| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Sequencing Tests
Cancer
Solid Tumor Gene Set
Hematopoietic Disorders Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Breast Tumor Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
CNS Tumors Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Genitourinary Tumor Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Gynecologic Tumor Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Head & Neck Tumor Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Melanoma Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81445 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Thoracic Tumor Gene Set
| Requisition | Cancer Sequencing Requisition |
| 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 by GPS 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% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81455 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Somatic and Related Disorders
Somatic Overgrowth Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of AKT1, AKT2, AKT3, GNA11, GNAQ, IDH1, IDH2, MAP2K1, MAP3K3, MTOR, PIK3CA, PIK3R2, PTEN, RASA1, SMO, TEK, TSC1 and TSC2. |
| Test Details | Extraction of 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 segmental overgrowth and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | **Primary specimen required: tissue from the affected area. Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab. Secondary specimen for comparative study: peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
PIK3CA-Related Overgrowth Gene Set
| Requisition | GPS SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of PIK3CA. |
| Test Details | Extraction of 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 segmental overgrowth and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | **Primary specimen required: tissue from the affected area. Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab. Secondary specimen for comparative study: peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81406 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
McCune Albright Gene Set
| Requisition | GPS SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of GNAS. |
| Test Details | Extraction of 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 McCune Albright and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | Formalin fixed paraffin embedded affected tissue; fresh affected tisse in transport or tissue culture media; peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81406 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Nevus Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of FGFR3, GNA11, GNAQ, HRAS, KRAS, MAP3K3, NRAS, PIK3CA and TEK. |
| Test Details | Extraction of 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 segmental overgrowth and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | **Primary specimen required: tissue from the affected area. Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab. Secondary specimen for comparative study: peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Curry-Jones Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of SMO. |
| Test Details | Extraction of 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 Curry-Jones Syndrome, segmental overgrowth, and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | **Primary specimen required: tissue from the affected area. Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab. Secondary specimen for comparative study: peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81406 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Maffucci Syndrome Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of IDH1 and IDH2. |
| Test Details | Extraction of 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 Maffucci Syndrome, Ollier Disease and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | **Primary specimen required: tissue from the affected area. Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab. Secondary specimen for comparative study: peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81406 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Rasopathies Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions ofBRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NF1, NRAS, PTPN11, RAF1, RIT1, SHOC2, SOS1 and SPRED1. |
| Test Details | Extraction of 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 Rasopathies and other potentially pathogenic non-synonymous variants are reported with interpretations. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 6-8 weeks from receipt of specimen |
| Specimen Requirements | **Primary specimen required: tissue from the affected area. Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab. Secondary specimen for comparative study: peripheral blood. |
| Sample Collection | Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. |
| Mininum Sample Volume | |
| 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: 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) |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Cardiac Disease
CardioGene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ABCC9, ACTC1, ACTN2, AKAP9, ANK2, ANKRD1, BAG3, BRAF, CACNA1C, CACNB2, CALM1, CASQ2, CAV3, CSRP3, CTF1, DES, DSC2, DSG2, DSP, DTNA, EMD, FHL1, FHL2, GATAD1, GLA, GPD1L, HCN4, HRAS, JUP, KCND3, KCNE1, KCNE2, KCNE3, KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, KRAS, LAMP2, LDB3, LMNA, MAP2K1, MAP2K2, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, NEXN, NRAS, PKP2, PLN, PRKAG2, PTPN11, RAF1, RBM20, RIT1, RYR2, SCN1B, SCN3B, SCN4B, SCN5A, SGCD, SHOC2, SNTA1, SOS1, TAZ, TCAP, TMEM43, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR and VCL. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Arrhythmia Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of AKAP9, ANK2, CACNA1C, CACNB2, CALM1, CASQ2, CAV3, GPD1L, HCN4, KCND3, KCNE1, KCNE2, KCNE3, KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, RYR2, SCN1B, SCN3B, SCN4B, SCN5A and SNTA1. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Brugada Syndrome Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of CACNA1C, CACNB2, GPD1L, HCN4, KCND3, KCNE3, KCNJ8, SCN1B, SCN3B and SCN5A. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Catecholaminergic polymorphic ventricular tachycardia (CPVT) Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ANK2, CALM1, CASQ2, KCNJ2 and RYR2. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Long QT Syndrome Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of AKAP9, ANK2, CACNA1C, CAV3, KCNE1, KCNE2, KCNH2, KCNJ2, KCNJ5, KCNQ1, SCN4B, SCN5A and SNTA1. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81280 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Short QT Syndrome Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of CACNA1C, CACNB2, KCNH2, KCNJ2 and KCNQ1. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Cardiomyopathy Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ABCC9, ACTC1, ACTN2, ANKRD1, BAG3, BRAF, CASQ2, CSRP3, CTF1, DES, DSC2, DSG2, DSP, DTNA, EMD, FHL1, FHL2, GATAD1, GLA, HRAS, JUP, KRAS, LAMP2, LDB3, LMNA, MAP2K1, MAP2K2, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, NEXN, NRAS, PKP2, PLN, PRKAG2, PTPN11, RAF1, RBM20, RIT1, RYR2, SCN5A, SGCD, SHOC2, SOS1, TAZ, TCAP, TMEM43, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR and VCL. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Arrhythmogenic right ventricular cardiomyopathy (ARVC) Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of DES, DSC2, DSG2, DSP, JUP, PKP2, RYR2, and TMEM43. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Dilated cardiomyopathy (DCM) Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ABCC9, ACTC1, ACTN2, ANKRD1, BAG3, CSRP3, CTF1, DES, EMD, FHL1, FHL2, GATAD1, LAMP2, LDB3, LMNA, MYBPC3, MYH6, MYH7, NEXN, PLN, RBM20, SCN5A, SGCD, TAZ, TCAP, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN and VCL. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Hypertrophic cardiomyopathy (HCM) Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ACTC1, ACTN2, BRAF, CSRP3, GLA, HRAS, KRAS, LAMP2, MAP2K1, MAP2K2, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, NEXN, NRAS, PLN, PRKAG2, PTPN11, RAF1, RIT1, SHOC2, SOS1, TNNC1, TNNI3, TNNT2, TPM1 and TTR. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Left ventricular noncompaction (LNVC) Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ACTC1, CASQ2, DTNA, LDB3, LMNA, MYBPC3, MYH7, TAZ, TNNT2 and VCL. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Neutropenia
Severe Congenital Neutropenia Gene Set
| Requisition | GPS Neutropenia Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of AP3B1, CSF3R, CXCR2, CXCR4, ELANE, G6PC3, GATA2, GFI1, HAX1, JAGN1, KRAS, LAMTOR2, LYST, NRAS, RAB27A, RUNX1, SBDS, SLC37A4, TAZ, TCIRG1, USB1, VPS13B, VPS45 and WAS. For some cases with negative results or isolated heterozygous mutations, additional deletion/duplication analysis by CGH array is performed. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing/CGH array |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen; 6 additional weeks for del/dup analysis. |
| Specimen Requirements | Peripheral blood |
| Sample Collection | EDTA (lavender top) tube containing 8 mL peripheral blood |
| Mininum Sample Volume | 8 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407; 81479, 81406 or 81408 (CGH array depending on gene tested) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Renal Disease
aHUS/TMA/C3 Glomerulopathy Gene Set
| Requisition | GPS Renal Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ADAMTS13, C3, CD46, CFB, CFH, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CFI, DGKE and THBD; CFHR3-CFHR1 deletion by multiplex ligation-dependent probe amplification (MLPA). |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing/MLPA |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407; 81479 (MLPA) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Alport Syndrome Gene Set
| Requisition | GPS Renal Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of COL4A3, COL4A4 and COL4A5. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Cystic disease and Nephronophthisis Gene Set
| Requisition | GPS Renal Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of AHI1, CEP290, GLIS2, INVS, IQCB1, NEK8, NPHP1, NPHP3, NPHP4, RPGRIP1L, TMEM67, TTC21B, XPNPEP3, BICC1, CRB2, EYA1, HNF1B, PAX2, PKD1, PKD2, PKHD1, SIX5 and UMOD. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Nephrotic Syndrome and Focal Segmental Glomerulosclerosis Gene Set
| Requisition | GPS Renal Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of ACTN4, ADCK4 (COQ8B), ANLN, APOL1, ARHGAP24, ARHGDIA, CD2AP, COL4A3, COL4A4, COL4A5, COQ2, COQ6, CRB2, CUBN, EMP2, INF2, ITGA3, ITGB4, LAMB2, LMX1B, MEFV, MYH9, MYO1E, NEIL1, NPHS1, NPHS2, PDSS2, PLCE1, PTPRO, SCARB2, SMARCAL1, TRPC6, TTC21B and WT1. |
| Test Details | Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing. |
| Methodology | Next Generation Sequencing |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen |
| Specimen Requirements | Peripheral blood |
| Sample Collection | 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood |
| Mininum Sample Volume | 2 ml |
| Storage/Transport Conditions | 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 | Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens. |
| Special Instructions | |
| CPT Code(s) | 81407 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |