Selective RET Targeted Agents and RET Testing in Non-Small-Cell Lung Carcinoma (NSCLC)

Table of contents

2 Executive summary

3 Introduction to NSCLC

3 Targeted therapies and biomarkers in NSCLC

5 Relevance of RET alterations in NSCLC

7 Evolution of RET targeted therapies in metastatic NSCLC

9 Molecular testing approaches for RET fusions and NSCLC biomarkers

12 Appendix

16 References

1 Executive summary

NSCLC is the most frequently diagnosed cancer and the leading cause of cancer-related deaths globally.1 Systematic genomic analyses have unveiled the complex genomic landscape within NSCLC, leading to the discovery of several oncogenic driver mutations and the associated development of molecularly targeted therapies for use in precision medicine–based cancer care. The expansive actionable biomarker landscape in NSCLC has driven the need for broad molecular profiling to enable a complete depiction of a patient’s disease to better guide clinical management. The oncogenic activation of RET (rearranged during transfection) by gene fusions is a primary driver in NSCLC, occurring in up to 2% of cases.2,3 With the recent approval of Retevmo (selpercatinib), a selective RET inhibitor in metastatic NSCLC, the need for RET identification has further expanded the list of biomarkers for characterization within NSCLC. A complete molecular profile is fundamental in guiding NSCLC treatment decisions, rendering the current iterative testing approach with multiple technologies unattainable. Comprehensive genomic profiling (CGP)-based next- generation sequencing (NGS) enables broad characterization and simultaneous detection of multiple prognostic and predictive biomarkers such as RET, genomic signatures such as tumor mutation burden (TMB) and homologous recombination deficiency (HRD), and emerging biomarkers within NSCLC in a single test. In this document, we review currently known oncogenic driver mutations of NSCLC, the role of RET alterations in NSCLC, and selective RET inhibitors in metastatic NSCLC.

In this document, reference to actionable genomic alterations and biomarkers are considered to be: predictive biomarkers linked to a Food and Drug Administration (FDA)-approved drug in a specific indicated tumor type, biomarkers predictive of response to a FDA-approved drug in another tumor type, biomarkers that are predictive of response and recommended by expert panels, and biomarkers linked to a mechanism-driven clinical trial.

2 Introduction to NSCLC

Lung cancer is the most frequently diagnosed cancer and the leading cause of cancer-related deaths globally, comprising 11.6% of cancer diagnoses within men and women combined.1 In 2018, there were over two million newly diagnosed lung cancer cases worldwide.1 The most recent Surveillance, Epidemiology, and End Results (SEER) data (2010-2016) reported the five-year survival rate in advanced NSCLC to be 6%.4 The World Health Organization (WHO) classifies lung cancer into two broad histological subtypes: NSCLC, which comprises 85% of cases, and small cell lung cancer (SCLC), which accounts for 15% of cases.5 NSCLC is further subdivided into adenocarcinoma, squamous cell carcinoma, and large cell carcinoma (Figure 1).6 The evolution of NSCLC management in the last decade has offered novel therapeutic approaches with molecules targeting drivers of lung tumorigenesis “driver mutations,” and immunotherapies that inhibit programmed death (PD)-1/PD- ligand(PD-L)-1 checkpoint.

10% Large cell carcinoma SCLC Other (rare subtypes such as 25% adenosquamous carcinoma)

NSCLC 25% Squamous cell cancer

40% Adenocarcinoma

Figure 1: Lung cancer classifications6

Driver mutations and molecularly targeted therapies in NSCLC

Driver mutations are causally implicated in oncogenesis. The oncogene-addicted biology of driver mutations and associated reliance on a signal tend to make driver mutations relevant molecular targets or biomarkers for the development and use of molecularly targeted therapies. A diverse spectrum of oncogenic drivers and targeted therapies has been identified in NSCLC (Figure 2, Table 1). Although the frequency of individual oncogenic drivers may be low, over 60% of NSCLCs may potentially harbor an actionable genomic alteration.7,8 A large OVER 60% retrospective study that evaluated tumor genomics and clinical outcomes in NSCLC patients observed an overall survival (OS) benefit in patients harboring of NSCLCs may an actionable driver mutation that were treated with the respective National potentially harbor Comprehensive Cancer Network® (NCCN®) recommended targeted therapy an actionable compared to patients treated alternatively (median overall survival, genomic alteration7,8 18.6 months [95% CI, 15.2-21.7] vs 11.4 months [95% CI, 9.7-12.5]; difference, 7.1 months [95% CI, 3.5-10.1]; P < .001).9

3 <1% MEK1

1% NTRK The NCCN Clinical Practice 2% HER2 Guidelines in Oncology (NCCN Guidelines®)for NSCLC recommends molecular testing 2% ROS1 for eligible patients with metastatic NSCLC and strongly 2% RET advises broader molecular profiling with the goal of 3% MET identifying rare driver mutations for which effective drugs may 4% PIK3CA already be available, or to appropriately counsel patients regarding the availability of 3-5% BRAF clinical trials.10

7% ALK NCCN® makes no warranties of any kind whatsoever regarding their content, use or application and disclaims any responsibility 10-20% EGFR for their application or use in any way.

25% KRAS

31% Unknown

Figure 2: Frequency of identified oncogenic drivers in NSCLC2,3,7,8,11-26

Therapeutic landscape in NSCLC Therapeutic advancements for NSCLC can be attributed to the expansive actionable biomarker landscape as well as the emergence of immunotherapy. Broad molecular profiling is a fundamental component of precision cancer care that enables the characterization of multiple therapeutically targetable oncogenic drivers and mutational signatures; such as TMB, MSI and HRD. Emerging data indicate that immune checkpoint inhibitors (ICIs), including PD-1/PD-L1 inhibitors, may be less efficacious in subsets of NSCLC Clinical activity patients with driver mutations.27 NCCN® recommendations include use of of ICIs is lower in first-line targeted therapies in patients with metastatic NSCLCs harboring a NSCLCs harboring targetable driver mutation over ICIs.10 a driver mutation27

4 Table 1: FDA-approved molecular-targeted therapies in NSCLC28

Molecular alteration Targeted therapy options Afatinib Erlotinib Sensitizing EGFR mutation positive Dacomitinib With the diverse Gefitinib spectrum of Osimertinib oncogenic drivers Alectinib in NSCLC, a Brigatinib complete molecular ALK gene fusion positive Ceritinib characterization Crizotinib is fundamental to Lorlatinib guiding treatment Ceritinib decisions ROS1 gene fusion positive Crizotinib Entrectinib

RET gene fusion positive Selpercatinib

Entrectinib NTRK gene fusion positive Larotrectinib

MET exon 14 skipping mutation Capmatinib

BRAF V600E mutation positive Dabrafenib + Trametinib

RET genomic alterations and molecularly targeted therapy

RET is a proto-oncogene involved in normal developmental and physiological processes.2,3,29 Oncogenic activation of RET by in-frame gene fusions or activating point mutations are implicated in the pathogenesis of multiple cancers and are typically mutually exclusive from other oncogenic drivers (Figure 3). In NSCLC, RET is a primary oncogenic driver with RET fusions occurring in up 2% of cases.2,3 Histologically, RET gene fusions are found in lung adenocarcinomas, are more common in nonsmokers, and tend not to overlap with other lung cancer driver mutations, such as EGFR, BRAF, METex14 skipping, KRAS, and ALK or ROS1 gene fusions.3,30,31 RET is known to partner with at least 12 different genes, with KIF5B-RET being the most frequently observed RET fusion in NSCLC.32,33 RET fusions occur in 10%-20% of papillary thyroid cancers (PTC).3,34,35 RET point mutations affect most medullary thyroid cancers (MTC), occurring in > 90% of hereditary cases and > 60% in sporadic cases. RET point mutations have not been broadly recognized in other cancers and are understood to only be a driver in MTC. 3,35,36

RET fusion identification has further expanded the need for molecular characterization within NSCLC

5 RET is activated by two major mechanisms in cancer

RET fusions RET mutations

Non-small cell lung cancer (2%) Medullary thyroid cancer Papillary and other thyroid sporadic (> 60%) cancers (10-20%) hereditary (> 90%)

Activation by ligand-independent Direct kinase Pancreatic cancer (<1%) dimerization activation Salivary gland cancer (<1%) Spitz tumors (<1%) Colorectal cancer (<1%) Covalent disulfide Ovarian cancer (<1%) bonds in Myeloproliferative disorders (<1%) cysteine-rich region Many others (<1%) Kinase domain mutation P P P P P P P Dimerization Kinase P P P P P P

P P P P P P P

KIF5B (most common in lung cancer) CCDC6 or NCOA4 (most common in thyroid cancer) Common mutation: RET M918T Drion et al. Nat Rev Clin Oncol 2018;15:151-67; Kato et al. Cin Cancer Res 2017; 23:1988-97; Pietrantonio et al. Ann Oncol 2018; FigureMar 10; Su 3: et RET al. PLoS is Oneactivated 2016;11(11) by two major mechanisms in cancer3,29,36,37

RET targeted therapy MKIs such as cabozantinib, vandetanib, lenvatinib, and sorafenib, are associated with significant off-target toxicities and have demonstrated a modest benefit inRET fusion–driven NSCLCs with objective response rates (ORR) from 18%-37% and, a median progression-free survival range of 2.2 months to 3.6 months.38 Selpercatinib and pralsetinib are novel selective RET inhibitors that have been developed to target the RET kinase.

Retevmo Retevmo (selpercatinib) is the first selective RET inhibitor to receive FDA approval and is indicated for the treatment of adult patients with metastatic RET fusion–positive NSCLC, the treatment of adult and pediatric patients > 12 years of age with advanced or metastatic RET-mutant MTC who require systemic therapy, and the treatment of adult and pediatric patients > 12 years of age with advanced or metastatic RET fusion–positive thyroid cancer who require systemic therapy and who are radioactive iodine refractory.39 The LIBRETTO-001 (NCT03157128), a phase I/II multicenter, open label, multicohort study, evaluated the efficacy of Retevmo in 105 patients with advanced RET fusion–positive NSCLC previously treated with platinum chemotherapy and 39 patients with treatment-naïve RET fusion–positive NSCLC (Figures 4-6).39

6 Total enrolled n = 531 Primary Endpoint RET fusion + NSCLC • ORR RET gene alteration Phase I n=253 determination by 20 mg QD- local accredited 240 mg BID RET fusion–positive Secondary laboratories using: metastatic NSCLC Endpoints • NGS • Primary analysis set • DoR Phase II • PCR with prior platinum • PFS 160 mg BID • FISH chemotherapy • Safety n = 105 • Treatment naïve n = 39

RET-mutant medullary thyroid cancer n = 226

RET fusion–positive thyroid cancer n = 27

Other n = 25

Figure 4: Schematic of the LIBRETTO-001 study evaluating the efficacy of Retevmo for patients withRET fusion–positive metastatic NSCLC40—Abbreviations: FISH = fluorescent in situ hybridization, QD = once daily, BID = twice daily, ORR = objective response rate, DoR = duration of response, PFS = progression-free survival

In the LIBRETTO-001 study, RET fusions were detected in 90% of patients using NGS, 8.6% using FISH, and 1.9% using PCR39

7 Patients with RET fusion positive metastatic NSCLC

Patients previously treated Treatment-naïve patients with platinum chemotherapy (n=105) (n=39) 64% ORR 85% ORR (95% CI: 54, 73) (95% CI: 70, 94) 1.9% CR + 62% PR 85% PR; all responses were partial Median DoR 17.5 months Median DoR (95% CI: 12, NE) not yet reached (95% CI: 12, NE)

Figure 5: Patient outcome of the LIBRETTO-001 study39—Abbreviations: ORR = objective response rate, DoR = duration of response, CR = complete response, PR = partial response, CI = confidence interval, NE = not evaluable

Severe adverse reactions (Grade 3-4) occurring in ≥ 15% of patients who received Retevmo in LIBRETTO-001, included hypertension (18%), prolonged QT interval (4%), diarrhea (3.4%), dyspnea (2.3%), fatigue (2%), abdominal pain (1.9%), hemorrhage (1.9%), headache (1.4%), rash (0.7%), constipation (0.6%), nausea (0.6%), vomiting (0.3%), and edema (0.3%).Common adverse reactions (all grades) occurring in ≥ 15% of patients who received Retevmo in LIBRETTO-001, were dry mouth (39%), diarrhea (37%), hypertension (35%), fatigue (35%), edema (33%), rash (27%), constipation (25%), nausea (23%), abdominal pain (23%), headache (23%), cough (18%), prolonged QT interval (17%), dyspnea (16%), vomiting (15%), and hemorrhage (15%).39

CCDC6 22%

KIF5B 59% NCOA4 2% Unknown 11% Other 6%

Figure 6: RET fusion partners detected in the LIBRETTO-001 study40—Other includes KIAA1468 (2), ARHGAP12, CCDC88C, CLIP1, DOCK1 +RBPMS, ERC1, PRKAR1A, and TRIM24 (1 each). Unknown includes FISH-positive or PCR-positive fusions.

8 Pralsetinib Pralsetinib (BLU-667) is an investigational, highly potent selective RET kinase inhibitor that targets oncogenic RET alterations including RET fusions.41 ARROW (NCT0307385) is an ongoing global phase I/II registrational study of pralsetinib in patients with advanced solid tumors and RET alterations, including RET fusion–positive NSCLC. Similar to LIBRETTO-001, efficacy is being evaluated in treatment of naïve patients and patients previously treated with a platinum chemotherapy and the primary endpoint is ORR (Table 2).42

Table 2: Efficacy summary in response-evaluable population to treatment with pralsetinib42

Intent-to-treat population Response-evaluated population All NSCLC Prior platinum Treatment naïve All NSCLC Prior platinum Treatment naïve (n = 132) (n = 92) (n = 29) (n = 116) (n = 80) (n = 26)

Overall response rate 58% 55% 66% 65% 61% 73%

95% CI 49-67% 45-66% 46-82% 55-73% 50-72% 52-88%

Best overall response

CR 6% 5% 10% 6% 5% 12%

PR 52% 50% 55% 59% 56% 62%

SD 30% 35% 14% 28% 34% 15%

PD 8% 4% 17% 7% 5% 12%

NE 5% 5% 3% 0% 0% 0%

Disease control rate 88% (81-93) 90% (82-85) 79% (60-92) 93% (87-97) 95% (88-99) 88% (70-98) (95% CI) Clinical benefit rate 68% (60-76) 70% (59-79) 66% (46-82) 72% (62-80) 71% (60-81) 73% (52-88) (95% CI)

Abbreviations: CI = confidence interval, CR = complete response, NE = not evaluable, NSCLC, PD = progressive disease, PR = partial response, SD = stable disease Severe adverse reactions (Grade 3-4) occurring in ≥ 10% of patients who received pralsetinib were hypertension and neutropenia.42

Molecular testing approaches for RET fusions

In NSCLC, a complete molecular profile is fundamental to guiding treatment decisions. Single-gene approaches are limited to a specific genomic alteration, requiring multiple parallel or iterative tests that often lead to tissue exhaustion, re-biopsies, and incomplete molecular profiles; particularly with sample limitations associated with fine needle aspirations.43 Current FDA-approved NSCLC companion diagnostic tests rely on one of four technologies: immunohistochemistry (IHC), FISH, PCR, and NGS.44 In this section, we review the merits and limitations of each technology and introduce the potential value of using comprehensive genomic profiling (CGP) to assess molecular aberrations (Table 3).

9 Table 3: Molecular testing approaches for RET aberrations and fusions

Technology Pros Cons

IHC • Fast turnaround time • Unable to identify RET fusion partner • May suggest gene fusions or amplifications • Protein detection only; does not provide • Used as a screening tool to detect fusions genetic information • Shows spatial localization of signal in cells and tissue • Low sensitivity (55%-65%) variable specificity (40%-85%) requiring confirmatory testing2,45 • Variability of cutoffs across assays • Usually a single-biomarker assay • May lead to tissue depletion if serial assays needed

Break-apart • Highly specific targeted genomic alteration • Unable to identify RET fusion partner45 FISH • May detect gene translocations regardless of fusion • Reduced sensitivity; high false-negative rate partner30,46 • Unstandardized cutoffs definingRET positivity, • Shows spatial localization of signal in cells and tissue limiting specificity; high false-positive rate • Expensive45 • Requires technical expertise45 • May lead to tissue depletion if serial assays needed

RT-PCR • May detect known RET fusion partners45 • Results depend on quality of extracted RNA • Low cost • Tests a limited number of genes per assay • Fast turnaround time • Targeted RT-PCR unable to detect novel/ unknown RET fusion partners • May lead to tissue depletion if serial assays needed

NGS (hot spot) • Highly specific targeted genomic alteration • Potential to miss new driver alterations • Provides sequence and orientation of rearrangement/ • Limited panel size fusion

NGS (broad) • Simultaneously detects multiple classes of alterations • Longer turnaround time than other methods in a single test • Requires technical expertise • Comprehensive profiling of prognostic and predictive • Complex analysis biomarkers • Able to detect in-frame RET fusions • Provides sequence and orientation of rearrangement/ fusion • Accurate profiling, even in low-quantity samples45 • May include DNA or DNA and RNA in one test • Consolidates multiple biomarkers, including those in guidelines and clinical trials, into a single assay47 • Can detect genomic signatures (ie, MSI and TMB) • Preserves tissue sample

NGS (DNA) • Detects oncogenic kinase fusions • Only detects gene fusions in short introns • Can identify precise genomic breakpoints and usually cannot detect fusions that arise in • Provides copy number and sequence information as longer introns well as rearrangements • Introns tend to contain repetitive sequences, challenging analysis • Can only identify rearrangements involving pre-specified fusion partners and breakpoint regions

NGS (RNA) • Excludes introns, ideal for fusion identification • Quality of RNA can impact sensitivity • Sensitive profiling ofRET gene • Agnostic to fusion partner and breakpoint- detects novel fusions and identifies unknown fusion partners

Overview of NGS pros and cons. Differences may arise when using different NGS methods (ie, amplicon vs hybrid-capture and DNA or RNA only vs DNA/RNA combined).

The NCCN Guidelines®for NSCLC recommends when feasible {molecular} testing be performed via a broad, panel-based approach, most typically performed by next-generation sequencing (NGS). For patients who, in broad panel testing don’t have identifiable driver oncogenes (especially in never smokers), consider RNA-based NGS if not already performed to maximize detection of fusion events.10 10 NCCN®makes no warranties of any kind whatsoever regarding their content, use or application and disclaims any responsibility for their application or use in any way. CGP NGS-based CGP using an integrated DNA and RNA workflow can enable simultaneous assessment of multiple variant types, including copy number variations (CNVs), indels, single nucleotide variations (SNVs), gene signatures like TMB and MSI, and gene fusions. Broad molecular testing with CGP is inclusive of relevant biomarkers with approved therapies and therapies under investigation. By replacing multiple, iterative tests with a single assay, CGP has the potential to offer faster, streamlined, and more economical results.47 Drilon et al. identified actionable genomic alterations previously missed by non-NGS testing strategies, supporting the use of CGP as a first-line strategy.48 Current molecular testing guidelines for lung cancer patients recommend RET testing as part of a larger panel screen with EGFR, ALK, and ROS1, or in the case when previous tests have been negative for these biomarkers.46

If you just know PDL1 and you don’t know ALK, EGFR and several other of the driver mutations, like “ RET, you can really do a disservice to the patient... Until you know all of them [the driver mutations] you really don’t know the best path for a patient.”

- Dr. Heather Wakelee49

11 Appendix Benefits of CGP

Consolidate testing CGP provides a hypothesis-neutral approach for assessment of actionable genomic alterations, including emerging biomarkers and those in guidelines and clinical trials, in a single assay, eliminating the burden and limitations of iterative testing (Figure 1).47

ITERATIVE TESTING CONSOLIDATED TESTING

Figure 1: CGP consolidates iterative testing into a single assay, saving time, sample, and money

Profile DNA and RNA biomarkers simultaneously Using a hybrid capture–based NGS workflow for CGP enables assessment of DNA alterations, including SNVs, CNVs, indels, known and novel RNA gene fusions, and additional oncogenic drivers in a single assay (Figure 2).

Detect biomarker signatures predictive of immunotherapy response Testing for immunotherapy biomarkers, along with the other guideline-recommended biomarkers for oncogene- targeted therapies, is essential for NSCLC therapy selection.50 CGP is the only molecular diagnostic method currently available that can simultaneously test for all known oncogenic biomarkers in NSCLC and key current and emerging predictive biomarkers of immunotherapy response, such as MSI and TMB.50

Fusion

Splice variant

Figure 2: NGS-based CGP enables assessment of all DNA and RNA variant classes, plus TMB and MSI, in a single test

12 Increase targeted therapy assignment and clinical trial enrollment CGP can inform precision medicine by matching patients with appropriate therapies based on the genomic composition of the tumor (Figure 3).43,46,51,55

TODAY Increased targeted therapy use

approved cancer 1000+ 50 therapies53 ongoing clinical trials52

POTENTIAL UTILITY OF CGP

Patient eligibility Patient assignment from 4% to from 6% to

54 54 Increased clinical trial enrollment Increased 54% 13%

Figure 3: Clinical utility of CGP in oncology treatment—Number of ongoing clinical trials defined by a search of clinicaltrials.gov using the following search terms: cancer, biomarker, and gene.52 Approved cancer therapies includes therapies used in solid tumors and hematologic oncology.53 Potential utility of CGP based on a predictive model study by Sabatini et al.54

In a prospective study of 10,000 patients, 37% had actionable alterations identified by CGP55

13 CGP and liquid biopsies Liquid biopsy enables comprehensive analysis of circulating tumor DNA (ctDNA) in plasma, providing a noninvasive approach for profiling solid tumors (Figure 4). It is currently believed that a liquid biopsy can provide significant tumor- related information and yield results comparable to those observed when using solid tissue biopsy for NSCLC and that NGS is a reliable technology for performing these studies.56 Using liquid biopsies has the added benefit of allowing clinicians to perform time-series evaluations throughout the course of patient care to measure response to a given therapy and any eventual relapse that may occur through the evolution of therapy-resistant mutations.56

iomarker iomarker

iomarker

PioM

PioM

DNA from tumors Cell-free DNA is extracted from plasma circulates in the blood

Figure 4: ctDNA can be used in CGP to identify actionable biomarkers

Reporting considerations for CGP results: CGP reports should present all actionable and clinically relevant results from NGS-based CGP in a salient and clinician-friendly manner. Commercially available CGP reports usually include findings on genomic alterations specific to all clinically relevant biomarkers, targeted and immunotherapies specific to a patient’s tumor genotype, and open clinical trials a patient may potentially qualify for based on the result of CGP test (Figure 5).57 Suggested components of a CGP report include:

Actionable genomic alterations Actionable genomic alterations, as defined by guidelines, include results for biomarkers with approved targeted therapies along with essential biomarkers for immunotherapy response, including MSI and TMB.57

Therapies for clinically relevant results Given the availability of targeted therapies for rare alterations, such as RET in NSCLC, it is vital to present commercially available therapies approved for treatment of genomic alterations specific to a patient’s cancer.57

Potential clinical trials Including novel targeted therapies that are not yet FDA approved but currently under investigation,57 enables patients to access potentially life-saving clinical trials and clinicians to continue improving treatment options for future patients.

14 Comprehensive Genomic PierianDx 77 Maryland Plaza Customized contact information Front page Report St. Louis, MO 63108 featuring your address and logo First half of front page Powered by Patient DOB Dieae Medical Record # Report Date Report tat summarizes key John Doe 02/04/1951 Non-small cell Lung Cancer 6563465346 09/19/2019 Final Easily identified sample information actionable information for the clinician Ret suay Executive Summary Other Biomarkers The patient tumor specimen harbors an NCOA4-RET fusion, KRAS G12D and PDGFRA D842V mutations and Biomarker LEVEL an ampliifcation in the MDM2 gene. RET fusions/rearrangements are an emerging biomarker and NCLC Biomarker LEVEL patients harboring these are recommended targeted therapies involving cabozantinib or vandetinib by NCCN. TMB High Presence of KRA mutations in NCLC patients indicates poor prognosis independent of therapy, reduced Highlighted status of new and responsiveness to EGFR TKI therapy and no impact on chemotherapeutic eiffcacy, as per recent NCCN Comprehensive overview; an MS Stable guidelines. Targeted therapies against RET fusions, KRA mutations, PDGFRA mutation or MDM2 ampliifcation emerging biomarkers open text field summarizing: are available in clinical trials for patients with NCLC. Genomic Findings • Identified variants Genomic Findings • Recommended IA IB IIC IID p.D842V NCOA4, RET NCOA4-RET PDGFRA p.D842V targeted therapies No variants reported. c.2525A>T No variants reported. fusion c.2525A>T MDM2 KRAS p.G12 D MDM MDM2 • Low-impact therapies KRAS p.G12 D ampliifcation c.35G>A ampliifcation • Possible clinical trials c.35G>A Relevant biomarkers sorted by 10 Clinical Trials 5 Clinical Trials strength of clinical significance

Clinically ReLevant Results

Tier I - Strong Clinical Signiifcance

Variant CLINICAL IMPACT

NCOA4, RET May bene椀ft from NCOA4-RET fusion - Cabozantinib or Vandatinib in non-small cell lung cance A A Interpretation

RET encodes a receptor tyrosine kinase involved in cell growth and differentiation which is known to undergo oncogenic activation in vivo and in vitro by cytogenetic rearrangement (Refeq, Jul 2008).

NCOA4 encodes an androgen receptor coactivator which interacts with the androgen receptor in a Description-/evidence-level tiering ligand-dependent manner to enhance its transcriptional activity. Chromosomal translocations between NCOA4 and RET, both located on chromosome 10, have been associated with papillary thyroid carcinoma for all detected variants: (Refeq, Feb 2009).

NCOA4-RET fusions have been reported in lung adenocarcinoma (COMIC, eptember 2019). NCCN • Variant interpretation recommends cabozantinib (FDA approved for treatment of advanced renal cell carcinoma (RCC) and • Clinical impact patients with hepatocellular carcinoma (CC) who have been previously treated with sorafenib) and vandetinib (FDA approved symptomatic or progressive medullary thyroid cancer in patients with • Possible therapies unresectable locally advanced or metastatic disease, category 2A) as targeted agents for NCLC patients harbouring RET rearrangements (NCCN, NCLC v.7.2019). • Indications • Prognosis • Literature

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Comprehensive Genomic Report Powered by Additional Content Patient DOB Disease Medical Record # Report Date Report Stats Jrhn Dre 02/04/1951 Nrn-soall cell Lung Cancef 6563465346 09/19/2019 Final Interpretation Easily identified sample information Other Biomarkers

Biomarker CLINICAL IMPACT

TMB May beneft fro - Nivolumab or Nivolumab + Ipilimumab in non-small cell lung cance High Interpretation and potential Interpretation 24 significance of new and muts/Mb muts/Mb Tumor mutational burden is an emerging quantitative genomic biomarker used to predict sensitivity to checkpoint inhibitors. NCCN recommends nivolumab with or without ipilimumab for patients with high emerging biomarkers TMB based on a recent study and the results of a Phase III clinical trial, NCT02477826 (NSCLC v7.209, PMID: 29658845, 286685).

MSI Interpretation

Stable Microsatellite Instability is caused by a failure of the DNA mismatch repair system (MMR) and a predictor of favorable response to immunotherapies (PMID: 26028255). This sample does not exhibit evidence of 5% high Microsatellite Instability (MSI). Unstable Sites high Microsatellite Instability (MSI).

UPotentialnstable Sites Clinical Trials

Clinical Trials associated with this patient’s genomic proifle and tumor type are displayed below.

Title Trial Identifier Phase Variant

Randomized Phase III Trial of Local Consolidation Therapy NCT03391869 III NCOA4, RET https:// clinicaltrials.gov/show/NCT09869 (LCT) After Nivolumab and Ipilimumab for https:// clinicaltrials.gov/show/NCT09869 NCOA4-RET fusion Immunotherapy- Naive Patients With Metastatic Non-Small Cell Lung Cancer (LONESTAR) - Strategic Alliance: BMS Clinical trial description: A Phase II Study of Cabozantinib in Patients With RET NCT01639508 II NCOA4, RET https://clinicaltrials.gov/show/NCT069508 Fusion- Positive Advanced Non- Small Cell Lung Cancer https://clinicaltrials.gov/show/NCT069508 NCOA4-RET fusion and Those With Other Genotypes: ROS or NTRK Fusions • Name of clinical trial or Increased MET or AXL Activity • Link to clinical trial A Phase /2 Study of the Highly-selective RET Inhibitor, NCT03037385 I/II NCOA4, RET https://clinicaltrials.gov/show/NCT00785 BLU-667, in Patients With Thyroid Cancer, Non-Small Cell https://clinicaltrials.gov/show/NCT00785 NCOA4-RET fusion • Phase of trial Lung Cancer (NSCLC) and Other Advanced Solid Tumors • Targeted variant

A Pilot Study of Nintedanib in Molecularly Selected NCT02299141 I NCOA4, RET https://clinicaltrials.gov/show/NCT022994 Patients With Advanced Non- Small Cell Lung Cancer https://clinicaltrials.gov/show/NCT022994 NCOA4-RET fusion (NSCLC) Note: Can be filtered by location

A Phase /b Study of MGCD56 in Patients With NCT02219711 I NCOA4, RET https://clinicaltrials.gov/show/NCT02297 Advanced Solid Tumor Malignancies https://clinicaltrials.gov/show/NCT02297 NCOA4-RET fusion

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Figure 5: Example of CGP report

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