| Requisition | Cancer Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 122 genes: 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 54 genes: 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 42 genes: 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) | 81445 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
CNS Tumors Gene Set
| Requisition | Cancer Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 48 genes: AKT1, 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 44 genes: 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) | 81445 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Gynecologic Tumor Gene Set
| Requisition | Cancer Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 50 genes: 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) | 81445 |
| 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 41 genes: 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) | 81445 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Melanoma Gene Set
| Requisition | Cancer Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 38 genes: 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 36 genes: 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) | 81445 |
| 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 25 genes: AKT1, AKT2, AKT3, BRAF, FGFR1, GNA11, GNAQ, HRAS, IDH1, IDH2, KRAS, MAP2K1, MAP3K3, MTOR, NRAS, PDGFRB, PIK3CA, PIK3R1, 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) | 81479 |
| 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) | 81479 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Nevus Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 12 genes: BRAF, FGFR1, FRFR2, 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) | 81479 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Maffucci Syndrome Gene Set
| Requisition | SOMA Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 2 genes: 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 of 14 genes: BRAF, 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) | 81442 |
| 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 163 genes: A2ML1, ABCC9, ACADVL, ACTA1, ACTA2, ACTC1, ACTN2, AGL, AKAP9, ALMS1, ALPK3, ANK2, ANKRD1, BAG3, BRAF, CACNA1C, CACNA2D1, CACNB2, CALM1, CALM2, CALM3, CALR3, CASQ2, CAV3, CBL, CHRM2, COL3A1, COL5A2, CPT2, CRYAB, CSRP3, CTF1, CTNNA3, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, DTNA, EFEMP2, ELAC2, EMD, EYA4, FBN1, FBN2, FHL1, FHL2, FKRP, FKTN, FLNC, GAA, GATA4, GATA6, GATAD1, GLA, GPD1L, HCN4, HFE, HRAS, ILK, JPH2, JUP, KCND3, KCNE1, KCNE2, KCNE3, KCNE5 (KCNE1L), KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, KRAS, LAMA4, LAMP2, LDB3, LMNA, LOX, LRRC10, MAP2K1, MAP2K2, MIB1, MTO1, MURC (CAVIN4), MYBPC3, MYH6, MYH7, MYH11, MYL2, MYL3, MYLK, MYLK2, MYOM1, MYOZ2, MYPN, NEBL, NEXN, NF1, NKX2-5, NOTCH1, NPPA, NRAS, PDLIM3, PKP2, PLEKHM2, PLN, PRDM16, PRKAG2, PTPN11, RAF1, RANGRF, RASA1, RBM20, RIT1, RRAS, RYR1, RYR2, SCN1B, SCN2B, SCN3B, SCN4B, SCN5A, SCN10A, SDHA, SEPN1 (SELENON), SGCD, SGCG, SHOC2, SLC22A5, SCL25A4, SLC2A10, SLMAP, SMAD3, SMAD4, SNTA1, SOS1, SOS2, SPRED1, TAZ, TBX20, TCAP, TGFB2, TGFB3, TGFBR1, TGFBR2, TMEM43, TMEM70, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TRDN, TRIM63, TRPM4, TTN, TTR, TXNRD2, VCL, YWHAE and ZBTB17. aCGH send out in certain cases: ALMS1, DSP, KCNH2, KCNQ1, PKP2, RYR2, SCL2A10 and TRDN. |
| 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; aCGH |
| 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 (NGS); 81479 x 8 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Arrhythmia Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components |
Next generation sequencing of all coding regions of 35 genes: AKAP9, ANK2, CACNA1C, CACNA2D1, CACNB2, CALM1, CALM2, CALM3, CASQ2, CAV3, GPD1L, HCN4, KCND3, KCNE1, KCNE2, KCNE3, KCNE5, KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, PKP2, RANGRF, RYR2, SCN1B, SCN2B, SCN3B, SCN4B, SCN5A, SCN10A, SLMAP, SNTA1, TRDN and TRPM4. aCGH send out in certain cases: KCNH2, KCNQ1, RYR2 and TRDN. |
| 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; aCGH |
| 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) |
81413 (NGS); 81479 x 4 (aCGH send out) |
| 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 18 genes: CACNA1C, CACNA2D1, CACNB2, GPD1L, HCN4, KCND3, KCNE3, KCNE5 (KCNE1L), KCNJ8, PKP2, RANGRF, SCN1B, SCN2B, SCN3B, SCN5A, SCN10A, SLMAP and TRPM4. |
| 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) | 81413 |
| 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 8 genes: ANK2, CALM1, CALM2, CALM3, CASQ2, KCNJ2, RYR2 and TRDN. aCGH send out in certain cases: RYR2 and TRDN. |
| 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; aCGH |
| 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 (NGS); 81479 x 2 (aCGH send out) |
| 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 16 genes: AKAP9, ANK2, CACNA1C, CALM2, CALM3, CAV3, KCNE1, KCNE2, KCNH2, KCNJ2, KCNJ5, KCNQ1, SCN4B, SCN5A, SNTA1 and TRDN. aCGH send out in certain cases: KCNH2 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; aCGH |
| 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) | 81413 (NGS); 81479 x 2 (aCGH send out) |
| 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 6 genes: CACNA1C, CACNA2D1, 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 115 genes: A2ML1, ABCC9, ACADVL, ACTA1, ACTC1, ACTN2, AGL, ALMS1, ALPK3, ANKRD1, BAG3, BRAF, CALR3, CASQ2, CBL, CHRM2, CPT2, CRYAB, CSRP3, CTF1, CTNNA3, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, DTNA, ELAC2, EMD, EYA4, FHL1, FHL2, FKRP, FKTN, FLNC, GAA, GATA4, GATA6, GATAD1, GLA, HFE, HRAS, ILK, JPH2, JUP, KRAS, LAMA4, LAMP2, LDB3, LMNA, LRRC10, MAP2K1, MAP2K2, MIB1, MTO1, MURC (CAVIN4), MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOM1, MYOZ2, MYPN, NEBL, NEXN, NF1, NKX2-5, NPPA, NRAS, PDLIM3, PKP2, PLEKHM2, PLN, PRDM16, PRKAG2, PTPN11, RAF1, RASA1, RBM20, RIT1, RRAS, RYR1, RYR2, SCN5A, SDHA, SEPN1 (SELENON), SGCD, SGCG, SHOC2, SLC22A5, SLC25A4, SOS1, SOS2, SPRED1, TAZ, TBX20, TCAP, TMEM43, TMEM70, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TRIM63, TTN, TTR, TXNRD2, VCL, YWHAE and ZBTB17. aCGH send out in certain cases: ALMS1, DSP and PKP2. |
| 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; aCGH |
| 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) | 81439 (NGS); 81479 x 3 (aCGH send out) |
| 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 11 genes: CTNNA3, DES, DSC2, DSG2, DSP, JUP, PDLIM3, PKP2, RYR1, RYR2 and TMEM43. aCGH send out in certain cases: DSP and PKP2. |
| 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; aCGH |
| 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) | 81439 (NGS); 81479 x 2 (aCGH send out) |
| 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 67 genes: ABCC9, ACADVL, ACTA1, ACTC1, ACTN2, ALMS1, ALPK3, ANKRD1, BAG3, CBL, CHRM2, CPT2, CRYAB, CSRP3, CTF1, DES, DMD, DNAJC19, DOLK, EMD, EYA4, FHL1, FHL2, FKRP, FKTN, FLNC, GATA4, GATA6, GATAD1, HFE, ILK, LAMP2, LDB3, LMNA, LRRC10, MURC (CAVIN4), MYBPC3, MYH6, MYH7, MYPN, NEBL, NEXN, NKX2-5, NPPA, PDLIM3, PLEKHM2, PLN, RBM20, SCN5A, SDHA, SEPN1 (SELENON), SGCD, SGCG, SLC22A5, TAZ, TBX20, TCAP, TMEM70, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TXNRD2, VCL and ZBTB17. aCGH send out in certain cases: ALMS1. |
| 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; aCGH |
| 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) | 81439 (NGS); 81479 (aCGH) |
| 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 62 genes: A2ML1, ACADVL, ACTA1, ACTC1, ACTN2, AGL, ALPK3, BRAF, CALR3, CBL, CPT2, CRYAB, CSRP3, ELAC2, FLNC, GAA, GATA4, GLA, HFE, HRAS, JPH2, KRAS, LAMP2, MAP2K1, MAP2K2, MTO1, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOM1, MYOZ2, MYPN, NEXN, NF1, NPPA, NRAS, PDLIM3, PLN, PRKAG2, PTPN11, RAF1, RASA1, RIT1, RRAS, SEPN1 (SELENON), SGCG, SHOC2, SLC22A5, SLC25A4, SOS1, SOS2, SPRED1, TNNC1, TNNI3, TNNT2, TPM1, TRIM63, TTR and ZBTB17 |
| 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) | 81439 |
| 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 15 genes: ACTC1, CASQ2, DNAJC19, DTNA, LAMA4, LDB3, LMNA, MIB1, MYBPC3, MYH7, PRDM16, TAZ, TNNT2, VCL and YWHAE. |
| 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) | 81439 |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Thoracic Aortic Aneurysm and Dissection (TAAD) Gene Set
| Requisition | GPS Cardiac Sequencing Requisition |
| Test Components |
Next generation sequencing of all coding regions of 17 genes: ACTA2, COL3A1, COL5A2, EFEMP2, FBN1, FBN2, LOX, MYH11, MYLK, NOTCH1, SLC2A10, SMAD3, SMAD4, TGFB2, TGFB3, TGFBR1 and TGFBR2. aCGH send out in certain cases: SCL2A10. |
| 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; aCGH |
| 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) | 81410 (NGS); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Diabetes, Hyperinsulinism and ER Stress
Rare and Atypical Diabetes Gene Set
| Requisition | Diabetes Sequencing Requisition |
| Test Components |
Next generation sequencing of all coding regions of 53 genes: ABCC8, AGPAT2, AIRE, APPL1, AKT2, BLK, CACNA1D, CEL, CISD2, CP, EIF2AK3, FOXA2, FOXP3, GATA4, GATA6, GCK, GLIS3, GLUD1, HADH, HFE, HNF1A, HNF1B, HNF4A, IER3IP1, INS, INSR, KCNJ11, KDM6A, KLF11, KMT2D, LRBA, MNX1, NEUROD1, NEUROG3, NKX2-2, PAX6, PAX4, PCBD1, PDX1, PGM1, PLAGL1, PPARG, PTF1A, RFX6, PMM2, SLC2A2, SLC16A1, SLC19A2, STAT3, TRMT10A, UCP2, WFS1 and ZFP57. aCGH send out in certain cases: HNF1B. |
| 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; aCGH |
| Performed | Mon-Fri |
| Turnaround | 4-6 weeks from receipt of specimen; 6 additional weeks for del/dup analysis. |
| 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 (NGS); 81404 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Endoplasmic Reticulum (ER) Stress Gene Set
| Requisition | Diabetes Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 5 genes: CISD2, EIF2AK3, IER3IP1, INS and WFS1.</ |
| 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 |
Hyperinsulinism Gene Set
| Requisition | Diabetes Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 18 genes: ABCC8, AKT2, CACNA1D, FOXA2, GCK, GLUD1, HADH, HNF1A, HNF4A, INSR, KCNJ11, KDM6A, KMT2D, PGM1, PMM2, SLC16A1, TRMT10A and UCP2.</ |
| 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 |
Permanent Neonatal Diabetes Mellitus (PNDM) Gene Set
| Requisition | Diabetes Sequencing Requisition |
| Test Components |
Next generation sequencing of all coding regions of 29 genes: ABCC8, CP, EIF2AK3, FOXP3, GATA4, GATA6, GCK, GLIS3, HNF1B, IER3IP1, INS, KCNJ11, LRBA, MNX1, NEUROD1, NEUROG3, NKX2-2, PAX6, PCBD1, PDX1, PLAGL1, PTF1A, RFX6, SLC2A2, SLC19A2, STAT3, TRMT10A, WFS1 and ZFP57. aCGH send out in certain cases: HNF1B. |
| 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; aCGH |
| 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 (NGS); 81404 (aCGH) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |
Monogenic Diabetes and MODY Gene Set
| Requisition | Diabetes Sequencing Requisition |
| Test Components |
Next generation sequencing of all coding regions of 43 genes: ABCC8, AGPAT2, AIRE, APPL1, AKT2, BLK, CEL, CISD2, CP, EIF2AK3, FOXP3, GATA4, GATA6, GCK, GLIS3, HFE, HNF1A, HNF1B, HNF4A, IER3IP1, INS, INSR, KCNJ11, KLF11, LRBA, MNX1, NEUROD1, NEUROG3, NKX2-2, PAX4, PAX6, PCBD1, PDX1, PLAGL1, PPARG, PTF1A, RFX6, SLC2A2, SLC19A2, STAT3, TRMT10A, WFS1 and ZFP57. aCGH send out in certain cases: HNF1B. |
| 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; aCGH |
| 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 (NGS); 81404 (aCGH) |
| 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 48 genes: AK2, AP3B1, ASXL1, CD40LG, CLPB, CSF3R, CXCR2, CXCR4, DNAJC21, DNM2, DOCK2, EFL1, EIF2AK3, ELANE, G6PC3, GATA1, GATA2, GFI1, GINS1, HAX1, IRAK4, JAGN1, KAT6A, KRAS, LAMTOR2, LYST, MYD88, NRAS, PGM3, PSTPIP1, RAB27A, RAC2, RUNX1, SBDS, SLC37A4, SMARCD2, SRP54, STK4, TAZ, TCIRG1, TCN2, TP53, USB1, VPS13B, VPS45, WAS, WDR1 and WIPF1. aCGH send out in certain cases: AP3B1, GATA2, HAX1, RAB27A, SLC37A4, TAZ, VPS13B, WAS. |
| 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; aCGH |
| 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 (NGS); 81407 x 1 and 81479 x 7 (aCGH send out) |
| 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 13 genes: 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) | 81479 |
| 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 3 genes: COL4A3, COL4A4 and COL4A5. aCGH send out in certain cases: 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; aCGH |
| 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 (NGS); 81407 (aCGH send out) |
| 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 33 genes: ACE, AGT, AGTR1, AHI1, BBS10, BICC1, CC2D2A, CEP290, CRB2, DNAJB11, EYA1, GANAB, GLIS2, HNF1B, INVS, IQCB1, MUC1, NEK8, NPHP1, NPHP3, NPHP4, PAX2, PKD1, PKD2, PKHD1, REN, RPGRIP1L, SIX5, TMEM67, TTC21B, UMOD, USH2A and XPNPEP3. |
| 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) | 81479 |
| 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 52 genes: ACE, ACTN4, ADCK4 (COQ8B), ANLN, APOL1, ARHGAP24, ARHGDIA, CD2AP, CLCN5, COL4A3, COL4A4, COL4A5, COQ2, COQ6, CRB2, CUBN, EMP2, FAT1, INF2, ITGA3, ITGB4, KANK1, KANK2, KANK4, LAGE3, LAMB2, LMX1B, MAGI2, MEFV, MYH9, MYO1E, NEIL1, NPHS1, NPHS2, NUP107, NUP205, NUP93, OCRL, OSGEP, PDSS2, PLCE1, PTPRO, REN, SCARB2, SMARCAL1, TP53RK, TPRKB, TRPC6, TTC21B, WDR73, WT1 and XPO5. aCGH send out in certain cases: CLCN5, COL4A5, NPHS1, NPHS2. |
| 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; aCGH |
| 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 (NGS); 81407 x 1 and 81479 x 3 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | GPS |