzed or FFPE block containing adequate amounts of tumor to be analyzed. A HE stained slide with areas of tumor marked should be submitted along with FFPE slides. Please include a copy of corresponding surgical pathology report. Sent at ambient temperature (18-25°C/64-77°F). Protect paraffin tissue from excessive heat. Ship in cooled container during summer months. Unacceptable Conditions include tumor in tissue or specimens fixed/processed in alternative fixatives.
Other Specimen type: Please contact the laboratory to discuss other specimen types that may be acceptable. Please note: if specimen contains less than 30% tumor content, please call our laboratory.
Turn Around Time
2 to 3 weeks
CPT Code 81455
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.
Comprehensive Hematological Cancer Panel (Heme + Fusion)
Testing Information
The CHOP Hematological Cancer Panel utilizes next-generation sequencing technology to simultaneously analyze a panel of genes known to be associated with hematological malignancies. Hematological malignancies results from accumulation of multiple genomic alterations that lead to aberrant hematopoietic proliferation and differentiation. These genomic alterations are important diagnostic, prognostic, and therapeutic biologic markers.
The CHOP Hematological Cancer Panel test can provide important genomic information regarding tumor development and progression, which facilitates more accurate disease diagnosis, risk stratification, and therapeutic decision. Ninety-nine genes known to be associated with cancer predisposition are analyzed using Next Generation Sequence (NGS) technology. All coding exons of the 99 genes and 5 base pairs of 5’ and 3’ flanking intronic sequences are analyzed. Certain known intronic mutations of these genes are also evaluated. Clinically actionable or potentially actionable variants detected by NGS are confirmed by Sanger sequencing or other methodologies. The genes included in this panel are listed below:
ABL1, ASXL1, ATRX, BCL11B, BCL6, BCOR, BCORL1, BRAF, CALR, CBL, CCND3, CDC25C, CDKN2A, CDKN2B, CEBPA, CREBBP, CRLF2, CSF1R, CSF3R, CTCF, DDX41, DNM2, DNMT3A, DOT1L, EBF1, EED, EP300, EPOR, ERG, ESR1, ETNK1, ETS1, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GATA3, HRAS, IDH1, IDH2, IKZF1, IKZF3, IL7R, JAK1, JAK2, JAK3, KDM6A, KIT, KRAS, LEF1, LYL1, KMT2D, MPL, MSH2, MSH6, MYB, NF1, NOTCH1, NPM1, NRAS, NT5C2, PAX5, PDGFRA, PHF6, PIK3R1, PRPF40B, PTEN, PTPN11, RB1, RELN, RPL10, RETEI1, RUNX1, SETBP1, SETD2, SF1, SF3A1, SF3B1, SH2B3, SRSF2, SUZ12, TAL1, TCF3, TERT, TET2, TINF2, TLX1, TLX3, TP53, U2AF1, U2AF2, UBA2, USH2A, USP7, WHSC1, WT1, ZRSR2
One hundred and six fusion gene partners are analyzed for over 500 fusions and many more novel fusions using anchored multiplex PCR technology followed by NGS. The technology allows detecting novel fusions associated with genes in this panel. Fusions are confirmed by FISH or Real Time PCR when necessary. This panel does not detect fusions not included in this panel. The panel should not be used for detecting residual fusions at present time. Customized Real Time PCR for monitoring residual fusions are available in our laboratory. The fusion partner genes included in this panel are listed below:
ABL1, ABL2, AKT3, ALK, ARHGAP26, AXL, BCL2, BCL6, BCR, BRAF, BRD3, BRD4, CAMTA1, CBFB, CCNB3, CCND1, CIC, CRFL2, CSF1R, DUSP22, EGFR, EPC1, EPOR, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FGR, FOXO1, FUS, GLI1, GLIS2, HMGA2, IL2RB, INSR, JAK2, JAZF1, KMT2A, MALT1, MAML2, MAST1, MAST2, MEAF6, MECOM, MET, MKL1, MKL2, MSMB, MUSK, MTB, NCOA2, NOTCH1, NOTCH2, NRG1, NTRK1, NTRK2, NTRK3, NUMBL, NUP214, NUP98, NUT, PAX5, PDGFB, PDGFRA, PDGFRB, PICALM, PIK3CA, PKN1, PLAG1, PPARG, PRKCA, PRKCB, PTK2B, RAF1, RARA, RBM15, RELA, RET, ROS1, RSPO2, RSPO3, RUNX1, RUNX1T1, SS18, STAT6, TAF15, TAL1, TCF12, TCF3, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TSLP, TYK2, USP6, YWHAE
Copy number variations (CNVs) of these genes are evaluated by analyzing NGS data. These CNVs are confirmed by MLPA, Real Time PCR, or aCGH when necessary. Certain genes or exons may not be evaluated for gross copy number variations, such as genes with no known gross deletion/duplication mutations, or genes or exons with pseudogenes or highly homologous sequences in the genome.
Methodology
Targeted Capture and anchored multiplex PCR (for fusions) followed by Massively Parallel Sequencing. MLPA, Real Time PCR, or aCGH may be used when needed.
Sample & Shipping Information
Submit 3-5 ml bone marrow or leukemic blood sample in an EDTA (purple-top) tube. Deliver to the laboratory immediately or ship at room temperature in an insulated container by overnight courier. Do not heat or freeze.
Other specimen type: Please contact the laboratory to discuss other specimen types that may be acceptable.
Turn Around Time
2 to 3 weeks
CPT Code 81455
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.
Solid Tumors Panel
Test Information
The CHOP Solid Tumor Panel utilizes next-generation sequencing technology to simultaneously analyze a panel of genes known to be associated with a variety of solid tumors including pediatric solid tumors. Most cancers result from accumulation of multiple genomic alterations that lead to dysfunction of cancer-associated genes. These genomic alterations are important diagnostic, prognostic, and therapeutic markers. The CHOP Solid Tumor Panel test can provide important genomic information regarding tumor development and progression, which facilitates more accurate disease diagnosis, risk strati cation, and therapeutic decision.
Two hundred thirty-seven genes known to be associated with cancer predisposition are analyzed using Next Generation Sequence (NGS) technology. All coding exons of the 237 genes and 5 base pairs of 5’ and 3’ flanking intronic sequences are analyzed. Certain known intronic mutations of these genes are also evaluated. Clinically actionable or potentially actionable variants detected by NGS are confirmed by Sanger sequencing or other methodologies when necessary. The genes included in this panel are listed below:
ABL1, ACVR1, AKT1, AKT2, AKT3, ALK,APC, AR, ARAF, ARID1A, ARID1B, ARID2, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXL, B2M, BAP1, BARD1, BCL2, BCL6, BCOR, BCORL1, BLM, BRAF, BRCA1, BCRA2, BRD4, BRIP1, CARD11, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD274, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CHEK1, CHEK2, CIC, CREBBP, CRKL, CRLF2, CSF1R, CTCF, CTNNB1, DAXX, DDR2, DNMT3A, DOT1L, EED, EGFR, EP300, EPHA3, EPHA5, EPHB1, ERBB2, ERBB3, ERBB4, ERG, ESR1, ETV6, EZH2, FAM46C, FANCA, FANCC, FBXW7, FGF19, FGF3, FGF4, FGFR1, FGFR2, FGFR3, FGFR4, FLCN, FLT1, FLT3, FLT4, FOXL2, FOXP1, FUBP1, GATA1, GATA2, GATA3, GNA11, GNAQ, GNAS, GRIN2A, GSK3B, H3F3A, HGF, HIST1H1C, HIST1H3B, HNF1A, HRAS, IDH1, IDH2, IGF1R, IKBKE, IKZF1, IL7R, INPP4B, IRF4, IRS2, JAK1, JAK2, JAK3, JMJD1C, JUN, KDM5A, KDM5C, KDM6A, KDR, KEAP1, KIT, KMT2A, KMT2C, KRAS, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAPK1, MCL1, MDM2, MDM4, MED12, MEF2B, MEN1, MET, MITF, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYB, MYC, MYCN, MYD88, MYOD1, NF1, NF2, NFE2L2, NKX2-1, NOTCH1, NOTCH2, NPM1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PAX5, PBRM1, PDCD1, PDGFRA, PDGFRB, PHOX2B, PIK3CA, PIK3CG, PIK3R1, PIK3R2, PIM1, PPM1D, PPP2R1A, PRDM1, PRKAR1A, PTCH1, PTEN, PTPN11, RAD50, RAD51, RAF1, RARA, RB1, RET, RHOA, RICTOR, RNF43, ROS1, RPTOR, RUNX1, SDHA, SDHB, SDHC, SDHD, SETD2, SF3B1, SMAD2, SMAD4, SMARCA4, SMARCB1, SMO, SOCS1, SOX2, SPEN, SPOP, SRC, STAG2, STK11, SUFU, SUZ12, TERT, TET2, TGFBR2, TNFAIP3, TNFRSF14, TOP1, TP53, TP63, TSC1, TSC2, TSHR, U2AF1, VHL, WHSC1, WT1, AMER1, XPO1
Copy number variations (CNVs) of these genes are evaluated by analyzing NGS data. These CNVs are confirmed by MLPA, Real Time PCR, or Array CGH Analysis (aCGH) when necessary. Certain genes or exons may not be evaluated for gross copy number variations, such as genes with no known gross deletion/duplication mutations, or genes or exons with pseudogenes or highly homologous sequences in the genome.
Methodology
Targeted Capture followed by Massively Parallel Sequencing. MLPA, Real Time PCR, or aCGH may be used when needed.
Sample & Shipping Information
Fresh Tissue: Submit 150 mg (0.5-2.0 cm3) Fresh tissue in transport media. Deliver to the laboratory within 24 hours at room temperature.
Fresh Frozen Tissue: Submit 150 mg (0.5-2.0 cm3) Fresh tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
FFPE tumor slides or block: Submit 10 unstained 10 um FFPE slides containing adequate amounts of tumor to be analyzed or FFPE block containing adequate amounts of tumor to be analyzed. A HE stained slide with areas of tumor marked should be submitted along with FFPE slides. Please include a copy of corresponding surgical pathology report. Sent at ambient temperature (18-25°C/64-77°F). Protect paraffin tissue from excessive heat. Ship in cooled container during summer months. Unacceptable conditions include no tumor in tissue or specimens fixed/processed in alternative fixatives.
Other Specimen type: Please contact the laboratory to discuss other specimen types that may be acceptable.
Turn Around Time
2 to 3 weeks
CPT Code 81455
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.
Hematological Cancer Panel
Test Information
The CHOP Hematological Cancer Panel utilizes next-generation sequencing technology to simultaneously analyze a panel of genes known to be associated with hematological malignancies. Hematological malignancies results from accumulation of multiple genomic alterations that lead to aberrant hematopoietic proliferation and differentiation. These genomic alterations are important diagnostic, prognostic, and therapeutic biologic markers. The CHOP Hematological Cancer Panel test can provide important genomic information regarding tumor development and progression, which facilitates more accurate disease diagnosis, risk stratification, and therapeutic decision.
Ninety-nine genes known to be associated with cancer predisposition are analyzed using Next Generation Sequence (NGS) technology. All coding exons of the 99 genes and 5 base pairs of 5’ and 3’ flanking intronic sequences are analyzed. Certain known intronic mutations of these genes are also evaluated. Clinically actionable or potentially actionable variants detected by NGS are confirmed by Sanger sequencing or other methodologies. The genes included in this panel are listed below:
ABL1, ASXL1, ATRX, BCL11B, BCL6, BCOR, BCORL1, BRAF, CALR, CBL, CCND3, CDC25C, CDKN2A, CDKN2B, CEBPA, CREBBP, CRLF2, CSF1R, CSF3R, CTCF, DDX41, DNM2, DNMT3A, DOT1L, EBF1, EED, EP300, EPOR, ERG, ESR1, ETNK1, ETS1, ETV6, EZH2, FBXW7, FLT3, GATA1, GATA2, GATA3, HRAS, IDH1, IDH2, IKZF1, IKZF3, IL7R, JAK1, JAK2, JAK3, KDM6A, KIT, KRAS, LEF1, LYL1, KMT2D, MPL, MSH2, MSH6, MYB, NF1, NOTCH1, NPM1, NRAS, NT5C2, PAX5, PDGFRA, PHF6, PIK3R1, PRPF40B, PTEN, PTPN11, RB1, RELN, RPL10, RETEI1, RUNX1, SETBP1, SETD2, SF1, SF3A1, SF3B1, SH2B3, SRSF2, SUZ12, TAL1, TCF3, TERT, TET2, TINF2, TLX1, TLX3, TP53, U2AF1, U2AF2, UBA2, USH2A, USP7, WHSC1, WT1, ZRSR2
Copy number variations (CNVs) of these genes are evaluated by analyzing NGS data. These CNVs are confirmed by MLPA, Real Time PCR, or aCGH when necessary. Certain genes or exons may not be evaluated for gross copy number variations, such as genes with no known gross deletion/duplication mutations, or genes or exons with pseudogenes or highly homologous sequences in the genome.
Methodology
Targeted Capture followed by Massively Parallel Sequencing. MLPA, Real Time PCR, or aCGH may be used when needed.
Sample & Shipping Information
Submit 3-5 ml bone marrow or leukemic blood sample in an EDTA (purple-top) tube. Deliver to the laboratory immediately or ship at room temperature in an insulated container by overnight courier. Do not heat or freeze.
Other specimen type: Please contact the laboratory to discuss other specimen types that may be acceptable.
Turn Around Time
2 to 3 weeks
CPT Code 81455
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.
Fusion Gene Panel
Test Information
The CHOP Cancer Fusion Panel utilizes anchored multiplex PCR and next-generation sequencing (NGS) technologies to simultaneously analyze a panel of genes known to be involved in over 500 cancer associated fusions and many more novel fusions.
The CHOP Cancer Fusion Panel test can provide important fusions information which facilitates disease diagnosis, risk stratification, and therapeutic decision. One hundred and six fusion gene partners are analyzed for over 500 fusions and many more novel fusions using anchored multiplex PCR technology followed by NGS. The technology allows detecting novel fusions associated with genes in this panel. Fusions are confirmed by FISH or Real Time PCR when necessary. This test does not detect fusions with no fusion partner included in this panel. The panel should not be used for detecting residual fusions at present time. Customized Real Time PCR assays for monitoring residual fusions are available in our laboratory. The fusion partner genes included in this panel are listed below:
ABL1, ABL2, AKT3, ALK, ARHGAP26, AXL, BCL2, BCL6, BCR, BRAF, BRD3, BRD4, CAMTA1, CBFB, CCNB3, CCND1, CIC, CRFL2, CSF1R, DUSP22, EGFR, EPC1, EPOR, ERG, ESR1, ESRRA, ETV1, ETV4, ETV5, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FGR, FOXO1, FUS, GLI1, GLIS2, HMGA2, IL2RB, INSR, JAK2, JAZF1, KMT2A, MALT1, MAML2, MAST1, MAST2, MEAF6, MECOM, MET, MKL1, MKL2, MSMB, MUSK, MTB, NCOA2, NOTCH1, NOTCH2, NRG1, NTRK1, NTRK2, NTRK3, NUMBL, NUP214, NUP98, NUT, PAX5, PDGFB, PDGFRA, PDGFRB, PICALM, PIK3CA, PKN1, PLAG1, PPARG, PRKCA, PRKCB, PTK2B, RAF1, RARA, RBM15, RELA, RET, ROS1, RSPO2, RSPO3, RUNX1, RUNX1T1, SS18, STAT6, TAF15, TAL1, TCF12, TCF3, TERT, TFE3, TFEB, TFG, THADA, TMPRSS2, TSLP, TYK2, USP6, YWHAE
Methodology
Anchored multiplex PCR followed by Massively Parallel Sequencing. Real Time PCR may be used when needed.
Sample & Shipping Information
Bone marrow and leukemic blood samples: Submit 3-5 ml bone marrow or leukemic blood sample in an EDTA (purple-top) tube. Deliver to the laboratory immediately or ship at room temperature in an insulated container by overnight courier. Do not heat or freeze.
Fresh Tissue : Submit 150 mg (0.5-2.0 cm3) Fresh tissue in transport media. Deliver to the laboratory within 24 hours at room temperature.
Fresh Frozen Tissue : Submit 150 mg (0.5-2.0 cm3) Fresh tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
FFPE tumor slides or block : Submit 10 unstained 10 um FFPE slides containing adequate amounts of tumor to be analyzed or FFPE block containing adequate amounts of tumor to be analyzed. A HE stained slide with areas of tumor marked should be submitted along with FFPE slides. Please include a copy of corresponding surgical pathology report. Sent at ambient temperature (18-25°C/64-77°F). Protect paraffin tissue from excessive heat. Ship in cooled container during summer months. Unacceptable conditions include no tumor in tissue or specimens fixed/processed in alternative fixatives.
Other Specimen type: Please contact the laboratory to discuss other specimen types that may be acceptable.
Turn Around Time
2 to 3 weeks
CPT Code 81455
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.
Comprehensive Hereditary Cancer Gene Panel
Test Information
The CHOP Hereditary Cancer Panel utilizes next-generation sequencing technology to simultaneously analyze a panel of genes known to be associated with increased risks for a wide range of cancers. This test should be used for patients whose medical and family histories strongly suggest an underlying genetic etiology of cancer and for at risk family members. One hundred twenty-eight genes known to be associated with cancer predisposition are analyzed using Next Generation Sequence (NGS) technology. The genes included in this panel are listed below:
ABCB11, ALK, APC, ARID5B, ATM, AXIN2, BAP1, BARD1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, BUB1B, CBL, CDC73, CDH1, CDK4, CDKN1C, CDKN1B, CDKN2A, CEBPA, CEBPE, CHEK2, COL7A1, CYLD, DDB2, DDX41, DICER1, DIS3L2, DKC1, DOCK8, EGFR, ELANE, EPCAM, ERCC2, ERCC3, ERCC4, ERCC5, ETV6, EXT1, EXT2, FAH, FANCA, FANCC, FANCG, FH, FLCN, G6PC3, GATA2, GBA, GJB2, GPC3, HABP2, HAX1, HFE, HMBS, HRAS, IKZF1, ITK, KIT, MAX, MEN1, MET, MLH1, MPL, MSH2, MSH6, MTAP, MUTYH, NBN, NF1, NF2, PALB2, PAX5, PDGFRA, PHOX2B, PMS2, POLD1, POLE, POLH, PRKAR1A, PRSS1, PTCH1, PTEN, PTPN11, RAD51, RAD51C, RAD51D, RB1, RECQL4, RET, RHBDF2, RMRP, RUNX1, SBDS, SDHA, SDHAF2, SDHB, SDHC, SDHD, SERPINA1, SH2D1A, SLC25A13, SMAD4, SMARCA4, SMARCB1, SMARCE1, SOS1, SRY, STAT3, STK11, SUFU, TERT, TGFBR1, TMEM127, FAS, TP53, TRIM37, TSC1, TSC2, UROD, VHL, WAS, WRN, WT1, XPA, XPC
All coding exons of the 128 genes and 20 base pairs of 5’ and 3’ flanking intronic sequences are analyzed. Certain known intronic mutations of these genes are also evaluated. Pathogenic/likely pathogenic variants detected by NGS are confirmed by Sanger sequencing.
The panel also evaluates gross copy number variations of these genes by analyzing NGS data, and by MLPA, Real Time PCR, or aCGH when necessary. Certain genes or exons may not be evaluated for gross copy number variations, such as genes with no known gross deletion/duplication mutations, or genes or exons with pseudogenes or highly homologous sequences in the genome.
Methodology
Targeted Capture followed by Massively Parallel Sequencing. Multiplex Ligation-dependent Probe Amplification (MLPA), Real Time PCR, or Array CGH Analysis (aCGH) when needed.
Sample & Shipping Information
Submit 3-5 ml blood sample in an EDTA (purple-top) tube. Deliver to the laboratory immediately or ship at room temperature in an insulated container by overnight courier. Do not heat or freeze.
Turn Around Time
8 weeks (shorter for smaller panels).
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.
Bone Marrow Failure Panel
Research
Learn more about the research being conducted at the Comprehensive Bone Marrow Failure Center at Children's Hospital of Philadelphia.
Test Information
The Bone Marrow Failure Panel is a next generation sequencing panel designed to identify underlying genetic variants associated with predisposition to bone marrow failure. Bone marrow failure disorders are characterized by inadequate production of one or more blood cell lineages by bone marrow, and results from either acquired immunologic, infectious or toxic insults, or from inherited mutations in genes (at least 90 at present time) associated with bone marrow failure. Identification of an underlying genetic cause is critical in establishing an inherited versus acquired etiology for bone marrow failure, which in turn has profound impacts on patient management and genetic counseling for families of affected patients.
Disorders associated with bone marrow failure can be inherited in an autosomal recessive, autosomal dominant, or x-linked manner. The Bone Marrow Failure Panel includes the following 90 genes:
ABCB7, ACD, AK2, ALAS2, ANKRD26, ATM, ATR, BLM, BRCA1, BRCA2, C15ORF41, CBL, CDAN1, CSF3R, CTC1, CXCR4, DDX11, DKC1, ELANE, ERCC4, ESCO2, ETV6, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ, FANCL, FANCM, G6PC3, GATA1, GATA2, GFI1, GLRX5, HAX1, KIF23, KLF1, LAMTOR2, LYST, MPL, NBN, NHP2, NOP10, PALB2, PARN, RAB27A, RAC2, RAD51, RAD51C, RBM8A, RMRP, RPL11, RPL15, RPL19, RPL26, RPL27, RPL35A, RPL5, RPS10, RPS17, RPS19, RPS24, RPS26, RPS27, RPS29, RPS7, RTEL1, RUNX1, SAMD9, SAMDL9, SBDS, SEC23B, SLC25A38, SLC37A4, SLX4, SRP72, TAZ, TERC, TERT, TINF2, USB1, VPS13B, VPS45, WAS, WIPF1, WRAP53.
Methodology
Ninety genes known to be associated with red blood cell disorders are analyzed using Next Generation Sequence (NGS) technology. All coding exons of the 90 genes and 20 base pairs of 5' and 3' flanking intronic sequences are analyzed. All known intronic mutations of these genes are also evaluated. Pathogenic/likely pathogenic variants detected by NGS are confirmed by Sanger sequencing.
The panel also evaluates gross copy number variations of these genes by analyzing NGS data. Pathogenic/likely pathogenic CNVs detected by NGS are confirmed by MLPA and/or ddPCR. Certain genes or exons may not be evaluated for gross copy number variations, such as genes with no known gross deletion/duplication mutations, or genes or exons with pseudogenes or highly homologous sequences in the genome.
Sample & Shipping Information
Storage / Transport Temperature: Room Temp
Volume Required: 3-5ml
Minimum Required: 1.5ml
Phlebotomy Draw: Yes
Turn Around Time
6-8 weeks
CPT Codes
81209, 81211, 81242, 81402, 81405, 81406 (x4), 81408 (x2), 81479
For more information contact Jason Roberts, Outreach Manager, Division of Pathology and Laboratory Medicine, at 215-590-0637 or robertsj1@email.chop.edu.