Isocitrate Dehydrogenase 2KRAS NGS: KRAS Proto-Oncogene, GTPaseLung Cancer Mutation Panel: AmpliSeq Cancer Hot Spot Panel
Next Generation Sequencing, Lung Cancer Panel NGSMicrosatellite Instability: Mismatch Repair Defect
MSIThyroid Cancer Mutation Panel: AmpliSeq Cancer Hot Spot Panel
Next Generation Sequencing, Thyroid Cancer Panel NGS
Test Includes
BRAF NGS - This is part of the Ion AmpliSeq Cancer Hot Spot Panel; the most common BRAF mutation is the V600E change in exon 15
Colorectal Cancer Mutation Panel - This assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants in five colorectal cancer-related genes (BRAF, KRAS, NRAS, PIK3CA, AKT1)
EGFR Gene Mutation Detection - EGFR can be tested by Ion Ampliseq Cancer Hot spot panel or Idylla EGFR Mutation Assay
IDH1 Mutation Detection - Identification of codon 132 mutations only in the IDH1 gene
IDH2 Mutation Detection - Identification of codon 172 mutations only in the IDH2 gene
KRAS NGS - This is part of the Ion AmpliSeq Cancer Hot Spot Panel
Lung Cancer Mutation Panel - This assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants in six lung cancer-related genes (EGFR, KRAS, BRAF, NRAS, PIK3CA, ERBB2)
Thyroid Cancer Mutation Panel - This assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants in ten thyroid cancer-related genes (BRAF, HRAS, KRAS, NRAS, AKT1, CTNNB1, PTEN, TP53, RET, and PIK3CA)
Performing Laboratory / Facility
UCLA Medical Center Clinical Laboratory (CHS)
Performing Section
Molecular Pathology
Availability
Monday through Friday, 0700-1700
Turnaround Time
14 days from receipt of specimen in performing lab
Methodology
BRAF NGS - For all solid tumor test by NGS: Ampliseq assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants
EGFR Gene Mutation Detection - Idylla Assay is a fully automated real- time PCR assay using a cartridge -based design for the detection of 51 somatic mutations in exon 18-21 of the human EGFR oncogene
Use
EGFR Gene Mutation Detection - A subset of NSCLC patients have point mutations, deletions, and insertions in the EGFR gene which allow them to respond to certain treatments (anti-EGFR tyrosine kinase inhibitors such as Erlotinib), resulting in a more favorable prognosis. However, other mutations (predominantly T790M) in the EGFR gene can result in resistance to anti-EGFR therapy. Thus, this test may be used, in conjunction with clinical and other laboratory findings, as an aid in selection of drug therapy
Limitations
BRAF NGS - This test has been validated by the UCLA Molecular Diagnostics Laboratories. The assay can detect approximately 5% to 10% of mutant in a background of wild-type genomic DNA. Preparation of DNA from tissue samples is dependent on the quality of the specimen provided. A negative (no mutation detected) result does not preclude the presence of such a mutation since results depend on, among other factors, mutant allele frequency, specimen integrity, absence of inhibitors and/or interfering polymorphisms, and availability of sufficient DNA for detection. Only variants that are known to be present in the Catalogue of Somatic Mutations in Cancer (COSMIC) database will be reported. Variants not included in the five targeted genes listed above will not be reported.
Specimen Type
Formalin-fixed paraffin-embedded (FFPE) slides
Container
Unstained slides
Volume
10 unstained slides from paraffin block in 5 µm (5-micrometer) sections or formalin-fixed paraffin-embedded tissue block containing >=20% tumor. Either option needs to be accompanied by an H&E reference slide.
Microsatellite Instability (MSI) requires 10 unstained and 1 H&E slides for the tumor tissue and 10 unstained and 1 H&E from the normal tissue.
Isocitrate Dehydrogenase 2KRAS NGS: KRAS Proto-Oncogene, GTPaseLung Cancer Mutation Panel: AmpliSeq Cancer Hot Spot Panel
Next Generation Sequencing, Lung Cancer Panel NGSMicrosatellite Instability: Mismatch Repair Defect
MSIThyroid Cancer Mutation Panel: AmpliSeq Cancer Hot Spot Panel
Next Generation Sequencing, Thyroid Cancer Panel NGS
Test Includes
BRAF NGS - This is part of the Ion AmpliSeq Cancer Hot Spot Panel; the most common BRAF mutation is the V600E change in exon 15
Colorectal Cancer Mutation Panel - This assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants in five colorectal cancer-related genes (BRAF, KRAS, NRAS, PIK3CA, AKT1)
EGFR Gene Mutation Detection - EGFR can be tested by Ion Ampliseq Cancer Hot spot panel or Idylla EGFR Mutation Assay
IDH1 Mutation Detection - Identification of codon 132 mutations only in the IDH1 gene
IDH2 Mutation Detection - Identification of codon 172 mutations only in the IDH2 gene
KRAS NGS - This is part of the Ion AmpliSeq Cancer Hot Spot Panel
Lung Cancer Mutation Panel - This assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants in six lung cancer-related genes (EGFR, KRAS, BRAF, NRAS, PIK3CA, ERBB2)
Thyroid Cancer Mutation Panel - This assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants in ten thyroid cancer-related genes (BRAF, HRAS, KRAS, NRAS, AKT1, CTNNB1, PTEN, TP53, RET, and PIK3CA)
Performing Laboratory / Facility
UCLA Medical Center Clinical Laboratory (CHS)
Performing Section
Molecular Pathology
Availability
Monday through Friday, 0700-1700
Turnaround Time
14 days from receipt of specimen in performing lab
Methodology
BRAF NGS - For all solid tumor test by NGS: Ampliseq assay utilizes Ion Torrent high throughput targeted sequencing technology to test for a panel of actionable oncogenic variants
EGFR Gene Mutation Detection - Idylla Assay is a fully automated real- time PCR assay using a cartridge -based design for the detection of 51 somatic mutations in exon 18-21 of the human EGFR oncogene
Use
EGFR Gene Mutation Detection - A subset of NSCLC patients have point mutations, deletions, and insertions in the EGFR gene which allow them to respond to certain treatments (anti-EGFR tyrosine kinase inhibitors such as Erlotinib), resulting in a more favorable prognosis. However, other mutations (predominantly T790M) in the EGFR gene can result in resistance to anti-EGFR therapy. Thus, this test may be used, in conjunction with clinical and other laboratory findings, as an aid in selection of drug therapy
Limitations
BRAF NGS - This test has been validated by the UCLA Molecular Diagnostics Laboratories. The assay can detect approximately 5% to 10% of mutant in a background of wild-type genomic DNA. Preparation of DNA from tissue samples is dependent on the quality of the specimen provided. A negative (no mutation detected) result does not preclude the presence of such a mutation since results depend on, among other factors, mutant allele frequency, specimen integrity, absence of inhibitors and/or interfering polymorphisms, and availability of sufficient DNA for detection. Only variants that are known to be present in the Catalogue of Somatic Mutations in Cancer (COSMIC) database will be reported. Variants not included in the five targeted genes listed above will not be reported.
Specimen Collection and Handling
Specimen Type
Formalin-fixed paraffin-embedded (FFPE) slides
Container
Unstained slides
Volume
10 unstained slides from paraffin block in 5 µm (5-micrometer) sections or formalin-fixed paraffin-embedded tissue block containing >=20% tumor. Either option needs to be accompanied by an H&E reference slide.
Microsatellite Instability (MSI) requires 10 unstained and 1 H&E slides for the tumor tissue and 10 unstained and 1 H&E from the normal tissue.
