April 2020 Case
Authors
Jong Taek Kim, MD (Fellow) : Eric Vail, MD (Faculty)
Subject: Molecular Genetics Pathology (Comprehensive Next Generation Sequencing)
Clinical History
A man in his 40’s with newly diagnosed stage 4 non-small cell lung cancer with metastasis to the brain, axial skeleton, and left supraclavicular lymph node presents for further evaluation and intervention.
Molecular Analysis
Molecular profiling of the patient's tumor tissue was first performed at an outside hospital. This included targeted testing for EGFR (Sanger Sequencing) and BRAF (PCR) both of which did not detect any targetable mutations. Additionally, FISH for ALK and ROS1 rearrangements could not be performed due to lack of available tissue. Subsequently repeat biopsy was performed on the left supraclavicular lymph node and was tested with the Cedars-Sinai Comprehensive Cancer Panel, which is a targeted amplicon based NGS assay that utilizes DNA and RNA to detect single nucleotide variations (SNV), indels, copy number variations (CNV) and select rearrangements (inter and intragenic) in 161 genes as well as tumor mutational burden (TMB). While the DNA sequencing did not reveal any targetable mutations, RNA analysis revealed transcripts with exon 25 of EGFR fused to exon 18 EGFR (Figure 1). This was diagnostic for an EGFR kinase domain duplication (EGFR-KDD). Tumor mutation burden was calculated to be 3 mutations/Mb. No other clinically relevant mutations were detected, including other fusions (ALK/RET/ROS1/NTRK) or pathogenic point mutations/indels (BRAF/EGFR/KRAS).
Figure 1: Visualization of EGFR‐KDD variant using the IGV Browser which shows NGS pileup data with coverage in both forward (orange) and reverse (blue) reads of a cDNA sequence (*) mapping to a combined sequence (†) of EGFR exon 25 (3') and 18 (5').
Diagnosis
EGFR Kinase Domain Duplication In A Patient with Metastatic Lung Cancer (Table 1: Variant Summary)
TABLE 1: RESULT SUMMARY |
||||||
|---|---|---|---|---|---|---|
|
Varient Detected |
FDA Approved Therapy Within Indication |
FDA Approved Therapy Outside Indication |
Resistance to Therapies |
NCCN Guidelines |
Clinical Trial Opportunity |
TMB |
|
EGFR Exon 18 to 25 Kinase Domain Duplication |
Osimertinib (Preferred), Erlotinib, Afatinib, Getfitnib |
No |
No |
Yes |
Yes |
3 Muts/Mb |
*161 Gene Panel: SNVs, Indels, CNV, Fusions
Discussion
An activating exon 18 to 25 EGFR kinase domain duplication (KDD) was detected. This mutation is not covered by most common EGFR testing methodologies and explains the prior negative result. Both preclinical and case report evidence suggest that EGFR KDD confers increased sensitivity to EGFR TKIs erlotinib, afatinib and osimertinib (afatinib being the most potent). In addition, osimertinib demonstrated most clinically meaningful efficacy against CNS metastases. NCCN recommends FDA approved osimertinib (preferred), erlotinib, gefitinib and afatinib (category 1) as first-line systemic therapy in locally advanced or metastatic NSCLC patients with sensitizing EGFR mutations (NCCN, NSCLC v6.2019).
Figure 2: NCCN Guidelines for Non-Small Cell Lung Cancer with Sensitizing EGFR Mutations.
In a patient with metastatic lung cancer, an EGFR kinase domain duplication (KDD) of exons 18 to 25 was detected with Cedars-Sinai Comprehensive Cancer Panel. Expanded multigene panel testing increases sensitivity with higher detection rate for rare variants that would otherwise be missed with frontline molecular testing in the community. This case highlights the advantages of a high throughput next generation sequencing technology over the traditional methods in finding an actionable mutation with therapeutic implications. After the NGS report was issued, the patient was placed on osimertinib therapy. A 5-month follow up imaging showed marked improvement in the size of lung mass well as lymph node, bone, and brain metastasis. The patient also reported significant symptomatic relief.
Figure 3: Brain repeating imaging
References
- Gallant JN, Sheehan JH, Shaver TM, et al. EGFR Kinase Domain Duplication (EGFR-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib. Cancer Discovery, 2015 Nov;5(11):1155-63.
- Goss G, Tsai CM, Shepherd FA, et al. CNS response to osimertinib in patients with T790M-positive advanced NSCLC: pooled data from two phase II trials. Ann Oncol. 2018 Mar 1;29(3):687-693.
- Wang J, Li X, Xue X, et al. Clinical outcomes of EGFR kinase domain duplication to targeted therapies in NSCLC. Int J Cancer. 2019 Jun 1;144(11):2677-2682.
- National Comprehensive Cancer Network Guidelines for Non-Small Cell Lung Cancer