Sequencing Tests

Cancer

Solid Tumor Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ABL1, AFF3, AKT1, AKT2, AKT3, ALK*, APC, AR, ATM, ATRX, BAP1, BCL2L1, BRAF, BRCA1, BRCA2, BRIP1, CCND1, CDH1, CDK12, CDK6, CDKN1A, CDKN1B, CDKN2A, CHEK2, CREBBP, CSF1R, CTNNB1, DAXX, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ERCC2, ESR1, ESR2, FANCA, FAT1, FBXW7, FGFR1, FGFR2*, FGFR3*, FGFR4, FLT1, FLT3, FLT4, FOXL2, GATA4, GNAS, H3F3A, HIST1H3B, HRAS, IDH1, IDH2, JAK1, JAK2, KDM5C, KDR, KEAP1, KIT, KLF4, KMT2C, KMT2D, KRAS, MAP2K1, MAP2K2, MAP3K3, MCL1, MED12, MET, MLH1, MN1, MTOR, MYB, MYBL1, MYC, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NRAS, NTRK1*, NTRK2, PALB2, PBRM1, PDGFRA, PDGFRB, PIK3C2B, PIK3CA, PIK3R1, PIK3R2, POLD1, POLE, PPARG, PPP2R1A, PTEN, RAD54B, RAF1, RB1, RET*, RIT1,ROS1*, RXRA, SETD2, SHOC2, SMAD2, SMAD4, SMARCA4, SMARCB1, SOS1, SPRED1, STK11, TEK, TERT, TGFBR2, TP53, TRAF7, TSC1, TSC2, VHL and WT1 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

Hematopoietic Disorders Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ABL1, ASXL1, ATM, BCOR, BIRC3, BRAF, CALR, CBL, CEBPA, CREBBP, CSF1R, CSF3R, DNMT3A, EP300, ETV6, EZH2, FBXW7, FGFR4, FLT3, GATA1, GATA2, GATA3, IDH1, IDH2, IL7R, JAK2, JAK3, KDM6A, KIT, KRAS, KMT2A*, MPL, NF1, NOTCH1, NOTCH2, NPM1, NRAS, NSD1, PAX5, PDGFRA, PDGFRB, PTPN11, RUNX1, SETB1, SF3B1, SRSF2, STAG2, TERT, TET1, TET2, TP53, TSLP, U2AF1 and ZRSR2 to detect single nucleotide variants and small insertions and deletions.*selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

Breast Tumor Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKT1, ATM, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDK6, CDKN2A, CHEK2, EGFR, ERBB2, ERBB3, ERBB4, ESR1, ESR2, FANCA, FBXW7, FGFR1, FGFR2*, GATA3, HRAS, IDH1, IDH2, KDR, KIT, KRAS, MAP2K1, MAP2K2, MET, PALB2, PIK3CA, PIK3R1, PTEN, RAC1, RAD54B, RB1, RET*, RUNX1, STK11 and TP53 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

CNS Tumors Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions ofAKT1, ATRX, BRAF, CDKN2A, CIC, CTNNB1, DAXX, DNMT3A, EGFR, ERBB2, FGFR1, FGFR2*, FUBP1, H3F3A, HIST1H3B, IDH1, IDH2, KLF4, KRAS, MED12, MET, MN1, MTOR, MYB, MYBL1, MYC, NF1, NF2, NOTCH1, NTRK1*, NTRK2, PDGFRA, PIK3CA, PIK3R1, PTCH1, PTEN, RB1, SETD2, SHH, SMARCA4, SMARCB1, SMO, SUFU, TERT, TP53, TRAF7, WNT1 and WT1 to detect single nucleotide variants and small insertions and deletions.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81445
Miscellaneous
Lab Area/Performed By GPS

Genitourinary Tumor Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKT1, AKT2, AKT3, AR, ATM, BAP1, BRAF, BRCA1, BRCA2, CDKN1A, CDKN2A, CREBBP, EGFR, ERBB2, ERBB3, ERCC2, FBXW7, FGFR2*, FGFR3*, HRAS, KDM5C, KDM6A, KMT2C, KMT2D, MED12, MET, MLH1, MTOR, NF1, NRAS, PBRM1, PIK3CA, PIK3R1, PPARG, PTCH1, PTEN, RXRA, SETD2, STAG2, TERT, TP53, TSC1, TSC2 and VHL to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

Gynecologic Tumor Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ABL1, AKT1, AKT2, AKT3, APC, ATM, BCOR, BRAF, BRCA1, BRCA2, CCND1, CDK12, CDKN2A, CTNNB1, EGFR, EP300, ERBB2, ERBB4, FAT1, FBXW7, FGFR1, FGFR2*, FGFR3*, FOXL2, HRAS, JAK3, KDR, KIT, KRAS, MAP2K1, MAP2K2, MED12, MET, MLH1, MTOR, NF1, NRAS, PIK3CA, PIK3R1, PIK3R2, POLD1, POLE, PPP2R1A, PTEN, RB1, SMAD4, SMO, STK11, TP53 and VHL to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

Head & Neck Tumor Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AFF3, AKT1, AKT2, AKT3, APC, ASXL1, ATM, BCL2L1, BRCA1, BRCA2, CCND1, CDKN2A, EGFR, EP300, ERBB2, FAT1, FBXW7, GATA4, HRAS, KDM6A, KMT2C, KMT2D, KRAS, MCL1, MTOR, NF1, NFE2L2, NOTCH1, NOTCH2, NRAS, NSD1, PIK3C2B, PIK3CA, PIK3R1, PTEN, RAC1, RB1, RHOA, SMAD4, TGFBR2 and TP53 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

Melanoma Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKT1, ALK*, BAP1, BRAF, CCND1, CDK4, CDKN2A, CTNNB1, EGFR, ERBB2, ERBB4, FGFR1, FGFR2*, FGFR3*, GNA11, GNAQ, HRAS, KIT, KMT2C, KMT2D, KRAS, MAP2K1, MAP2K2, MED12, MET, MTOR, NF1, NRAS, PDGFRA, PDGFRB, PIK3CA, PTEN, RAC1, RB1, RET*, ROS1*, TERT and TP53 to detect single nucleotide variants and small insertions and deletions.*selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Speciment Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81445
Miscellaneous
Lab Area/Performed By GPS

Thoracic Tumor Gene Set

Requisition Cancer Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKT1, AKT2, AKT3, ALK*, ATM, BAP1, BRAF, CDKN1B, CDKN2A, DDR2, ERBB2, ERBB3, FANCA, FGFR1, FLT1, FLT4, HRAS, KDR, KEAP1, KMT2C, KMT2D, KRAS, MED12, MET, NF1, NRAS, NTRK1*, RB1, RET*, RIT1, ROS1*, SMARCA4, STK11, TP53, TSC1 and TSC2 to detect single nucleotide variants and small insertions and deletions. *selected introns also sequenced to detect rearrangements.
Test Details Pathologist review to identify neoplastic tissue is followed by extraction of tumor DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in cancer and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 3 weeks from receipt of specimen
Specimen Requirements Tumor-containing formalin fixed paraffin embedded tissue; bone marrow aspirate; disease-involved peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing viable tumor with tumor cells. Tumor cells must account for at least 10% of cell nuclei in the tumor-containing regions of the block. One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). For molecular analysis, tumor cells will be excised by GPS in the form of tissue cores or 10 µm sections. Unstained Slides: Ten (10) 5-10 µm unstained sections on positively charged, unbaked slides from a single tumor-containing formalin fixed paraffin embedded block AND One (1) corresponding hematoxylin and eosin (H&E) stained slide (if available). Note: For smaller tissues (less than 5mm x 5mm) please send 15 slides. For molecular analysis, tumor cells will be excised by microdissection. Cell Block: One (1) formalin fixed paraffin embedded (FFPE) cell block containing sufficient tumor (preferably with large groupings of tumor cells and/or without significant admixture by non-neoplastic nucleated cells). For molecular analysis, tumor cells will be excised in the form of tissue cores or 10 µm sections. Bone Marrow or Involved Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL. Note: Greater than 10% tumor-involvement required.
Minimum Sample Volume 3- 1mm punches (cores); 5- 5µm scrolls; 10 – 5µm slides; 2 ml bone marrow or peripheral blood
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood and marrow: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable); Minimum tumor cellularity must be >10% in tumor involved regions of the specimen. Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81455
Miscellaneous
Lab Area/Performed By GPS

Somatic and Related Disorders

Somatic Overgrowth Gene Set

Requisition SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKT1, AKT2, AKT3, GNA11, GNAQ, IDH1, IDH2, MAP2K1, MAP3K3, MTOR, PIK3CA, PIK3R2, PTEN, RASA1, SMO, TEK, TSC1 and TSC2.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in segmental overgrowth and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements **Primary specimen required: tissue from the affected area.  Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab.  Secondary specimen for comparative study: peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

PIK3CA-Related Overgrowth Gene Set

Requisition GPS SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions of PIK3CA.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in segmental overgrowth and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements **Primary specimen required: tissue from the affected area.  Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab.  Secondary specimen for comparative study: peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 81406
Miscellaneous
Lab Area/Performed By GPS

McCune Albright Gene Set

Requisition GPS SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions of GNAS.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in McCune Albright and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements Formalin fixed paraffin embedded affected tissue; fresh affected tisse in transport or tissue culture media; peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 81406
Miscellaneous
Lab Area/Performed By GPS

Nevus Gene Set

Requisition SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions of FGFR3, GNA11, GNAQ, HRAS, KRAS, MAP3K3, NRAS, PIK3CA and TEK.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in segmental overgrowth and related syndromes and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements **Primary specimen required: tissue from the affected area.  Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab.  Secondary specimen for comparative study: peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Curry-Jones Gene Set

Requisition SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions of SMO.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in Curry-Jones Syndrome, segmental overgrowth, and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements **Primary specimen required: tissue from the affected area.  Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab.  Secondary specimen for comparative study: peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 81406
Miscellaneous
Lab Area/Performed By GPS

Maffucci Syndrome Gene Set

Requisition SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions of IDH1 and IDH2.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in Maffucci Syndrome, Ollier Disease and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements **Primary specimen required: tissue from the affected area.  Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab.  Secondary specimen for comparative study: peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 81406
Miscellaneous
Lab Area/Performed By GPS

Rasopathies Gene Set

Requisition SOMA Sequencing Requisition
Test Components Next generation sequencing of all coding regions ofBRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NF1, NRAS, PTPN11, RAF1, RIT1, SHOC2, SOS1 and SPRED1.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing of the entire coding region and select introns on the Illumina platform. Identified variants previously described in Rasopathies and other potentially pathogenic non-synonymous variants are reported with interpretations.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 6-8 weeks from receipt of specimen
Specimen Requirements **Primary specimen required: tissue from the affected area.  Formalin fixed paraffin embedded affected tissue; fresh affected tissue in transport or tissue culture media; buccal swab.  Secondary specimen for comparative study: peripheral blood.
Sample Collection Routine Tissue Block: One (1) formalin fixed paraffin embedded (FFPE) block containing affected tissue. Peripheral Blood: One (1) EDTA (lavender top) tube containing 2-5 mL.
Mininum Sample Volume
Storage/Transport Conditions FFPE blocks: ambient /room temperature. Place in a sealed container (bag). Place primary container in a padded envelope. Recommend shipping by overnight. In seasonal warmer weather, include cold pack (DO NOT FREEZE).; Blood: Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Specimens processed using acid decalcification are not acceptable (EDTA is acceptable)
Special Instructions
CPT Code(s) 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 ABCC9, ACTC1, ACTN2, AKAP9, ANK2, ANKRD1, BAG3, BRAF, CACNA1C, CACNB2, CALM1, CASQ2, CAV3, CSRP3, CTF1, DES, DSC2, DSG2, DSP, DTNA, EMD, FHL1, FHL2, GATAD1, GLA, GPD1L, HCN4, HRAS, JUP, KCND3, KCNE1, KCNE2, KCNE3, KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, KRAS, LAMP2, LDB3, LMNA, MAP2K1, MAP2K2, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, NEXN, NRAS, PKP2, PLN, PRKAG2, PTPN11, RAF1, RBM20, RIT1, RYR2, SCN1B, SCN3B, SCN4B, SCN5A, SGCD, SHOC2, SNTA1, SOS1, TAZ, TCAP, TMEM43, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR and VCL.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Arrhythmia Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKAP9, ANK2, CACNA1C, CACNB2, CALM1, CASQ2, CAV3, GPD1L, HCN4, KCND3, KCNE1, KCNE2, KCNE3, KCNH2, KCNJ2, KCNJ5, KCNJ8, KCNQ1, RYR2, SCN1B, SCN3B, SCN4B, SCN5A and SNTA1.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS
Brugada Syndrome Gene Set
Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of CACNA1C, CACNB2, GPD1L, HCN4, KCND3, KCNE3, KCNJ8, SCN1B, SCN3B and SCN5A.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Catecholaminergic polymorphic ventricular tachycardia (CPVT) Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ANK2, CALM1, CASQ2, KCNJ2 and RYR2.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Long QT Syndrome Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AKAP9, ANK2, CACNA1C, CAV3, KCNE1, KCNE2, KCNH2, KCNJ2, KCNJ5, KCNQ1, SCN4B, SCN5A and SNTA1.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81280
Miscellaneous
Lab Area/Performed By GPS

Short QT Syndrome Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of CACNA1C, CACNB2, KCNH2, KCNJ2 and KCNQ1.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Cardiomyopathy Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ABCC9, ACTC1, ACTN2, ANKRD1, BAG3, BRAF, CASQ2, CSRP3, CTF1, DES, DSC2, DSG2, DSP, DTNA, EMD, FHL1, FHL2, GATAD1, GLA, HRAS, JUP, KRAS, LAMP2, LDB3, LMNA, MAP2K1, MAP2K2, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, NEXN, NRAS, PKP2, PLN, PRKAG2, PTPN11, RAF1, RBM20, RIT1, RYR2, SCN5A, SGCD, SHOC2, SOS1, TAZ, TCAP, TMEM43, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN, TTR and VCL.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Arrhythmogenic right ventricular cardiomyopathy (ARVC) Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of DES, DSC2, DSG2, DSP, JUP, PKP2, RYR2, and TMEM43.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Dilated cardiomyopathy (DCM) Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ABCC9, ACTC1, ACTN2, ANKRD1, BAG3, CSRP3, CTF1, DES, EMD, FHL1, FHL2, GATAD1, LAMP2, LDB3, LMNA, MYBPC3, MYH6, MYH7, NEXN, PLN, RBM20, SCN5A, SGCD, TAZ, TCAP, TMPO, TNNC1, TNNI3, TNNT2, TPM1, TTN and VCL.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Hypertrophic cardiomyopathy (HCM) Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ACTC1, ACTN2, BRAF, CSRP3, GLA, HRAS, KRAS, LAMP2, MAP2K1, MAP2K2, MYBPC3, MYH6, MYH7, MYL2, MYL3, MYLK2, MYOZ2, NEXN, NRAS, PLN, PRKAG2, PTPN11, RAF1, RIT1, SHOC2, SOS1, TNNC1, TNNI3, TNNT2, TPM1 and TTR.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Left ventricular noncompaction (LNVC) Gene Set

Requisition GPS Cardiac Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ACTC1, CASQ2, DTNA, LDB3, LMNA, MYBPC3, MYH7, TAZ, TNNT2 and VCL.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Neutropenia

Severe Congenital Neutropenia Gene Set

Requisition GPS Neutropenia Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AP3B1, CSF3R, CXCR2, CXCR4, ELANE, G6PC3, GATA2, GFI1, HAX1, JAGN1, KRAS, LAMTOR2, LYST, NRAS, RAB27A, RUNX1, SBDS, SLC37A4, TAZ, TCIRG1, USB1, VPS13B, VPS45 and WAS. For some cases with negative results or isolated heterozygous mutations, additional deletion/duplication analysis by CGH array is performed.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing/CGH array
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen; 6 additional weeks for del/dup analysis.
Specimen Requirements Peripheral blood
Sample Collection EDTA (lavender top) tube containing 8 mL peripheral blood
Mininum Sample Volume 8 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407; 81479, 81406 or 81408 (CGH array depending on gene tested)
Miscellaneous
Lab Area/Performed By GPS

Renal Disease

aHUS/TMA/C3 Glomerulopathy Gene Set

Requisition GPS Renal Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ADAMTS13, C3, CD46, CFB, CFH, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CFI, DGKE and THBD; CFHR3-CFHR1 deletion by multiplex ligation-dependent probe amplification (MLPA).
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing/MLPA
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407; 81479 (MLPA)
Miscellaneous
Lab Area/Performed By GPS

Alport Syndrome Gene Set

Requisition GPS Renal Sequencing Requisition
Test Components Next generation sequencing of all coding regions of COL4A3, COL4A4 and COL4A5.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Cystic disease and Nephronophthisis Gene Set

Requisition GPS Renal Sequencing Requisition
Test Components Next generation sequencing of all coding regions of AHI1, CEP290, GLIS2, INVS, IQCB1, NEK8, NPHP1, NPHP3, NPHP4, RPGRIP1L, TMEM67, TTC21B, XPNPEP3, BICC1, CRB2, EYA1, HNF1B, PAX2, PKD1, PKD2, PKHD1, SIX5 and  UMOD.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS

Nephrotic Syndrome and Focal Segmental Glomerulosclerosis Gene Set

Requisition GPS Renal Sequencing Requisition
Test Components Next generation sequencing of all coding regions of ACTN4, ADCK4 (COQ8B), ANLN, APOL1, ARHGAP24, ARHGDIA, CD2AP, COL4A3, COL4A4, COL4A5, COQ2, COQ6, CRB2, CUBN, EMP2, INF2, ITGA3, ITGB4, LAMB2, LMX1B, MEFV, MYH9, MYO1E, NEIL1, NPHS1, NPHS2, PDSS2, PLCE1, PTPRO, SCARB2, SMARCAL1, TRPC6, TTC21B and WT1.
Test Details Extraction of DNA, capture of the genes to be assayed, and sequencing on the Illumina platform. Identified variants are categorized using the ACMG/AMP guidelines for the interpretation of sequence variants. An interpretation of results is provided based on the medical literature and in the context of the indication for testing.
Methodology Next Generation Sequencing
Performed Mon-Fri
Turnaround 4-6 weeks from receipt of specimen
Specimen Requirements Peripheral blood
Sample Collection 1 EDTA (lavender top) tube containing 2-5 mL peripheral blood
Mininum Sample Volume 2 ml
Storage/Transport Conditions Ambient / room temperature preferred. However, if delivery / shipment of specimen is greater than four (4) hours, refrigerate at 4 degrees until delivery / shipment by overnight delivery. In seasonal warmer weather, include cold pack (DO NOT FREEZE).
Unacceptable Conditions Frozen specimens, use of inappropriate tube type, and clotted or hemolyzed specimens.
Special Instructions
CPT Code(s) 81407
Miscellaneous
Lab Area/Performed By GPS