MayoComplete Lung Cancer Panel - Clinical Genetic Test - GTR

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MayoComplete Lung Cancer Panel

Clinical Genetic Test

offered by

Mayo Clinic Laboratories

View lab's test page

GTR Test Accession: GTR000613224.1

INHERITED DISEASERESPIRATORY DISEASECANCER ... View more

Registered in GTR: 2024-05-01

Last annual review date for the lab: 2024-05-28

At a Glance

Test purpose:

Diagnosis; Therapeutic management

Conditions (1):

Lung cancer

Genes (15):

ALK (2p23.2-23.1); BRAF (7q34); EGFR (7p11.2); ERBB2 (17q12); HRAS (11p15.5) more...

Methods (2):

Molecular Genetics - RNA analysis: RT-qPCR; ...

Target population:

Diagnosis and management of patients with lung cancer. Assessing microsatellite …

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Mayo Clinic Laboratories
View lab's website
View lab's test page

Test short name:

MCLNG

Specimen Source:

tissue slides and cytology slides
Paraffin block
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Dentist
Licensed Physician
Nurse Practitioner
Physician Assistant
Public Health Mandate
Registered Nurse

Test Order Code:

MCLNG
View other test codes

LOINC codes:

**LOINC codes notice

CPT codes:

81457
88381

**AMA CPT codes notice

Lab contact:

Samantha Wiley, CGC, Certified Genetic counselor, CGC, Genetic Counselor
wiley.samantha@mayo.edu

Contact Policy:

Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.

How to Order:

https://www.mayocliniclabs.com/test-catalog/overview/616486#Specimen
Order URL

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Based on applicable state law

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test strategy

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 15

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 2

Method Category

Test method

Instrument *

RNA analysis

RT-qPCR

Sequence analysis of the entire coding region

Next-Generation (NGS)/Massively parallel sequencing (MPS)

* Instrument: Not provided

Clinical Information

Test purpose:

Diagnosis; Therapeutic management

Target population:

Diagnosis and management of patients with lung cancer. Assessing microsatellite instability.

View citations (17)

Eberhard DA, Johnson BE, Amler LC, Goddard AD, Heldens SL, Herbst RS, Ince WL, Jänne PA, Januario T, Johnson DH, Klein P, Miller VA, Ostland MA, Ramies DA, Sebisanovic D, Stinson JA, Zhang YR, Seshagiri S, Hillan KJ. Mutations in the epidermal growth factor receptor and in KRAS are predictive and prognostic indicators in patients with non-small-cell lung cancer treated with chemotherapy alone and in combination with erlotinib. J Clin Oncol. 2005;23(25):5900-9. doi:10.1200/JCO.2005.02.857. Epub 2005 Jul 25. PMID: 16043828.
Somatic mutations of epidermal growth factor receptor signaling pathway in lung cancers. Shigematsu H, et al. Int J Cancer. 2006;118(2):257-62. doi:10.1002/ijc.21496. PMID: 16231326.
Epidermal growth factor receptor mutations in lung cancer. Sharma SV, et al. Nat Rev Cancer. 2007;7(3):169-81. doi:10.1038/nrc2088. PMID: 17318210.
Mok TS. Personalized medicine in lung cancer: what we need to know. Nat Rev Clin Oncol. 2011;8(11):661-8. doi:10.1038/nrclinonc.2011.126. Epub 2011 Aug 23. PMID: 21862980.
Gao G, Ren S, Li A, Xu J, Xu Q, Su C, Guo J, Deng Q, Zhou C. Epidermal growth factor receptor-tyrosine kinase inhibitor therapy is effective as first-line treatment of advanced non-small-cell lung cancer with mutated EGFR: A meta-analysis from six phase III randomized controlled trials. Int J Cancer. 2012;131(5):E822-9. doi:10.1002/ijc.27396. Epub 2012 Jan 27. PMID: 22161771.
Cheng L, Alexander RE, Maclennan GT, Cummings OW, Montironi R, Lopez-Beltran A, Cramer HM, Davidson DD, Zhang S. Molecular pathology of lung cancer: key to personalized medicine. Mod Pathol. 2012;25(3):347-69. doi:10.1038/modpathol.2011.215. Epub 2012 Jan 27. PMID: 22282308.
Shaw AT, Kim DW, Nakagawa K, Seto T, Crinó L, Ahn MJ, De Pas T, Besse B, Solomon BJ, Blackhall F, Wu YL, Thomas M, O'Byrne KJ, Moro-Sibilot D, Camidge DR, Mok T, Hirsh V, Riely GJ, Iyer S, Tassell V, Polli A, Wilner KD, Jänne PA. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med. 2013;368(25):2385-94. doi:10.1056/NEJMoa1214886. Epub 2013 Jun 01. PMID: 23724913.
Vaishnavi A, Capelletti M, Le AT, Kako S, Butaney M, Ercan D, Mahale S, Davies KD, Aisner DL, Pilling AB, Berge EM, Kim J, Sasaki H, Park S, Kryukov G, Garraway LA, Hammerman PS, Haas J, Andrews SW, Lipson D, Stephens PJ, Miller VA, Varella-Garcia M, Jänne PA, Doebele RC. Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer. Nat Med. 2013;19(11):1469-1472. doi:10.1038/nm.3352. Epub 2013 Oct 27. PMID: 24162815.
Frampton GM, Ali SM, Rosenzweig M, Chmielecki J, Lu X, Bauer TM, Akimov M, Bufill JA, Lee C, Jentz D, Hoover R, Ou SH, Salgia R, Brennan T, Chalmers ZR, Jaeger S, Huang A, Elvin JA, Erlich R, Fichtenholtz A, Gowen KA, Greenbowe J, Johnson A, Khaira D, McMahon C, Sanford EM, Roels S, White J, Greshock J, Schlegel R, Lipson D, Yelensky R, Morosini D, Ross JS, Collisson E, Peters M, Stephens PJ, Miller VA. Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. Cancer Discov. 2015;5(8):850-9. doi:10.1158/2159-8290.CD-15-0285. Epub 2015 May 13. PMID: 25971938.
Current practices and guidelines for clinical next-generation sequencing oncology testing. Strom SP, et al. Cancer Biol Med. 2016;13(1):3-11. doi:10.28092/j.issn.2095-3941.2016.0004. PMID: 27144058.
Clay R, Kipp BR, Jenkins S, Karwoski RA, Maldonado F, Rajagopalan S, Voss JS, Bartholmai BJ, Aubry MC, Peikert T. Computer-Aided Nodule Assessment and Risk Yield (CANARY) may facilitate non-invasive prediction of EGFR mutation status in lung adenocarcinomas. Sci Rep. 2017;7(1):17620. doi:10.1038/s41598-017-17659-6. Epub 2017 Dec 15. PMID: 29247171.
Spurr L, Li M, Alomran N, Zhang Q, Restrepo P, Movassagh M, Trenkov C, Tunnessen N, Apanasovich T, Crandall KA, Edwards N, Horvath A. Systematic pan-cancer analysis of somatic allele frequency. Sci Rep. 2018;8(1):7735. doi:10.1038/s41598-018-25462-0. Epub 2018 May 16. PMID: 29769535.
Targeting . Sehgal K, et al. Transl Cancer Res. 2018;7(Suppl 7):S779-S786. doi:10.21037/tcr.2018.08.11. PMID: 30327756.
NTRK fusion-positive cancers and TRK inhibitor therapy. Cocco E, et al. Nat Rev Clin Oncol. 2018;15(12):731-747. doi:10.1038/s41571-018-0113-0. PMID: 30333516.
Marcus L, Lemery SJ, Keegan P, Pazdur R. FDA Approval Summary: Pembrolizumab for the Treatment of Microsatellite Instability-High Solid Tumors. Clin Cancer Res. 2019;25(13):3753-3758. doi:10.1158/1078-0432.CCR-18-4070. Epub 2019 Feb 20. PMID: 30787022.
Efficacy of Selpercatinib in . Drilon A, et al. N Engl J Med. 2020;383(9):813-824. doi:10.1056/NEJMoa2005653. PMID: 32846060.
Metal substitutions incarbonic anhydrase: a halide ion probe study. Smith RJ, et al. Biochem Biophys Res Commun. 1975;66(4):1281-6. doi:10.1016/0006-291x(75)90498-2. PMID: 3. US Food and Drug Administration (FDA). Table of Pharmacogenomic Biomarkers in Drug Labeling. Updated August 11, 2022, Accessed July 31, 2023. Available at www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling.

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
No.

Will the lab re-contact the ordering physician if variant interpretation changes?
No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Research:

Is research allowed on the sample after clinical testing is complete?
Research testing is only performed under IRB approved protocol with an opt-out policy in place.

Recommended fields not provided:

Clinical validity, Clinical utility, Sample negative report, Sample positive report

Technical Information

Test Procedure:

Next-generation sequencing is performed to determine microsatellite instability (MSI) status and evaluate the presence of a mutation in all coding regions of the ALK, BRAF, EGFR, ERBB2, HRAS, KRAS, MDM2, MET, NRAS, RET, ROS1 and STK11 genes. Qualitative detection using the Idylla GeneFusion Assay is performed to detect rearrangements (fusions) … View more

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions-insertions [delis, formerly indels]) is 5% variant allele frequency and having at least 500x deduplicated coverage. Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delis is 99.7% (699/701) … View more

Assay limitations:

This test cannot differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk. DNA variants of uncertain significance may be identified. A negative result does not rule out the presence of a variant or fusion that … This test cannot differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk. DNA variants of uncertain significance may be identified. A negative result does not rule out the presence of a variant or fusion that may be present below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 5% mutant allele frequency with a minimum coverage of 500X in a sample with 20% or more tumor content. Point mutations and small insertion/deletion mutations will be detected in the ALK, BRAF, EGFR, ERBB2, HRAS, KRAS, MDM1, MET, NRAS, RET, ROS1, and STK11 genes only. This test may detect single exon deletions but does not detect multi-exon deletions, duplications, or genomic copy number variants. This test does not detect point mutations, insertion/deletion mutations, large single or multi-exon deletions or duplications, or genomic copy number variants for the NTRK1, NTRK2, and NTRK3 genes. Variant allele frequency (VAF) is the percentage of sequencing reads supporting a specific variant divided by the total sequencing reads at that position. In somatic testing, VAF should be interpreted in the context of several factors including, but not limited to, tumor purity/heterogeneity/copy number status (ploidy, gains/losses, loss of heterozygosity) and sequencing artifact/misalignment.(1,2) Gene fusions (rearrangements) and expression imbalance will be detected when involving the ALK, ROS1, RET, NTRK1, NTRK2, and NTRK3 genes only. Rare polymorphisms may be present that could lead to false-negative or false-positive results. The presence or absence of a variant may not be predictive of response to therapy in all patients. Test results should be interpreted in the context of clinical, tumor sampling, histopathological, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. Reliable results are dependent on adequate specimen collection and processing. This test has been validated on cytology slides and formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause polymerase chain reaction failure. SUPPORTIVE DATA Performance Characteristics: The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions-insertions [delins, formerly indels]) is 5% variant allele frequency and having at least 500x deduplicated coverage. Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delins is 99.7% (699/701) and 96.6% (226/234) of variants, respectively. Concordance for the detection of delins was 98.9% (186/188) in variants 1 to 10 base pairs (bp) in size, 95.8% (23/24) in variants 11 to 50 bp in size, and 88.9% (8/9) in variants 51 to 200 bp in size. Microsatellite instability (MSI) evaluation is accurate at a tumor purity of at least 10% for colorectal tumors and 20% for other tumor types. During verification studies, 98% (200/204) concordance for MSI status was observed between this test and the reference method. View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Alternative Assessment

Description of PT method:
Internal Blind

VUS:

Software used to interpret novel variations
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, gene-specific online databases, ISCA, UCSC Genome Browser

Laboratory's policy on reporting novel variations
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.

Recommended fields not provided:

Test Confirmation, Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, PT Provider, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Category: FDA exercises enforcement discretion

Additional Information

Reviews:

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View FASLG variations in ClinVar

View BRAF variations in ClinVar

View CASP8 variations in ClinVar

View MAP3K8 variations in ClinVar

View CYP2A6 variations in ClinVar

View EGFR variations in ClinVar

View ERBB2 variations in ClinVar

View ERCC6 variations in ClinVar

View IRF1 variations in ClinVar

View KRAS variations in ClinVar

View SLC22A18 variations in ClinVar

View PRKN variations in ClinVar

View PIK3CA variations in ClinVar

View PPP2R1B variations in ClinVar

RefSeqGene

Coriell Institute for Medical Research

Practice guidelines:

NICE, 2023

Consumer resources:

MalaCards

MedlinePlus

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.