Please see a list of acceptable specimens below. Any specimen submitted should be accompanied by a pathology report. Also, please indicate the percentage of the specimen estimated to be tumor tissue.
Bone marrow or Leukemic Blood: 3-5 ml in an EDTA (purple-top) tube.
Fresh Tumor Tissue: 150 mg or 0.5-2.0 cm3 fresh tissue in transport media. Deliver the specimen at room temperature within 24 hours.
Frozen Tumor Tissue: 150 mg or 0.5-2.0 cm3 tissue snap frozen in liquid nitrogen. Store at -80°C and prevent thawing. Ship the specimen on a minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
Formalin-Fixed, Paraffin-Embedded (FFPE) Tumor Slides or Block: preferred sample is a block of five 20-um scrolls 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.
RNA extracted in a CLIA/CAP certified laboratory: 200 ng
Unacceptable Conditions
Unacceptable conditions include specimens lacking tumor tissue and/or specimens fixed/processed in alternative fixatives.
Storage/Transport Temperature
See "Collect" section.
Minimum Required
See "Collect" section.
Phlebotomy Draw
Phlebotomy draw is only for blood specimens.
Performing Lab
Divison of Genomic Diagnostics
Performed
Monday through Friday 9:00am - 4:00pm
Reported
21 days
Detection Rate
The CHOP Cancer Transcriptome Analysis (RNA Sequencing) test is designed to detect gene fusions in tumor specimens by screening for abundant and abnormal RNA sequences in tumor tissue.
Utility
This test is not intended as a first tier analysis and should only be considered after completion of the Cancer Gene-Fusion panel. The Cancer Gene-Fusion Panel is the first tier test as it specifically targets fusion gene partners known to be associated with cancer to facilitate disease diagnosis, risk stratification, and therapeutic decisions https://www.testmenu.com/chop/Tests/785504.
Synonyms
Cancer Transcriptome Analysis, RNA Sequencing, RNASeq
RNASQ
LIS Mnemonic
RNASQ
Available STAT
Yes
Test Notes
Next generation sequencing (NGS) and data analysis: Total RNA is extracted from the patient's sample following standard RNA extraction protocols. Extracted RNA is fragmented and transcribed into cDNA using random priming using the Illumina TruSeq RNA Exome kit. Index adapters are then ligated to double stranded cDNA fragments. The coding regions of the transcriptome are captured with specific probes. Libraries are then enriched and pooled for sequencing on Illumina NovaSeq 6000 system using 100bp paired-end reads. Mapping and analysis were based on the GRCh37 reference sequence. Sequence data are analyzed using the home brewed software ConcordR V1.0.0 NGS Analysis Pipeline. Cancer gene fusions data are analyzed using IGV and Alamut. Clinically significant fusion genes are confirmed by Sanger sequencing, Real-Time PCR, or other methodologies when necessary.
Molecular Testing Notes
This is the first version of this test. The current test is not a comprehensive transcriptome, only fusion results are reported. Expression of the transcriptome is variable by sample/tissue and not all genes are expressed in a given sample. For gene specific expression information, please contact the laboratory by emailing DGDGeneticCounselor@email.chop.edu. Fusions with a low level of expression may not be detected by this technology. This assay is at risk of false negatives when tumor cells are less than 30% of total cellularity. In rare situations some fusions may not be detectable by this test due to local sequence characteristics. This test is not designed to detect minimal residual diseases (MRD).
CPT Codes
81456
Collection
Collect
Please see a list of acceptable specimens below. Any specimen submitted should be accompanied by a pathology report. Also, please indicate the percentage of the specimen estimated to be tumor tissue.
Bone marrow or Leukemic Blood: 3-5 ml in an EDTA (purple-top) tube.
Fresh Tumor Tissue: 150 mg or 0.5-2.0 cm3 fresh tissue in transport media. Deliver the specimen at room temperature within 24 hours.
Frozen Tumor Tissue: 150 mg or 0.5-2.0 cm3 tissue snap frozen in liquid nitrogen. Store at -80°C and prevent thawing. Ship the specimen on a minimum of 10 lbs. of dry ice in an insulated container by overnight courier.
Formalin-Fixed, Paraffin-Embedded (FFPE) Tumor Slides or Block: preferred sample is a block of five 20-um scrolls 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.
RNA extracted in a CLIA/CAP certified laboratory: 200 ng
Unacceptable Conditions
Unacceptable conditions include specimens lacking tumor tissue and/or specimens fixed/processed in alternative fixatives.
Storage/Transport Temperature
See "Collect" section.
Minimum Required
See "Collect" section.
Phlebotomy Draw
Phlebotomy draw is only for blood specimens.
Ordering
Performing Lab
Divison of Genomic Diagnostics
Performed
Monday through Friday 9:00am - 4:00pm
Reported
21 days
Detection Rate
The CHOP Cancer Transcriptome Analysis (RNA Sequencing) test is designed to detect gene fusions in tumor specimens by screening for abundant and abnormal RNA sequences in tumor tissue.
Utility
This test is not intended as a first tier analysis and should only be considered after completion of the Cancer Gene-Fusion panel. The Cancer Gene-Fusion Panel is the first tier test as it specifically targets fusion gene partners known to be associated with cancer to facilitate disease diagnosis, risk stratification, and therapeutic decisions https://www.testmenu.com/chop/Tests/785504.
Synonyms
Cancer Transcriptome Analysis, RNA Sequencing, RNASeq
RNASQ
LIS Mnemonic
RNASQ
Available STAT
Yes
Test Notes
Next generation sequencing (NGS) and data analysis: Total RNA is extracted from the patient's sample following standard RNA extraction protocols. Extracted RNA is fragmented and transcribed into cDNA using random priming using the Illumina TruSeq RNA Exome kit. Index adapters are then ligated to double stranded cDNA fragments. The coding regions of the transcriptome are captured with specific probes. Libraries are then enriched and pooled for sequencing on Illumina NovaSeq 6000 system using 100bp paired-end reads. Mapping and analysis were based on the GRCh37 reference sequence. Sequence data are analyzed using the home brewed software ConcordR V1.0.0 NGS Analysis Pipeline. Cancer gene fusions data are analyzed using IGV and Alamut. Clinically significant fusion genes are confirmed by Sanger sequencing, Real-Time PCR, or other methodologies when necessary.
Molecular Testing Notes
This is the first version of this test. The current test is not a comprehensive transcriptome, only fusion results are reported. Expression of the transcriptome is variable by sample/tissue and not all genes are expressed in a given sample. For gene specific expression information, please contact the laboratory by emailing DGDGeneticCounselor@email.chop.edu. Fusions with a low level of expression may not be detected by this technology. This assay is at risk of false negatives when tumor cells are less than 30% of total cellularity. In rare situations some fusions may not be detectable by this test due to local sequence characteristics. This test is not designed to detect minimal residual diseases (MRD).
