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.
FFPE preferred sample: minimum three 20-um scrolls or 5 slides that are freshly cut before shipping to us via overnight delivery. It would be best to cut and ship Wednesday to arrive on Thursday. Alternatively, a whole FFPE block can be sent.
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.
Unacceptable Conditions
Unacceptable conditions include no tumor in tissue or specimens fixed/processed in alternative fixatives.
Storage/Transport Temperature
See "Collect" section above.
Volume Required
See "Collect" section above.
Minimum Required
See "Collect" section above or call the lab.
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 - 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.
Utility
Facilitates disease diagnosis, risk stratification, and therapeutic decision-making.
Next generation sequencing (NGS) and data analysis: Genomic DNA is extracted from the patient’s samples following standard DNA 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. Clinically significant variants including single nucleotide variants (SNVs), indels, and CNVs 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.
FFPE preferred sample: minimum three 20-um scrolls or 5 slides that are freshly cut before shipping to us via overnight delivery. It would be best to cut and ship Wednesday to arrive on Thursday. Alternatively, a whole FFPE block can be sent.
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.
Unacceptable Conditions
Unacceptable conditions include no tumor in tissue or specimens fixed/processed in alternative fixatives.
Storage/Transport Temperature
See "Collect" section above.
Volume Required
See "Collect" section above.
Minimum Required
See "Collect" section above or call the lab.
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 - 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.
Utility
Facilitates disease diagnosis, risk stratification, and therapeutic decision-making.
Next generation sequencing (NGS) and data analysis: Genomic DNA is extracted from the patient’s samples following standard DNA 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. Clinically significant variants including single nucleotide variants (SNVs), indels, and CNVs are confirmed by Sanger sequencing, MLPA, Real-Time PCR, or ddPCR only when necessary.
