Must submit both tumor/affected tissue AND a normal/germline specimen.
For Solid Tumor Specimens:
Fresh Tissue: 150 mg or 0.5-2.0 cm3 fresh tissue in transport media. Delivery within 24 hours at room temperature.
Fresh Frozen Tissue: 150 mg or 0.5-2.0 cm3 tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
Formalin-fixed, paraffin embedded (FFPE) tissue: a minimum of freshly cut 6 20-um scrolls or 10 slides can be shipped overnight to the laboratory. It would be best to cut and ship Wednesday to arrive on Thursday. The laboratory may reach out if additional material is required in case of extraction failure. Please note: unlike the other specimens in which isolated RNA is extracted, only Total Nucleic Acid (DNA and RNA) is extracted from FFPE tissue.
For Normal/Unaffected Specimens:
Blood: 3-5 ml whole blood in an EDTA (lavender top) tube
Fresh tissue, such as a skin biopsy, is also acceptable as a germline specimen.
Specimen Preparation
See "Collect" section above.
Storage/Transport Temperature
See "Collect" section above.
Volume Required
See "Collect" section above.
Minimum Required
See "Collect" section above.
Phlebotomy Draw
No
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
21 days.
Detection Rate
The Paired Tumor/Normal - Comprehensive Solid Tumor Panel includes the V2.1 Solid Tumor Panel for sequence and copy number analyses of 237 cancer genes and two genes associated with cancer pharmacogenomics in paired tumor and normal samples, and V3 Fusion Panel which targets over 700 exons of 117 cancer genes in tumor sample only.
Utility
Facilitates disease diagnosis, risk stratification, and therapeutic decision-making.
Synonyms
COMPC
Solid Tumor, Fusion panel, Tumor / Normal Paired Test, T/ N, T/N, Comprehensive
Next generation sequencing (NGS) and data analysis: Nucleic acid is extracted from the patient’s samples following standard DNA and RNA extraction protocols. Extracted DNA is fragmented and tagged using SureSelect QXT target enrichment to generate adapter-tagged libraries. Biotin-labeled probes specific to the targeted regions are used for capture hybridization. Libraries are enriched for the desired regions using streptavidin beads. Enriched libraries are then indexed and pooled for sequencing. Libraries are subject to sequence analysis on Illumina NovaSeq 6000 system for 150 bp paired end reads. All coding exons and the flanking intron sequences of targeted genes in the panel are sequenced, and selected promoter regions and known intronic variants are also evaluated. Sequence data are analyzed using the home brew software ConcordS V4.0.0 and NextGENe V2 NGS Analysis Software. Sequence variants within exons and 5 bp flanking intron sequences are annotated. Copy number variation (CNV) analysis for gross deletions and duplications are evaluated using NGS data. For the tumor sample only, RNA sequencing libraries are prepared using Archer Universal RNA Reagent Kit with CHOP fusion panel custom-designed primers with target specific molecular barcode. Sequencing data are analyzed using ArcherTM Analysis for fusion genes. Clinically significant variants including single nucleotide variants (SNVs), indels, CNVs and fusion genes are confirmed by Sanger sequencing, MLPA, Real-Time PCR, or ddPCR only when necessary.
Must submit both tumor/affected tissue AND a normal/germline specimen.
For Solid Tumor Specimens:
Fresh Tissue: 150 mg or 0.5-2.0 cm3 fresh tissue in transport media. Delivery within 24 hours at room temperature.
Fresh Frozen Tissue: 150 mg or 0.5-2.0 cm3 tissue snap frozen at -20°C. Store at -20°C. Ship on minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
Formalin-fixed, paraffin embedded (FFPE) tissue: a minimum of freshly cut 6 20-um scrolls or 10 slides can be shipped overnight to the laboratory. It would be best to cut and ship Wednesday to arrive on Thursday. The laboratory may reach out if additional material is required in case of extraction failure. Please note: unlike the other specimens in which isolated RNA is extracted, only Total Nucleic Acid (DNA and RNA) is extracted from FFPE tissue.
For Normal/Unaffected Specimens:
Blood: 3-5 ml whole blood in an EDTA (lavender top) tube
Fresh tissue, such as a skin biopsy, is also acceptable as a germline specimen.
Specimen Preparation
See "Collect" section above.
Storage/Transport Temperature
See "Collect" section above.
Volume Required
See "Collect" section above.
Minimum Required
See "Collect" section above.
Phlebotomy Draw
No
Ordering
Performing Lab
Division of Genomic Diagnostics
Performed
Monday-Friday 9:00am - 4:00pm
Reported
21 days.
Detection Rate
The Paired Tumor/Normal - Comprehensive Solid Tumor Panel includes the V2.1 Solid Tumor Panel for sequence and copy number analyses of 237 cancer genes and two genes associated with cancer pharmacogenomics in paired tumor and normal samples, and V3 Fusion Panel which targets over 700 exons of 117 cancer genes in tumor sample only.
Utility
Facilitates disease diagnosis, risk stratification, and therapeutic decision-making.
Synonyms
COMPC
Solid Tumor, Fusion panel, Tumor / Normal Paired Test, T/ N, T/N, Comprehensive
Next generation sequencing (NGS) and data analysis: Nucleic acid is extracted from the patient’s samples following standard DNA and RNA extraction protocols. Extracted DNA is fragmented and tagged using SureSelect QXT target enrichment to generate adapter-tagged libraries. Biotin-labeled probes specific to the targeted regions are used for capture hybridization. Libraries are enriched for the desired regions using streptavidin beads. Enriched libraries are then indexed and pooled for sequencing. Libraries are subject to sequence analysis on Illumina NovaSeq 6000 system for 150 bp paired end reads. All coding exons and the flanking intron sequences of targeted genes in the panel are sequenced, and selected promoter regions and known intronic variants are also evaluated. Sequence data are analyzed using the home brew software ConcordS V4.0.0 and NextGENe V2 NGS Analysis Software. Sequence variants within exons and 5 bp flanking intron sequences are annotated. Copy number variation (CNV) analysis for gross deletions and duplications are evaluated using NGS data. For the tumor sample only, RNA sequencing libraries are prepared using Archer Universal RNA Reagent Kit with CHOP fusion panel custom-designed primers with target specific molecular barcode. Sequencing data are analyzed using ArcherTM Analysis for fusion genes. Clinically significant variants including single nucleotide variants (SNVs), indels, CNVs and fusion genes are confirmed by Sanger sequencing, MLPA, Real-Time PCR, or ddPCR only when necessary.
