| 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 | NGS |
Sequencing Tests
**Please note that all of our orderable tests include a professional molecular interpretation. Please contact our laboratory if you have additional questions regarding the test interpretation.
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 | NGS |
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 | NGS |
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 | NGS |
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 | NGS |
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 | NGS |
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 | NGS |
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 |
| 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 | NGS |
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 | NGS |
Mosaicism Disorders
Somatic Overgrowth Panel
| 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
PIK3CA-Related Overgrowth Spectrum Disorders
| Requisition | 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
McCune Albright Syndrome
| Requisition | 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
Nevus Panel
| 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
Curry-Jones Syndrome
| 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
Maffucci Syndrome Panel
| 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
Rasopathies Panel
| 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 | 3 weeks from receipt of specimen (Sanger sequencing, if applicable, is an additional 3 weeks after completion of the NGS testing). |
| 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 | NGS |
Cardiac Disease
Cardiac Diseases Gene panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components |
CORE: 82 genes sequenced: ACADVL, ACTA2, ACTC1, ACTN2, AGL, ALMS1, ALPK3, BAG3, BGN, CACNA1C, CALM1, CALM2, CALM3, CASQ2, COL3A1, COL5A2, CPT2, CRYAB, CSRP3, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, EFEMP2, ELAC2, EMD, FBN1, FBN2, FHL1, FKRP, FKTN, FLNC, FOXE3, GAA, GLA, JPH2, JUP, KCNE1, KCNH2, KCNJ2, KCNQ1, LAMP2, LMNA, LOX, MFAP5, MTO1, MYBPC3, MYH7, MYH11, MYL2, MYL3, MYLK, NEXN, PKP2, PLN, PRKAG2, PRKG1, RBM20, RYR2, SCN5A, SDHA, SGCD, SLC25A4, SMAD2, SMAD3, TAZ, TECRL, TGFB2, TGFBR1, TGFBR2, TMEM43, TNNC1, TNNI3, TNNT2, TPM1, TRDN, TTN, TTR and VCL. EXPANDED: 150 genes sequenced: ABCC9, ACADVL, ACTA2, ACTC1, ACTN2, AGL, AKAP9, ALMS1, ALPK3, ANKRD1, BAG3, BGN, CACNA1C, CACNA2D1, CACNB2, CALM1, CALM2, CALM3, CALR3, CASQ2, CAV3, CDH2, CHRM2, COL3A1, COL5A2, COL9A1, CPT2, CRYAB, CSRP3, CTF1, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, DTNA, EFEMP2, ELAC2, EMD, EYA4, FBN1, FBN2, FHL1, FKRP, FKTN, FLNA, FLNC, FOXE3, GAA, GATA4, GATA6, GATAD1, GLA, GPD1L, HAND1, HCN4, ILK, JPH2, JUP, KCND3, KCNE1, KCNE2, KCNE3, KCNE5, KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, KLF10, LAMA4, LAMP2, LDB3, LMNA, LOX, MAT2A, MFAP5, MIB1, MTO1, MYBPC3, MYH6, MYH7, MYH11, MYL2, MYL3, MYLK, MYLK2, MYLK3, MYOM1, MYOZ2, MYPN, NEBL, NEXN, NKX2-5, NOTCH1, NRAP, OBSCN, PDLIM3, PKP2, PLEKHM2, PLN, PPCS, PRDM16, PRKAG2, PRKG1, PSEN2, RAF1, RANGRF, RBM20, RYR2, SCN1B, SCN2B, SCN3B, SCN4B, SCN5A, SCN10A, SDHA, SGCD, SLC2A10, SLC25A4, SLMAP, SMAD2, SMAD3, SNTA1, TAZ, TBX20, TCAP, TECRL, TGFB2, TGFB3, TGFBR1, TGFBR2, TJP1, TMEM43, TNNC1, TNNI3, TNNI3K, TNNT2, TPM1, TRDN, TRIM63, TRPM4, TTN, TTR, TXNRD2, VCL, YWHAE and ZBTB17. aCGH send out in certain cases: ALMS1, BGN, DSP, KCNH2, KCNQ1, PKP2, 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81479 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Arrhythmia panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 13 genes sequenced: CACNA1C, CALM1, CALM2, CALM3, CASQ2, KCNE1, KCNH2, KCNJ2, KCNQ1, RYR2, SCN5A, TECRL and TRDN.
EXPANDED: 35 genes sequenced: AKAP9, 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, TECRL, 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81479 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Brugada Syndromes panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 1 gene sequenced: SCN5A
EXPANDED: 17 genes sequenced: CACNA2D1, CACNB2, GPD1L, HCN4, KCND3, KCNE3, KCNE5, 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 | 3 – 4 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 (Core panel); 81479 (Expanded panel); 81479 (aCGH Send Out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Catecholaminergic polymorphic ventricular tachycardia (CPVT) panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 7 genes sequenced: CALM1, CALM2, CALM3, CASQ2, RYR2, TECRL 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Long QT Syndromes panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 10 genes sequenced: CACNA1C, CALM1, CALM2, CALM3, KCNE1, KCNH2, KCNJ2, KCNQ1, SCN5A and TRDN.
EXPANDED: 16 genes sequenced: AKAP9, CACNA1C, CALM1, 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81479 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Cardiomyopathy panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 52 genes sequenced: ACADVL, ACTC1, ACTN2, AGL, ALMS1, ALPK3, BAG3, CPT2, CRYAB, CSRP3, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, ELAC2, EMD, FHL1, FKRP, FKTN, FLNC, GAA, GLA, JPH2, JUP, LAMP2, LMNA, MTO1, MYBPC3, MYH7, MYL2, MYL3, NEXN, PKP2, PLN, PRKAG2, RBM20, SCN5A, SDHA, SGCD, SLC25A4, TAZ, TMEM43, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR and VCL.
EXPANDED: 96 genes sequenced: ABCC9, ACADVL, ACTC1, ACTN2, AGL, ALMS1, ALPK3, ANKRD1, BAG3, CALR3, CAV3, CDH2, CHRM2, CPT2, CRYAB, CSRP3, CTF1, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, DTNA, ELAC2, EMD, EYA4, FHL1, FKRP, FKTN, FLNC, GAA, GATA4, GATA6, GATAD1, GLA, HAND1, ILK, JPH2, JUP, KLF10, LAMA4, LAMP2, LDB3, LMNA, MIB1, MTO1, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYLK3, MYOM1, MYOZ2, MYPN, NEBL, NKX2-5, NEXN, NRAP, OBSCN, PDLIM3, PKP2, PLEKHM2, PLN, PPCS, PRDM16, PRKAG2, PSEN2, RAF1, RBM20, RYR2, SCN5A, SDHA, SGCD, SLC25A4, TAZ, TBX20, TCAP, TGFB3, TJP1, TMEM43, TNNC1, TNNI3, TNNI3K, TNNT2, TPM1, TRIM63, TTN, TTR, TXNRD2, YWHAE, VCL 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81439 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Arrhythmogenic right ventricular cardiomyopathy (ARVC) Gene Set
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 11 genes sequenced: DES, DSC2, DSG2, DSP, JUP, LMNA, PKP2, PLN, SCN5A, TMEM43 and TTN.
EXPANDED: 17 genes sequenced: CDH2, DES, DSC2, DSG2, DSP, JUP, LMNA, MYBPC3, MYH7, MYL3, PKP2, PLN, SCN5A, TGFB3, TJP1, TMEM43 and TTN. 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81439 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Dilated cardiomyopathy (DCM) panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 33 genes sequenced: ACADVL, ACTC1, ACTN2, ALMS1, BAG3, CPT2, CRYAB, DES, DMD, DNAJC19, DOLK, DSP, EMD, FKRP, FKTN, FLNC, JPH2, LAMP2, LMNA, MYH7, NEXN, PLN, RBM20, SCN5A, SDHA, SGCD, TAZ, TNNC1, TNNI3, TNNT2, TPM1, TTN and VCL.
EXPANDED: 68 genes sequenced: ABCC9, ACADVL, ACTC1, ACTN2, ALMS1, ANKRD1, BAG3, CHRM2, CPT2, CRYAB, CTF1, DES, DMD, DNAJC19, DOLK, DSC2, DSG2, DSP, DTNA, EMD, EYA4, FKRP, FKTN, FLNC, GATA4, GATA6, GATAD1, HAND1, ILK, JPH2, LAMA4, LAMP2, LDB3, LMNA, MIB1, MYH6, MYH7, MYLK3, MYPN, NEBL, NEXN, NKX2-5, NRAP, OBSCN, PLEKHM2, PLN, PPCS, PRDM16, PSEN2, RAF1, RBM20, RYR2, SCN5A, SDHA, SGCD, TAZ, TBX20, TCAP, TNNC1, TNNI3, TNNI3K, TNNT2, TPM1, TTN, TXNRD2, VCL, YWHAE 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81479 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Hypertrophic Cardiomyopathy (HCM) panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 28 genes sequenced: ACADVL, ACTC1, ACTN2, AGL, ALPK3, BAG3, CSRP3, DES, ELAC2, FHL1, FLNC, GAA, GLA, JPH2, LAMP2, MTO1, MYBPC3, MYH7, MYL2, MYL3, PLN, PRKAG2, SLC25A4, TNNC1, TNNI3, TNNT2, TPM1 and TTR.
EXPANDED: 42 genes sequenced: ACADVL, ACTC1, ACTN2, AGL, ALPK3, ANKRD1, BAG3, CALR3, CAV3, CSRP3, DES, ELAC2, FHL1, FLNC, GAA, GATA4, GLA, JPH2, KLF10, LAMP2, MTO1, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOM1, MYOZ2, MYPN, PDLIM3, PLN, PRKAG2, RYR2, SLC25A4, TCAP, TNNC1, TNNI3, TNNT2, TPM1, TRIM63 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 | 3 – 4 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 (Core panel); 81479 (Expanded panel) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Familial Thoracic Aortic Aneurysm and Dissection panel
| Requisition | Cardiac Sequencing Requisition |
| Test Components | CORE: 18 genes sequenced: ACTA2, BGN, COL3A1, COL5A2, EFEMP2, FBN1, FBN2, FOXE3, LOX, MFAP5, MYH11, MYLK, PRKG1, SMAD2, SMAD3, TGFB2, TGFBR1 and TGFBR2.
EXPANDED: 25 genes sequenced: ACTA2, BGN, COL3A1, COL5A2, COL9A1, EFEMP2, FBN1, FBN2, FLNA, FOXE3, HCN4, LOX, MAT2A, MFAP5, MYH11, MYLK, NOTCH1, PRKG1, SLC2A10, SMAD2, SMAD3, TGFB2, TGFB3, TGFBR1 and TGFBR2. aCGH send out in certain cases: BGN. |
| 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 | 3 – 4 weeks from receipt of specimen – NGS (aCGH send out is an additional 3 weeks after completion of NGS) |
| 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 (Core panel); 81410 (Expanded panel); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Diabetes, Hyperinsulinism and ER Stress
Atypical Diabetes and ER Stress Disorders Gene Panel
| Requisition | Diabetes Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 54 genes: ABCC8, AGPAT2, AIRE, APPL1, AKT2, BLK, CACNA1D, CEL, CISD2, CP, EIF2AK3, FOXA2, FOXP3, GATA4, GATA6, GCK, GLIS3, GLUD1, HADH, HNF1A, HNF1B, HNF4A, IER3IP1, INS, INSR, KCNJ11, KDM6A, KLF11, KMT2D, LMNA, LRBA, MNX1, NEUROD1, NEUROG3, NKX2-2, PAX6, PAX4, PCBD1, PDX1, PGM1, PLAGL1, PPARG, PTF1A, RFX6, PLIN1, 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) | 81479 x 2(NGS and aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Endoplasmic Reticulum (ER) Stress Disorders Panel
| 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) | 81479 |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Hyperinsulinism Panel
| 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) | 81479 |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Permanent Neonatal Diabetes Mellitus (PNDM) Panel
| 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) | 81479 x 2 (NGS and aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Monogenic Diabetes and MODY Panel
| Requisition | Diabetes Sequencing Requisition |
| Test Components | Next generation sequencing of all coding regions of 44 genes: ABCC8, AGPAT2, AIRE, APPL1, AKT2, BLK, CEL, CISD2, CP, EIF2AK3, FOXP3, GATA4, GATA6, GCK, GLIS3, HNF1A, HNF1B, HNF4A, IER3IP1, INS, INSR, KCNJ11, KLF11, LMNA, LRBA, MNX1, NEUROD1, NEUROG3, NKX2-2, PAX4, PAX6, PCBD1, PDX1, PLAGL1, PLIN1, 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) | 81479 x 2 (NGS and aCGH Send Out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Renal Disease
Complement-mediated Renal Disease panel
| Requisition | NGS 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 x 2 (NGS and MLPA send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Alport Syndrome panel
| Requisition | NGS 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); 81479 (aCGH send out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Cystic disease and Nephronophthisis panel
| Requisition | NGS 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 | NGS |
Nephrotic Syndrome and Focal Segmental Glomerulosclerosis panel
| Requisition | NGS 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) | 81479 (NGS); 81479 (aCGH Send Out) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |
Clinical Whole Exome Sequencing
Whole Exome Sequencing
| Requisition | Whole Exome Sequencing |
| Test Components | Next generation sequencing of the coding regions of the genome |
| Test Details | Extraction of DNA, capture 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 | 8 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) | 81415 (proband); 81416 (each comparator) |
| Miscellaneous | |
| Lab Area/Performed By | NGS |