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Test Code EGFRW EGFR Targeted Mutation Analysis with ALK Reflex, Tumor


Specimen Required


Pathology report must accompany specimen for testing to be performed.

 

Preferred:

Specimen Type: Tissue

Container/Tube: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block.

 

Acceptable:

Specimen Type: Tissue

Container/Tube: Slides

Specimen Volume: 12 unstained, positively charged, unbaked slides or 2 hematoxylin and eosin-stained slides (will not be returned) and 10 unstained, positively charged, unbaked slides

Collection Instructions: Submit 12 unstained, positively charged, unbaked slides cut at 5-microns or 2 hematoxylin and eosin-stained slides and 10 unstained, positively charged, unbaked slides with 5-micron thick sections of the tumor tissue.


Useful For

Identifying non-small cell lung cancers that may benefit from treatment with epidermal growth factor receptor -targeted therapies or anaplastic lymphoma kinase inhibitors

Additional Tests

Test ID Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
LCAF ALK (2p23), Lung Cancer, FISH, Ts Yes No

Testing Algorithm

When this test is ordered, the EGFR Gene, Mutation Analysis, 51 Mutation Panel, Tumor will always be performed. All specimens without an EGFR mutation will be automatically reflexed to testing for the ALK (2p23) rearrangement. Specimens with an identified EGFR mutation will result in cancellation of the LCAF test.

 

When this test is ordered, slide review will always be performed at an additional charge.

Method Name

Polymerase Chain Reaction (PCR)

Reporting Name

EGFR with ALK Reflex, Tumor

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Reject Due To

Specimens that have been decalcified (all methods)
Low tumor percentage
Insufficient amount of tumor
Specimens that have not been formalin-fixed, paraffin-embedded
Reject

Clinical Information

Targeted cancer therapies are defined as antibody or small molecule drugs that block the growth and spread of cancer by interfering with specific cell molecules involved in tumor growth and progression. Multiple targeted therapies have been approved by the FDA for treatment of specific cancers. Molecular genetic profiling is often needed to identify targets amenable to targeted therapies and to minimize treatment costs and therapy-associated risks. Epidermal growth factor receptor (EGFR) protein is activated by the binding of specific ligands, resulting in activation of the RAS/MAPK pathway. Activation of this pathway induces a signaling cascade, ultimately leading to cell proliferation. Dysregulation of the RAS/MAPK pathway is a key factor in tumor progression for many solid tumors. Targeted therapies directed to tumors harboring activating mutations within the EGFR tyrosine kinase domain (exons 18-21) have demonstrated some success in treating a subset of patients with non-small cell lung cancer (NSCLC). As a result, the mutation status of EGFR can be a useful marker by which patients are selected for EGFR-targeted therapy.

 

Rearrangements of the anaplastic lymphoma kinase (ALK) locus are found in a subset of lung carcinomas (generally EGFR wildtype tumors) and their identification by fluorescence in situ hybridization (FISH) may guide important therapeutic decisions for the management of these tumors. The fusion of the echinoderm microtubule-associated protein-like 4 (EML4) gene with the ALK gene results from an inversion of chromosome band 2p23. The ALK-EML4 rearrangement has been identified in 3% to 5% of NSCLC with the majority occurring in adenocarcinoma and younger male patients who were light or nonsmokers. Recent studies have demonstrated that lung cancers harboring ALK rearrangements are resistant to EGFR tyrosine kinase inhibitors but may be highly sensitive to ALK inhibitors, like crizotinib (Xalkori). The drug crizotinib works by blocking certain kinases, including those produced by the abnormal ALK gene. Clinical studies have demonstrated that crizotinib treatment of patients with tumors exhibiting ALK rearrangements can halt tumor progression or result in tumor regression. The ALK/EML4 FISH assay is an FDA-approved companion diagnostic test for crizotinib, which was recently approved by the FDA to treat certain patients with late-stage (locally advanced or metastatic), non-small cell lung cancers that harbor ALK gene rearrangements. It is useful for the identification of patients with lung cancer who will benefit from crizotinib therapy.

Reference Values

An interpretive report will be provided.

Interpretation

An interpretive report will be provided.

Cautions

A negative (wildtype) EGFR result does not rule out the presence of a mutation that may be present but is below the limits of detection for this assay (approximately 10%).

 

A negative (wildtype) EGFR result does not rule out the presence of other activating mutations in the EGFR

gene.

 

Rare polymorphisms exist that could lead to false-negative or false-positive EGFR results.

 

The ALK fluorescence in situ hybridization (FISH) test is intended to be used for therapeutic purposes in pulmonary carcinoma. This FISH assay does not rule out other chromosome abnormalities.

 

While results of these tests may indicate the likely response to EGFR-targeted therapies or  anaplastic lymphoma kinase (ALK)-inhibitor therapies, selection of treatment remains a clinical decision.

Method Description

All ordered specimens will undergo EGFR testing. The EGFR test is a qualitative polymerase chain reaction (PCR)-based assay employing fluorescently labeled probes that are used to detect exon 18 (G719A/C/S), exon 21 (L858R,

L861Q), exon 20 (T790M, S768I) mutations, exon 19 deletions and exon 20 insertions of the EGFR gene.

 

Exon

Mutation

Protein change

Nucleotide change

Genotyp

18

G719A

p.Gly719Ala

c.2156G>C

G719A/C/S

G719C

p.Gly719Cys

c.2155G>T

G719C

p.Gly719Cys(2)

c.2154_2155delinsTT

G719S

p.Gly719Ser

c.2155G>A

19

Deletion 9

p.Leu747_Ala750delinsPro

c.2238_2248delinsGC

Exon 19 deletion

c.2239_2248delinsC

p.Leu747_Ala750delinsSer

c.2240_2248del

p.Leu747_Glu749del

c.2239_2247del

Deletion 12

p.Leu747_Thr751delinsPro

c.2239_2251delinsC

p.Leu747_Thr751delinsSer

c.2240_2251del

Deletion 15

p.Glu746_Ala750del

c.2235_2249del

c.2236_2250del

p.Leu747_Thr751del

c.2239_2253del

c.2240_2254del

c.2238_2252del

p.Glu746_Thr751delinsAla

c.2237_2251del

p.Glu746_Thr751delinsIle

c.2235_2252delinsAAT

p.Glu746_Thr751delinsVal

c.2237_2252delinsT

p.Lys745_Ala750delinsThr

c.2234_2248del

p.Glu746_Thr751delinsLeu

c.2236_2253delinsCTA

p.Glu746_Thr751delinsVal

c.2237_2253delinsTA

p.Glu746_Thr751delinsAla

c.2235_2251delinsAG

p.Glu746_Thr751delinsGln

c.2236_2253delinsCAA

p.Ile744_Ala750delinsValLys

c.2230_2249delinsGTCAA

Deletion 18

p.Leu747_Pro753delinsSer

c.2240_2257del

p.Glu746_Ser752delinsVal

c.2237_2255delinsT

p.Leu747_Ser752del

c.2239_2256del

p.Glu746_Thr751del

c.2236_2253del

p.Leu747_Pro753delinsGln

c.2239_2258delinsCA

p.Glu746_Ser752delinsAla

c.2237_2254del

p.Glu746_Ser752delinsAsp

c.2238_2255del

p.Glu746_Pro753delinsValSer

c.2237_2257delinsTCT

p.Glu746_Ser752delinsIle

c.2236_2255delinsAT

c.2236_2256delinsATC

p.Glu746_Ser752delinsVal

c.2237_2256delinsTT

c.2237_2256delinsTC

c.2235_2255delinsGGT

p.Leu747_Pro753del

c.2238_2258del

p.Glu746_Ser752del

c.2236_2256del

p.Ser752_Ile759del

c.2253_2276del

p.Thr790Met

c.2369C>T

p.Ser768Ile

c.2303G>T

p.Asp770_Asn771insGly

c.2310_2311insGGT

p.Val769_Asp770insAlaSerVal

c.2307_2308insGCCAGCGTG

p.Val769_Asp770insAlaSerVal

c.2309_2310delinsCCAGCGTGGAT

p.Asp770_Asn771insSerValAsp

c.2311_2312insGCGTGGACA

p.His773_Val774insHis

c.2319_2320insCAC

p.Leu858Arg

c.2573T>G

c.2573_2574delinsGT

c.2573_2574delinsGA

p.Leu861Gln

c.2582T>A

 

 

A pathology review and macrodissection to enrich for tumor cells is performed prior to slide scraping.

 

The ALK fluorescence in situ hybridization (FISH) test uses an FDA-approved ALK dual-color, break-apart rearrangement probe kitset. The ALK probe consists of 2 probes that flank the ALK gene region at 2p23 (Abbott Molecular). Five-micron sections of formalin-fixed, paraffin-embedded tissue specimens are cut and mounted on positively-charged glass slides. The selection of tissue and the identification of target areas on the hematoxylin and eosin-stained slide are performed by a pathologist. The probe set is hybridized to the appropriate target areas and 2 technologists analyze 25 interphase nuclei each (50 total). Results are reported based on the guidelines include with the probe kit and package insert with the results expressed as the percent abnormal nuclei.(Unpublished Mayo method)

Day(s) Performed

Monday through Friday

Report Available

5 to 14 days

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

81235-EGFR (epidermal growth factor receptor) (eg, non-small cell lung cancer) gene analysis, common variants(eg, exon 19 deletions, L858R, T790M, G719S, L861Q)

88381-Microdissection, manual

88271 x 2-DNA Probe (if appropriate)

88274-Interphase in situ hybridization (if appropriate)

88291-Interpretation and report (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
EGFRW EGFR with ALK Reflex, Tumor 21665-5

 

Result ID Test Result Name Result LOINC Value
616130 Result Summary 50397-9
616131 Result 21665-5
616132 Interpretation 69047-9
616133 Specimen 31208-2
616134 Source 31208-2
616135 Tissue ID 80398-1
616136 Released By 18771-6

Disease States

  • Non-small cell lung cancer

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.