Rapidly bridge the gap between outsourcing and insourcing next generation sequencing testing with a comprehensive, turnkey menu of CLIA/CAP validated assays for cancer and germline testing.
Click below to learn more about each service.
| Test Components | Next generation sequencing of all coding regions of ABL1, AFF3, AKT1, AKT2, AKT3, ALK*, APC, AR, ATM, ATRX, BAP1, BCL2L1, BRAF, BRCA1, BRCA2, BRIP1, CCND1, CDH1, CDK12, CDK6, CDKN1A, CDKN1B, CDKN2A, CHEK2, CREBBP, CSF1R, CTNNB1, DAXX, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ERCC2, ESR1, ESR2, FANCA, FAT1, FBXW7, FGFR1, FGFR2*, FGFR3*, FGFR4, FLT1, FLT3, FLT4, FOXL2, GATA4, GNAS, H3F3A, HIST1H3B, HRAS, IDH1, IDH2, JAK1, JAK2, KDM5C, KDR, KEAP1, KIT, KLF4, KMT2C, KMT2D, KRAS, MAP2K1, MAP2K2, MAP3K3, MCL1, MED12, MET, MLH1, MN1, MTOR, MYB, MYBL1, MYC, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NRAS, NTRK1*, NTRK2, PALB2, PBRM1, PDGFRA, PDGFRB, PIK3C2B, PIK3CA, PIK3R1, PIK3R2, POLD1, POLE, PPARG, PPP2R1A, PTEN, RAD54B, RAF1, RB1, RET*, RIT1,ROS1*, RXRA, SETD2, SHOC2, SMAD2, SMAD4, SMARCA4, SMARCB1, SOS1, SPRED1, STK11, TEK, TERT, TGFBR2, TP53, TRAF7, TSC1, TSC2, VHL and WT1 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of ABL1, ASXL1, ATM, BCOR, BIRC3, BRAF, CALR, CBL, CEBPA, CREBBP, CSF1R, CSF3R, DNMT3A, EP300, ETV6, EZH2, FBXW7, FGFR4, FLT3, GATA1, GATA2, GATA3, IDH1, IDH2, IL7R, JAK2, JAK3, KDM6A, KIT, KRAS, KMT2A*, MPL, NF1, NOTCH1, NOTCH2, NPM1, NRAS, NSD1, PAX5, PDGFRA, PDGFRB, PTPN11, RUNX1, SETB1, SF3B1, SRSF2, STAG2, TERT, TET1, TET2, TP53, TSLP, U2AF1 and ZRSR2 to detect single nucleotide variants and small insertions and deletions.*selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of AKT1, ATM, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDK6, CDKN2A, CHEK2, EGFR, ERBB2, ERBB3, ERBB4, ESR1, ESR2, FANCA, FBXW7, FGFR1, FGFR2*, GATA3, HRAS, IDH1, IDH2, KDR, KIT, KRAS, MAP2K1, MAP2K2, MET, PALB2, PIK3CA, PIK3R1, PTEN, RAC1, RAD54B, RB1, RET*, RUNX1, STK11 and TP53 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions ofAKT1, ATRX, BRAF, CDKN2A, CIC, CTNNB1, DAXX, DNMT3A, EGFR, ERBB2, FGFR1, FGFR2*, FUBP1, H3F3A, HIST1H3B, IDH1, IDH2, KLF4, KRAS, MED12, MET, MN1, MTOR, MYB, MYBL1, MYC, NF1, NF2, NOTCH1, NTRK1*, NTRK2, PDGFRA, PIK3CA, PIK3R1, PTCH1, PTEN, RB1, SETD2, SHH, SMARCA4, SMARCB1, SMO, SUFU, TERT, TP53, TRAF7, WNT1 and WT1 to detect single nucleotide variants and small insertions and deletions. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of AKT1, AKT2, AKT3, AR, ATM, BAP1, BRAF, BRCA1, BRCA2, CDKN1A, CDKN2A, CREBBP, EGFR, ERBB2, ERBB3, ERCC2, FBXW7, FGFR2*, FGFR3*, HRAS, KDM5C, KDM6A, KMT2C, KMT2D, MED12, MET, MLH1, MTOR, NF1, NRAS, PBRM1, PIK3CA, PIK3R1, PPARG, PTCH1, PTEN, RXRA, SETD2, STAG2, TERT, TP53, TSC1, TSC2 and VHL to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of ABL1, AKT1, AKT2, AKT3, APC, ATM, BCOR, BRAF, BRCA1, BRCA2, CCND1, CDK12, CDKN2A, CTNNB1, EGFR, EP300, ERBB2, ERBB4, FAT1, FBXW7, FGFR1, FGFR2*, FGFR3*, FOXL2, HRAS, JAK3, KDR, KIT, KRAS, MAP2K1, MAP2K2, MED12, MET, MLH1, MTOR, NF1, NRAS, PIK3CA, PIK3R1, PIK3R2, POLD1, POLE, PPP2R1A, PTEN, RB1, SMAD4, SMO, STK11, TP53 and VHL to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of AFF3, AKT1, AKT2, AKT3, APC, ASXL1, ATM, BCL2L1, BRCA1, BRCA2, CCND1, CDKN2A, EGFR, EP300, ERBB2, FAT1, FBXW7, GATA4, HRAS, KDM6A, KMT2C, KMT2D, KRAS, MCL1, MTOR, NF1, NFE2L2, NOTCH1, NOTCH2, NRAS, NSD1, PIK3C2B, PIK3CA, PIK3R1, PTEN, RAC1, RB1, RHOA, SMAD4, TGFBR2 and TP53 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of AKT1, ALK*, BAP1, BRAF, CCND1, CDK4, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2*, FGFR3*, GNA11, GNAQ, HRAS, KIT, KMT2C, KMT2D, KRAS, MAP2K1, MAP2K2, MED12, MET, MTOR, NF1, NRAS, PDGFRA, PDGFRB, PIK3CA, PTEN, RAC1, RB1, RET*, ROS1*, TERT and TP53 to detect single nucleotide variants and small insertions and deletions.*selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Speciment Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
| Test Components | Next generation sequencing of all coding regions of AKT1, AKT2, AKT3, ALK*, ATM, BAP1, BRAF, CDKN1B, CDKN2A, DDR2, ERBB2, ERBB3, FANCA, FGFR1, FLT1, FLT4, HRAS, KDR, KEAP1, KMT2C, KMT2D, KRAS, MED12, MET, NF1, NRAS, NTRK1*, RB1, RET*, RIT1, ROS1*, SMARCA4, STK11, TP53, TSC1 and TSC2 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements. |
| Test Details | Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 3 weeks from receipt of specimen |
| Specimen Requirements | Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required. |
| Minimum Sample Volume | 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood |
| Storage/Transport Conditions | FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE). |
| Unacceptable Conditions | Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be <10% tumor cells content in the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous |
|
Gene |
Analysis |
Region |
RefSeq |
|
ABL1 |
Hot Spots |
Codons 244-493 |
NM_005157 |
|
ASXL1 |
Hot Spots |
Codons 630-643, 1102-1107 |
NM_015338 |
|
ATM |
Whole Gene |
All protein coding regions plus splice sites |
NM_000051 |
|
ATRX |
Partial Gene |
Exons 8-31 |
NM_000489 |
|
BCORL1 |
Whole Gene |
All protein coding regions plus splice sites |
NM_021946 |
|
BRAF |
Hot Spots |
Codons 464-472, 581-602 |
NM_004333 |
|
CALR |
Partial Gene |
Exon 9 |
NM_004343 |
|
CBL |
Hot Spots |
Codons 371-384, 416-420 |
NM_005188 |
|
CCND1 |
Partial Gene |
Exon 1, 2 |
NM_053056 |
|
CCND3 |
Hot Spots |
Codons 260-289 |
NM_001760 |
|
CDKN2A |
Whole Gene |
All protein coding regions plus splice sites |
NM_000077 |
|
CEBPA |
Whole Gene |
All protein coding regions plus splice sites |
NM_004364 |
|
CRLF2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_022148 |
|
CSF3R |
Partial Gene |
Exons 14-17 |
NM_156039 |
|
CTNNB1 |
Hot Spots |
Codons 23-66 |
NM_001904 |
|
CUX1 |
Whole Gene |
All protein coding regions plus splice sites |
NM_001913 |
|
DDX3X |
Hot Spots |
Codons 330-341, 410-411 |
NM_001356 |
|
DNMT3A |
Whole Gene |
All protein coding regions plus splice sites |
NM_022552 |
|
ETV6 |
Whole Gene |
All protein coding regions plus splice sites |
NM_001987 |
|
EZH2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_152998 |
|
FGFR3 |
Hot Spots |
Codons 248-250, 370-393, 650-652, 697 |
NM_000142 |
|
FLT3 |
Hot Spots |
Codons 569-613 (ITD), 835 |
NM_004119 |
|
GATA1 |
Hot Spots |
Codons 1-30 |
NM_002049 |
|
GATA2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_032638 |
|
GATA3 |
Hot Spots |
Codons 309-445 |
NM_001002295 |
|
GNAS |
Partial Gene |
Exons 8,9 |
NM_000516 |
|
HRAS |
Hot Spots |
Codons 12-13, 61, 117 |
NM_005343 |
|
IDH1 |
Hot Spots |
Codon 132 |
NM_005896 |
|
IDH2 |
Hot Spots |
Codons 140, 172 |
NM_002168 |
|
IKZF1 |
Whole Gene |
All protein coding regions plus splice sites |
NM_006060 |
|
IL7R |
Hot Spots |
Codons 237-245 |
NM_002185 |
|
JAK2 |
Partial Gene |
Exons 12-14 |
NM_004972 |
|
KDM6A |
Whole Gene |
All protein coding regions plus splice sites |
NM_021140 |
|
KIT |
Hot Spots |
Exons 9, 14, codons 416-422, 541-546, 550-592, 642, 796-850 |
NM_000222 |
|
KRAS |
Hot Spots |
Codons 12-13, 61, 117, 146 |
NM_004985 |
|
MAP2K1 |
Hot Spots |
Codons 56-67, 121-124 |
NM_002755 |
|
MPL |
Hot Spots |
Codons 490-522 |
NM_005373 |
|
NF1 |
Whole Gene |
All protein coding regions plus splice sites |
NM_000267 |
|
NF2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_000268 |
|
NOTCH1 |
Hot Spots |
Codons 1574-1578, 1585-1607, 1674-1680, 2438-2444, 2459-2467, 2492-2503, 2512-2523 |
NM_017617 |
|
NPM1 |
Hot Spots |
Codons 287-292 |
NM_002520 |
|
NRAS |
Hot Spots |
Codons 12-13, 61, 117, 146 |
NM_002524 |
|
PHF6 |
Whole Gene |
All protein coding regions plus splice sites |
NM_032458 |
|
PRDM1 |
Hot Spots |
Codons 59-62 |
NM_001198 |
|
PTEN |
Whole Gene |
All protein coding regions plus splice sites |
NM_000314 |
|
PTPN11 |
Hot Spots |
Codons 60-76, 502-503 |
NM_002834 |
|
RAD21 |
Whole Gene |
All protein coding regions plus splice sites |
NM_006265 |
|
RUNX1 |
Whole Gene |
All protein coding regions plus splice sites |
NM_001754 |
|
SETBP1 |
Hot Spots |
Codons 852-892 |
NM_015559 |
|
SETD2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_014159 |
|
SF3A1 |
Hot Spots |
Codon 478 |
NM_005877 |
|
SF3B1 |
Partial Gene |
Exons 13-16 |
NM_012433 |
|
SH2B3 |
Partial Gene |
Exons 1-3 |
NM_005475 |
|
SMC1A |
Whole Gene |
All protein coding regions plus splice sites |
NM_006306 |
|
SMC3 |
Whole Gene |
All protein coding regions plus splice sites |
NM_005445 |
|
SRSF2 |
Hot Spots |
Codons 95-107 |
NM_003016 |
|
STAG2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_006603 |
|
STK11 |
Hot Spots |
Codons 36-37, 60-66, 170-171, 194-199, 281-282, 354 |
NM_000455 |
|
SUZ12 |
Whole Gene |
All protein coding regions plus splice sites |
NM_015355 |
|
TET2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_017628 |
|
TP53 |
Whole Gene |
All protein coding regions plus splice sites |
NM_000546 |
|
U2AF1 |
Hot Spots |
Codons 34-35, 156-160 |
NM_006758 |
|
U2AF2 |
Hot Spots |
Codons 143, 190 |
NM_007279 |
|
WT1 |
Hot Spots |
Codons 298-314, 390-397 |
NM_024426 |
|
ZRSR2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_005089 |
|
Gene |
Analysis |
Region |
RefSeq |
|
AKT1 |
Hot Spots |
Codons 17, 32-52 |
NM_005163 |
|
ALK |
Hot Spots |
Codons 542, 1152-1278 |
NM_004304 |
|
ATM |
Whole Gene |
All protein coding regions plus splice sites |
NM_000051 |
|
B2M |
Hot Spots |
Codons 1-5 |
NM_004048 |
|
BCL2 |
Hot Spots |
Codons 7-20, 57-60, 129-135 |
NM_000633 |
|
BCL6 |
Hot Spots |
Codons 587-615 |
NM_001706 |
|
BCOR |
Whole Gene |
All protein coding regions plus splice sites |
NM_017745 |
|
BIRC3 |
Hot Spots |
Codon 123 |
NM_001165 |
|
BRAF |
Hot Spots |
Codons 464-472, 581-602 |
NM_004333 |
|
BTK |
Hot Spots |
Codons 1-47, 175-196, 281-298, 327-367, 426-450, 463-522 |
NM_000061 |
|
CALR |
Partial Gene |
Exon 9 |
NM_004343 |
|
CARD11 |
Hot Spots |
Codons 230-251 |
NM_032415 |
|
CCND3 |
Hot Spots |
Codons 260-289 |
NM_001760 |
|
CD79A |
Hot Spots |
Codons 167-214 |
NM_001783 |
|
CD79b |
Hot Spots |
Codon 196 |
NM_000626 |
|
CDKN2A |
Whole Gene |
All protein coding regions plus splice sites |
NM_000077 |
|
CREBBP |
Whole Gene |
All protein coding regions plus splice sites |
NM_004380 |
|
CRLF2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_022148 |
|
CTNNB1 |
Hot Spots |
Codons 23-66 |
NM_001904 |
|
DDX3X |
Hot Spots |
Codons 330-341, 410-411 |
NM_001356 |
|
DNMT3A |
Whole Gene |
All protein coding regions plus splice sites |
NM_022552 |
|
EP300 |
Hot Spots |
Codons 1625-1639 |
NM_001429 |
|
EZH2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_152998 |
|
FBXW7 |
Partial Gene |
Exons 7-11 (Codons 297-332, 450-468, 478-525, 576-618) |
NM_018315 |
|
ID3 |
Hot Spots |
Codon 56 |
NM_002167 |
|
IDH1 |
Hot Spots |
Codon 132 |
NM_005896 |
|
IDH2 |
Hot Spots |
Codons 140, 172 |
NM_002168 |
|
IL7R |
Hot Spots |
Codons 237-245 |
NM_002185 |
|
JAK1 |
Hot Spots |
Codons 652-658 |
NM_002227 |
|
JAK2 |
Partial Gene |
Exons 12-14 |
NM_004972 |
|
JAK3 |
Hot Spots |
Codons 501-511, 572-576, 657 |
NM_000215 |
|
KMT2A |
Partial Gene |
Exons 4-8, codons 2462, 3440 (exon 27) |
NM_005933 |
|
KMT2D |
Whole Gene |
All protein coding regions plus splice sites |
NM_003482 |
|
KRAS |
Hot Spots |
Codons 12-13, 61, 117, 146 |
NM_004985 |
|
MAP2K1 |
Hot Spots |
Codons 56-67, 121-124 |
NM_002755 |
|
MEF2B |
Hot Spots |
Codons 77-81 |
NM_005919 |
|
MPL |
Hot Spots |
Codons 490-522 |
NM_005373 |
|
MYD88 |
Partial Gene |
Exons 3, 4, 5 (Codons 219-220, 265) |
NM_002468 |
|
NOTCH1 |
Hot Spots |
Codons 1574-1578, 1585-1607, 1674-1680, 2438-2444, 2459-2467, 2492-2503, 2512-2523 |
NM_017617 |
|
NOTCH2 |
Hot Spots |
Codon 2400 |
NM_024408 |
|
NPM1 |
Hot Spots |
Codons 287-292 |
NM_002520 |
|
NRAS |
Hot Spots |
Codons 12-13, 61, 117, 146 |
NM_002524 |
|
PAX5 |
Hot Spots |
Codons 75-80 |
NM_016734 |
|
PHF6 |
Whole Gene |
All protein coding regions plus splice sites |
NM_032458 |
|
PIK3CA |
Hot Spots |
Codons 88, 539-549, 1020-1025, 1043-1049 |
NM_006218 |
|
PIM1 |
Hot Spots |
Codons 1-16, 28-56, 68-171, 210-251 |
NM_002648 |
|
PIM2 |
Hot Spots |
Codons 199-232, 270-312 |
NM_006875 |
|
PLCG2 |
Hot Spots |
Codons 161-188, 256-322, 330-355, 496-519, 526-569, 646-676, 686-724, 746-769, 864-908, 961-1005 |
NM_002661 |
|
PTPN11 |
Hot Spots |
Codons 60-76, 502-503 |
NM_002834 |
|
RHOA |
Partial Gene |
Exon 1 |
NM_001664 |
|
RUNX1 |
Whole Gene |
All protein coding regions plus splice sites |
NM_001754 |
|
SF3B1 |
Partial Gene |
Exons 13-16 |
NM_012433 |
|
STAT3 |
Hot Spots |
Codons 640-661 |
NM_139276 |
|
STAT5A |
Whole Gene |
All protein coding regions plus splice sites |
NM_003152 |
|
STK11 |
Hot Spots |
Codons 36-37, 60-66, 170-171, 194-199, 281-282, 354 |
NM_000455 |
|
SYK |
Hot Spots |
Codons 67-116, 306-372, 395-407, 426-463, 534-574 |
NM_003177 |
|
TET2 |
Whole Gene |
All protein coding regions plus splice sites |
NM_017628 |
|
TNFAIP3 |
Whole Gene |
All protein coding regions plus splice sites |
NM_006290 |
|
TP53 |
Whole Gene |
All protein coding regions plus splice sites |
NM_000546 |
|
TRAF3 |
Hot Spots |
Codon 118 |
NM_145725 |
|
XPO1 |
Hot Spots |
Codon 571 |
NM_003400 |
AIP, ALK, APC, ATM, BAP1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, BUB1B, CDC73, CDH1, CDK4, CDKN1C, CDKN2A, CEBPA, CEP57, CHEK2, CYLD, DDB2, DICER1, DIS3L2, EGFR, EPCAM, ERCC2, ERCC3, ERCC4, ERCC5, EXT1, EXT2, EZH2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FH, FLCN, GATA2, GPC3, HNF1A, HRAS, KIT, MAX, MEN1, MET, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, NF2, NSD1, PALB2, PHOX2B, PMS1, PMS2, PRF1, PRKAR1A, PTCH1, PTEN, RAD51C, RAD51D, RB1, RECQL4, RET, RHBDF2, RUNX1, SBDS, SDHAF2, SDHB, SDHC, SDHD, SLX4, SMAD4, SMARCB1, STK11, SUFU, TMEM127, TP53, TSC1, TSC2, VHL, WRN, WT1, XPA, XPC
ABCC9, ACTC1, ACTN2, ALMS1, ALPK3, ANKRD1, BAG3, BRAF, CAV3, CHRM2, CRYAB, CSRP3, DES, DMD, DOLK, DSC2, DSG2, DSP, DTNA, EMD, FHL1, FKRP, FKTN, GATAD1, GLA, HCN4, HRAS, ILK, JPH2, JUP, KRAS, LAMA4, LAMP2, LDB3, LMNA, MAP2K1, MAP2K2, MIB1, MTND1, MTND5, MTND6, MTTD, MTTG, MTTH, MTTI, MTTK, MTTL1, MTTL2, MTTM, MTTQ, MTTS1, MTTS2, MURC, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, MYPN, NEBL, NEXN, NKX2-5, NRAS, PDLIM3, PKP2, PLN, PRDM16, PRKAG2, PTPN11, RAF1, RBM20, RIT1, RYR2, SCN5A, SGCD, SOS1, TAZ, TCAP, TGFB3, TMEM43, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR, TXNRD2, VCL
The following additional germline tests are available upon request:
Above is a graphic of the next generation sequencing testing workflow. The CAP Distributive Model of Next Generation Sequencing Testing enables any CLIA/CAP lab to outsource individual components to one or more additional CLIA/CAP labs.
Begin insourcing genomic testing immediately without the upfront validation expenditures and while capital budgets are still being approved.
Develop core competencies and stronger collaboration with your clinical providers to better evaluate ordering patterns and learn which assays have the highest utility.
Access all raw and processed genomic data in discrete formats to begin building your repository of diagnostic validation samples and to facilitate subsequent serial testing for your patients.
A practiced based guide.
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A rapid, economical approach to building your clinical next generation sequencing testing program.
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"I knew that with the resources we had, there was no way to create something that would rival a system like the CGW. As we've set up reflex testing in various cancer types, we have been well supported to scale the massive undertaking..."
- Nikoletta Sidiropoulos, MD - Medical Director, University of Vermont Medical Center
“There's going to be a bottleneck in the professional component as well sometimes. PierianDx allowed us to widen that bottleneck and to have more uniformity of reporting.”
- Eric Loo, MD - Asst. Professor, Pathology and Lab Medicine, Dartmouth-Hitchcock
“We chose PierianDx because their technology combined with expert scientific and clinical services will help accelerate TriCore’s ability to expand our NGS test offerings and provide enhanced clinically actionable information.”
- Eric Carbonneau - Director Core Laboratory Operations, TriCore Reference Laboratories
“A new partnership with PierianDx expands our reporting to include current clinical trials and up-to- the-minute treatment options, all linked to NorthShore’s Electronic Medical Record.”
- NorthShore University HealthSystem Kellogg Cancer Center 2017 Annual Report
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