EGFR Sequencing Test
The LMM performs bi-directional sequence analysis of the kinase domain of the EGFR gene as a clinical test to help predict tumor response to tyrosine kinase inhibitors.
The LMM has the limited right to offer EGFR mutation testing solely to patients of Massachusetts General Hospital (MGH), Dana-Farber Cancer Institute (DFCI) and Brigham and Women's Hospital (BWH).
Genzyme Corporation is the exclusive provider of EGFR mutation testing for all other institutions.
EGFR GENE SEQUENCING TEST
Gene: EGFR at 7p12.3-p12.1
Methodology: Bi-directional DNA sequencing of 7 exons (18-24)
and splice sites
Clinical Sensitivity: Variable
Turn-Around-Time: 2 weeks for clients within the Partners
Healthcare system.
Sample Requirements:
- Tissue block (formalin-fixed, paraffin-embedded) OR
13-15 paraffin-embedded tissue slides and
one hematoxylin-eosin stained reference slide
- 7 ml blood sample collected in a lavender top (K3EDTA) blood tube
- Copy of the original pathology report
Cost: $850
How to order test | Resources | Clinical Services
Background
The epidermal growth factor receptor gene, EGFR, encodes a receptor tyrosine kinase,
and is the target of tyrosine kinase inhibitors (TKIs). In three separate studies,
somatic mutations in the kinase domain of EGFR were found in 25/31 (81%) individuals
with non-small cell lung cancer (NSCLC) responsive to TKIs, while no mutations were found
in 29/29 (100%) individuals with NSCLC that did not respond to
TKIs[1], [2], [3]
The LMM offers sequencing of the kinase domain of EGFR to identify patients that may
respond to TKIs. Somatic mutations found in the kinase domain of tumor tissue are likely to
be associated with altered protein function and therefore with TKI-responsiveness. However,
the likelihood of TKI-responsiveness cannot precisely be determined for variants that have
not been previously reported in a TKI-responder.
DNA is prepared from either frozen or paraffin-embedded tissue and exons 18 through 21 of
EGFR are amplified by nested PCR reactions. The second round PCR products are sequenced
bi-directionally to identify mutations. Any variants found are confirmed by repeating
sequencing of the tumor sample and when appropriate, a blood sample from the patient.
Variants found in tumor samples that have already been described in other patient samples
and/or not found in the corresponding blood samples represent somatic alterations in the
tumor tissue.
EGFR sequencing by the LMM must be accompanied by pathology consultations performed by
either Brigham and Women's Hospital or Massachusetts General Hospital; contact the
laboratory for more details.
Methodology Bi-directional sequence analysis is performed on 4 exons and splice sites
encoding the tyrosine kinase domain of EGFR. This test does not detect deletions
encompassing entire exons of the gene.
·
Four exons of the EGFR kinase domain, exons 18-21, are amplified in 2 rounds of PCR using nested primers.
·
Direct DNA sequencing is performed on the products of the second round PCR.
Sample requirements
EGFR analysis is most appropriate for individuals with adenocarcinoma of the lung. Tissue that can be used includes primary tumor, metastases, or cell block of pleural fluid.
Viable tumor must be present.
Please send:
1. Tissue block (formalin-fixed, paraffin-embedded), which will be returned upon request.
If originating hospital policy prevents send-out of tissue blocks, please send 13-15
paraffin-embedded tissue slides and one hematoxylin-eosin stained reference slide
Note: If tissue has been saved frozen, this tissue should be saved for one month. If technical problems develop with the fixed tissue analysis, the frozen tissue may be requested. Do not send frozen tissue without prior approval.
2. Include a copy of the original pathology report.
3. All pathology specimens should be accompanied by a blood specimen. The preferred blood specimen
is a 7 ml blood sample collected in a lavender top (K3EDTA) blood tube. Smaller blood samples may
be acceptable. Saliva samples
may also be acceptable. Please contact the lab for more information
and/or to request a saliva collection kit.
4. All samples should be accompanied by a requisition form
Epidemiology:
·
Approximately 10-20% of NSCLCs tested have been found to respond to TKIs.
·
EGFR kinase domain mutations have been found in approximately 13% of NSCLCs tested.
Test Indications
·
Non-small cell lung cancer
Test Outcomes
·
The detection of a somatic mutation previously reported in a TKI-responder predicts likely responsiveness to TKIs.
·
The detection of a somatic mutation not previously reported in a TKI-responder is likely associated with altered EGFR function, but the likelihood of TKI-responsiveness cannot be precisely determined.
Turn-Around-Time: 2 weeks for clients within the Partners Healthcare system.
Analytical Sensitivity: This assay has greater than 99.9% accuracy to detect mutations in the sequence analyzed.
Clinical Sensitivity: Preparation of DNA from tissue samples is dependent upon the quality and quantity of the initial tissue sample. Inadequate DNA extraction may occur for up to 25% of paraffin-embedded samples. Tumor samples can be a mix of cell types. The composition of the tumor cannot be determined until a pathological analysis is performed. A minimum of 50% tumor cells is required to ensure the accuracy of the EGFR sequencing assay.
Price and CPT codes:
EGFR Sequencing (exons 18 - 21)
- Price: $850 (including pathology services)
- CPT codes: 83891(1), 83898(8), 83894(1), 83904(8), 83909(1), 83912(1)
If you have any questions, please call the Laboratory for Molecular Medicine at 617-768-8500, or email us at lmm@partners.org
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