Must submit both tumor cells (typically bone marrow or leukemic blood specimen) and a normal specimen via the Normal specimen for Paired Tumor / Normal – Hematologic Cancer Panels’ order available in relevant Epic Order Sets and on the test requisition form.
Tumor specimen:
Bone marrow or leukemic blood sample in an EDTA (purple-top) tube. Fresh, frozen, or FFPE tumor tissue is also acceptable. FFPE preferred sample: minimum six 20-um scrolls or 10 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.
Normal specimen:
The typically submitted ‘normal specimen’ in this scenario is a skin biopsy. For fresh tissue specimens such as skin, collect 150 mg or 0.5-2.0 cm3 fresh tissue in transport media and deliver within 24 hours at room temperature.
Performing Lab
Division of Genomic Diagnostics
Reported
21 days
Detection Rate
The Paired Tumor/Normal - Comprehensive Hematologic Cancer Panel includes the V2.3 Hematologic Cancer Panel for sequence and copy number analyses of 117 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.
Next generation sequencing (NGS) and data analysis: Nucleic acid is extracted from the patient’s sample 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 cells (typically bone marrow or leukemic blood specimen) and a normal specimen via the Normal specimen for Paired Tumor / Normal – Hematologic Cancer Panels’ order available in relevant Epic Order Sets and on the test requisition form.
Tumor specimen:
Bone marrow or leukemic blood sample in an EDTA (purple-top) tube. Fresh, frozen, or FFPE tumor tissue is also acceptable. FFPE preferred sample: minimum six 20-um scrolls or 10 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.
Normal specimen:
The typically submitted ‘normal specimen’ in this scenario is a skin biopsy. For fresh tissue specimens such as skin, collect 150 mg or 0.5-2.0 cm3 fresh tissue in transport media and deliver within 24 hours at room temperature.
Ordering
Performing Lab
Division of Genomic Diagnostics
Reported
21 days
Detection Rate
The Paired Tumor/Normal - Comprehensive Hematologic Cancer Panel includes the V2.3 Hematologic Cancer Panel for sequence and copy number analyses of 117 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.
Next generation sequencing (NGS) and data analysis: Nucleic acid is extracted from the patient’s sample 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.
