Dr Kate Goodhealth Goodhealth Medical Clinic 123 Address Road SUBURBTOWN NSW 2000 Referring Doctor Your ref Address Dr John Medico 123 Main Street, SUBURBTOWN NSW 2000 Phone 02 9999 9999 Requested 17 May 2018 Collected 18 May 2018 09:00 am Received 18 May 2018 12:27 pm Reported 25 May 2018 15:46 pm Contextual Genomics Report Colorectal Panel Interpretation summary - Treatment with anti-egfr monoclonal antibodies is contraindicated by mutation status of the tumour specimen. - Utility of MEK/ERK pathway, PI3K/AKT/mTOR pathway and CDK inhibitors is under investigation; further clinical studies are required. Test results summary TABLE 1: KEY MUTATIONS PRESENT Gene KRAS cdna change c.35g>a (NM_004985) Amino Acid Change G12D (p.gly12asp) Exon Allelic ratio (%) Therapeutic implication 2 24.6 Contraindication for treatment with panitumumab or cetuximab Level of evidence Tier: I.A NCCN PBS May respond to MEK/ERK, PI3K/AKT/mTOR or CDK4/6 inhibitors Tier: II.D Literature PIK3CA c.1633g>a (NM_006218) E545K (p.glu545lys) 10 26.9 Possible resistance mutation to treatment with cetuximab or panitumumab Tier: II.D Literature Targeted therapies could not be identified. Standard therapies are available; clinical trials may be available. Tier: II.D Literature Page 1 of 65
TABLE 2: KEY MUTATIONS ABSENT Gene Therapeutic implication Level of evidence None found. Interpretation PRESENCE of a KRAS mutation An activating KRAS mutation, as described in the table above, was detected in the tumour DNA of this patient. The presence of a KRAS activating mutation in exons 2, 3 or 4 predicts lack of response to anti-egfr monoclonal antibody treatment in metastatic colorectal cancer (mcrc). Clinical trials have reported that patients with mcrc and KRAS or NRAS activating mutations in exon 2, 3 or 4 are unlikely to benefit from anti-egfr antibody therapy (Douillard et al., 2013; Peeters et al., 2013; Bokemeyer et al., 2015; Van Cutsem et al., 2015a). The National Comprehensive Cancer Network (NCCN) recommends testing mcrc tumours at exons 2, 3 and 4 of KRAS and NRAS genes at diagnosis of stage IV disease and only recommends cetuximab or panitumumab containing treatment for wild-type patients (NCCN Guidelines; Colon Cancer). Currently there are no approved first-line therapies that target the identified KRAS mutation. Preliminary data inidcates that KRAS mutated tumours may respond to MEK, PI3K/AKT/mTOR pathway or CDK inhibitors (Engelman et al., 2008; Zhang et al., 2009, Riely et al., 2012, Temraz et al., 2015, Pek et al, 2017). Combination therapy of a MEK inhibitor with an additional agent such as PI3K/AKT/mTOR pathway or CDK inhibitor, chemotherapy or immunotherapy may be a more efficient treatment strategy than monotherapy. Clinical trials are ongoing to evaluate the efficacy of these treatments, but these have not been approved for the treatment of metastatic colorectal cancer. PRESENCE of a PIK3CA mutation An activating PIK3CA mutation, as described in the table above, was detected in the colorectal tumour DNA of this patient. PIK3CA mutations have been significantly associated with non-response or a low response rate and a shorter PFS to anti-egfr monoclonal antibody therapy of mcrc in some studies (Sartore-Bianchi et al., 2009; De Roock et al., 2010); however, contradictory evidence has also been observed (Prenen et al., 2009). PIK3CA mutations have also been associated with poor prognosis in patients with colorectal cancer (He et al., 2009; Kato et al., 2007; Sartore-Bianchi et al., 2009). Furthermore, preclinical studies suggest that activating PIK3CA mutations are associated with reduced sensitivity to MEK inhibitors (Wee et al., 2009). Currently, there are no approved drugs for the targeted treatment of PIK3CA mutations. Preliminary studies suggest that PI3K/AKT/mTOR pathway inhibitors are potential therapeutics (Janku et al., 2014; Juric et al, 2018). In addition, regular use of aspirin has been associated with longer survival among patients with mutated PIK3CA colorectal cancer compared to patients with non-mutated PIK3CA (Liao et al., 2012; Gu et al, 2017). Clinical trials are needed to evaluate the clinical efficacy of these treatments for the treatment of colorectal cancer. Page 21 of 65
Clinical trials Australia KRAS Mutation Present Study A Phase 1 Study of an ERK1/2 Inhibitor (LY3214996) Administered Alone or in Combination With Other Agents in Advanced Cancer A Phase I/II Study of Safety and Efficacy of Ribociclib (LEE011) in Combination With Trametinib (TMT212) in Patients With Metastatic or Advanced Solid Tumors NCT02857270 NCT02703571 Other Relevant Trials A Phase III Study of BBI-608 in Combination With 5-Fluorouracil, Leucovorin, Irinotecan (FOLFIRI) in Adult Patients With Previously Treated Metastatic Colorectal Cancer (CRC). An Open-label Early Access Phase IIIb Study of Trifluridine / Tipiracil (S 95005/TAS-102) in Patients With a Pretreated Metastatic Colorectal Cancer (PRECONNECT) TABLE3: Clinical Studies. NCT02753127 NCT03306394 The clinical trials included in the report are sourced from Australian trials listed on clinicaltrials.gov and anzctr.org.au. We select trials based on tumour histotype and mutation status, with a specific focus on trials of targeted therapy. The inclusion of a trial in our report does not necessarily mean that the patient would be eligible. Patients eligibility for a trial, and the benefit that they may derive from it, will depend on additional factors that must be assessed by the oncologist. Conversely, the list of potentially relevant trials in our report may not be complete. We may have overlooked relevant trials on these websites, or there may be relevant trials listed elsewhere. Please let us know if you identify a trial of targeted therapy that could have been included in a patient s report. Specimen Information Specimen Collection Date: 2018-Mar-01 Specimen Source: Resection Tumour Cellularity: 40% Histologic Type: Adenocarcinoma Report ID: 123 Methodology Block ID #: 12345 Specimen Type: FFPE Block Primary Site of Tumour: Colon Sample Name: 12345 Patient ID: 12345 This test includes targeted sequence analysis of hotspot mutations/coding exons of the requested genes and transcripts (listed below). FFPE slides and/or tissue blocks undergo pathology evaluation, and tumour cell enrichment through macro-dissection is performed, if appropriate. Genomic DNA is extracted and targets of interest amplified using a highly multiplexed in-house designed PCR assay. The targeted regions are sequenced using Illumina technology with 151bp paired-end reads. Sequence reads that pass defined quality threshold metrics are aligned to the reference sequence (Genome Build hg19) and variants are identified and annotated using a validated, custom-built bioinformatics pipeline. Standard acceptance criteria for reporting of analytical runs are a minimum read depth of 500, a variant allele fraction of 5%, a base quality score of 30, and a probability score of 0.90 for single nucleotide changes or a quality score of 400 for insertion/deletion events. The probability score is the likelihood that a detected mutation is a true positive. The variant allele fraction (VAF) is defined as the proportion of alleles with a mutation to the total number of alleles present in a sample, expressed as a percentage. Hotspot variants are categorised into clinical significance tiers as per Li et al, J Mol Diagn 2017, 19(1):4-23. Page 31 of 65
HOTSPOT PANEL Gene Hotspot Transcript Gene Hotspot Transcript BRAF Q201, G466, F468, G469, Y472, D594, G596, L597, V600, K601 NM_004333.4 PIK3CA KRAS G12, G13, A59, Q61, K117, A146 NM_004985.4 NRAS G12, G13, A59, Q61, K117, A146 NM_002524.4 TABLE4: Hotspot Panel: CG001.v3.4_Hotspot_Manifest_Panel3.4.5_20170921.tsv R88, E542, E545, Q546, D549, M1043, N1044, A1046, H1047, G1049 NM_006218.2 Page 41 of 65
Quality metrics The figure below displays the correlation between the expected variant allelic fraction (VAF) and the observed VAF for the quality control sample. The table below summarises the average amplicon coverage for this patient. Status Coverage depth FIGURE1: Correlation between the expected and observed variant allelic fraction (VAF) for the quality control sample for this run. Limitations All 14 amplicons > 1000 TABLE5: Amplicon Coverage Single nucleotide changes, insertions and deletions at the targeted hotspots and exons will be reported. The size limit for the detection of insertion and deletion events is 1 to 24 base pairs for deletions and 1 to 18 base pairs for insertions. Variants with 5% allele ratio will be reported. Rare genetic variation can interfere with this assay. The presence of gene amplification and gene rearrangement events will not be detected by this assay. The ability to detect a particular variant in a given specimen will depend upon the allele proportion of the variant in the extracted DNA combined with the lower limit of detection of the assay. This assay does not differentiate between germline (hereditary) and somatic mutations. This assay does not detect copy number variation (CNV) including amplification of HER2/neu nor does it detect gene fusions such as those leading to ALK gene rearrangements. In addition, the assay does not assess for mutations in BRCA or other genes associated with homologous recombination and DNA damage repair which could be associated with response to PARP inhibitors. Page 51 of 65
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