Breast Cancer PAGE 1 OF 7 Patient: DOB: Patient #: Gender: Customer Ref.: SPECIMEN Requisition: Collection Date: Date Received: Report Date: Specimen Site: Tumor Origin: Unspecified Breast PHYSICIAN Ordering Physician: Account: Address: City, St., Zip: Country: RESULT INTERPRETATION 43 y/o female with newly diagnosed Grade III TNBC breast cancer by core needle biopsy. T1b,NX,MX with Risk Basal signature by BluePrint and Mammaprint. ERBB2 signature was also co-expressed(+0.308) on BluePrint but without corresponding positive expression of HER2 by TargetPrint. TargetPrint was consistent with TNBC. Endocrine Therapy: There is no mrna expression for any endocrine gene activation including the androgen receptor. No mrna expression evidence for any meaningful responsiveness to endocrine therapy. Chemotherapy: no clear chemotherapy class sensitivity, by mrna expression. There appears to be average sensitivity to alkylators and anti-metabolites. There appears to be a stronger mrna expression signal for sensitivity to anthracyclines, platinum agants and topoisomerase inhibitors. Taxanes do not appear to uniquely sensitive but there is an mrna expression for sensitivity to eribulin mesylate in this basal tumor that appears to have up-regulation of the mesenchymal-stemcell component. Targeted Therapy: Wildtype for EGFR, KRAS, BRAF and PIK3CA. There is very low expression of BRCA1 suggesting that PARP inhibitors may be beneficial. There is moderately high expression of ERBB2 mrna consistent with the positive ERBB2 signature seen on BluePrint as well as a very high expression of both EGFR and PIK3CA mrna. This patient may have a low level Her2 activating mutation and if anti-her2 therapy were considered, there might be consideration of using TDM-1 or Trastuzumab in combination with an irreversible inhibitor to Her2 such as neratinib as opposed to lapatinib as these functional mutations are frequently resistant to reversible inhibitors such as lapatinib. The high PIK3CA mrna expression suggests benefit from a PIK3CA inhibitor. Clinical trials are listed on the website. THERAPRINT OVERVIEW TheraPrint for breast cancer patients provides an individualized genomic fingerprint of the patient s tumor and correlates the results with a likely response to a variety of hormonal, chemo and biological therapies. TheraPrint provides gene expression results for 55 biomarkers and variant analysis results for 4 genes that have been identified as potential markers for predicting response. Some of these markers are directly targeted by existing drugs or a drug class; others have been shown to be involved in resistance or response mechanisms. Within categories, the gene biomarkers are listed according to drug class. The clinical relevance statement is a short description of how expression and mutation presence is linked to response or resistance to the associated drugs. TheraPrint biomarkers have been investigated in research and clinical studies for their potential involvement in the context of cancer therapy. The quality and quantity of the supporting literature for each biomarker are indicated by the level of evidence. Detailed information about each biomarker, reference lists and more information can be found in the appendix or via the link www.agendia.com/theraprint/breastcancerinformation. The selection of any, all or none of the matched drugs/agents resides solely with the discretion of the treating physician.
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PAGE 3 OF 7 THERAPRINT RESULTS SERM (e.g. tamoxifen, raloxifene, fulvestrant) BCL2 X BCL2 expression in ER-positive patients is correlated with positive response to endocrine therapy. ESR1 X expression of Estrogen Receptor 1 (ESR1) is correlated to response to endocrine therapies. ESR2 X ESR2 expression is directly correlated with prognosis and response to endocrine therapies. PR (PGR) X expression of Progesterone Receptor (PR) is correlated to response to endocrine therapies. CCND1 X ER-positive breast cancer patients with high expression of cyclin D1 may not benefit from endocrine therapy. EPHA2 X expression of EPHA2 in ER-positive breast cancer is linked to poor prognosis and poor response to endocrine therapy. HIF1A X expression of HIF1A is a marker of poor prognosis and is linked to poor endocrine therapy response. PDGFRA X expression of PDGFRA may be predictive for resistance to tamoxifen treatment in ER-positive patients. TIMP1 X expression of TIMP1 is linked to endocrine therapy resistance. VEGFR2 (KDR) X expression of VEGFR2 is linked to endocrine therapy resistance in ER-positive patients. ERBB4 (HER4) X Loss of HER4 expression is a marker for resistance to endocrine therapy. Aromatase Inhibitors (e.g. anastrozole, letrozole, exemestane) ESR1 X expression of ESR1 is linked to response to Aromatase Inhibitors in post menopausal patients. PR (PGR) X expression of PR is correlated to response to endocrine therapies. ER-positive and PR-positive expression are linked to a greater response than PR alone. Anti-androgen (e.g. abitarone, bicalutamide, flutamide) AR X expression of androgen receptor (AR) might be linked to response to anti-androgen treatment. Alkylating Agents (e.g. temozolomide, cyclophosphamide) MGMT X In triple negative patients, low expression of MGMT is correlated with response to alkylation drugs. TIMP1 X TIMP1 expression is linked to lack of response to alkylation agent therapy. ABCB1 X ABCB1 expression is linked to resistance to alkylating agents. Anti-Metabolites (e.g. 5-fluorouracil, gemcitabine, methotrexate) CES2 X CES2 expression is linked to response to anti-metabolite chemotherapy. DCK X expression levels of DCK are indicative for positive response to nucleoside analogs. TYMP X TYMP expression is linked to response to anti-metabolite chemotherapy. TS (TYMS) X expression of TYMS is linked to a better response and survival benefit from anti-metabolite chemotherapy. ABCG2 X ABCG2 expression is linked to resistance to anti-metabolite chemotherapy. RRM1 X expression of RRM1 is suspected to be indicator of poor response to anti-metabolite chemotherapy. RRM2B X expression levels of RRM2B might be linked to anti-metabolite therapy resistance. TIMP1 X TIMP1 expression is linked to lack of response to anti-metabolite chemotherapy.
PAGE 4 OF 7 Anthracyclines (e.g. doxorubicin, epirubicin) TOP2A X expression levels of TOP2A in HER2-positive patients are linked to poor prognosis and better response to anthracycline based chemotherapy. BRCA1 X Patients with low BRCA1 expression level may benefit from anthracycline based chemotherapy. GRB7 X expression level of GRB7 is associated with poor prognosis and in triple negative patients and may be indicative for resistance to anthracycline based chemotherapy. YWHAZ X expression of YWHAZ is linked to resistance to anthracycline based chemotherapy. Mitotic Inhibitors/ Taxanes (e.g. docetaxel, ixabepilone, eribulin mesylate) BCL2 X expression of BCL2 is linked to response to taxane based chemotherapy. SPARC X SPARC expression is linked to response to taxane based chemotherapy, especially nab-paclitaxel. GRB7 X expression of GRB7 is linked to resistance to taxane based chemotherapy. Platinum Based (e.g. carboplatin, cisplatin) CES2 X expression of CES2 might be linked to positive response to platinum based chemotherapy. BRCA1 X Patients with low BRCA1 expression level may benefit from platinum based chemotherapy. ERCC1 X expression of ERCC1 is linked to better response to platinum based chemotherapy. Topoisomerase Inhibitors (e.g. irinotecan, etoposide) AURKA X levels of AURKA indicate proliferative activity and more likely response to anti-proliferative chemotherapy. MKI67 X levels of MKI67 indicate proliferative activity and more likely response to anti-proliferative chemotherapy. TOP2A X expression levels of TOP2A might be linked to better response to toposoimerase II inhibitors. ral TOP1 X expression of TOP1 is associated with poor prognosis and linked to resistance to topoisomerase inhibitors. ABCB1 X expression of ABCB1 may predict multidrug resistance. ABCG2 X expression levels of ABCG2 might be linked to multidrug resistance. HIF1A X expression of HIF1A is a marker of poor prognosis and is linked to poor chemotherapy response. NFKB1 X expression of NFKB1 is involved in tumor growth, progression and resistance to chemotherapy. TIMP1 X expression of TIMP1 is linked to chemotherapy resistance.
PAGE 5 OF 7 Angiogenesis Inhibitor (e.g. bevacizumab) PECAM1 X PECAM1 expression is associated with poor prognosis and might be linked to response to bevacizumab. VEGFA X expression of VEGFA is weakly linked to response to angiogenesis inhibitors. VEGFB X expression of VEGFB is weakly linked to response to angiogenesis inhibitors. VEGFR1 (FLT1) X VEGFR1 expression may be an indicator for poor prognosis and indicative for response to anti-vegfr antibodies. VEGFR2 (KDR) X expression of VEGFR2 is a sign of increased vascularization and is linked to response to angiogenesis inhibitors. HIF1A X expression of HIF1A is linked to acquired anti-angiogenesis inhibitor resistance. HER2/ EGFR Inhibitors (e.g. trastuzumab, lapatinib, cetuximab, gefitinib, pertuzumab) ERBB2 (HER2) X Amplification and high expression of ERBB2/HER2 is correlated to response to Herceptin and other HER2-inhibitors. ERBB3 (HER3) X expression of ERBB3 is correlated to poor prognosis and might be indicative for improved response to HER2/HER3 targeting agents. ERBB4 (HER4) X expression of ERBB4 might be a favorable prognostic marker and an indication for efficient response to Herceptin treatment in HER2-positive patients. EGFR X EGFR expression might be linked to better response to anti-egfr antibodies like pertuzumab. EGFR variant analysis wt Tumors without EGFR mutations may be sensitive to anti-egfr monoclonal antibody therapy. PIK3CA variant analysis wt PIK3CA mutations in exon 9 (p.glu542, p.glu545) and exon 20 (p.his1047) may be indicative for resistance to anti- HER2 inhibitors. Patients wildtype for PIK3CA may benefit. EPHA2 X expression of EPHA2 in HER2-positive patients indicate poor prognosis and poor response to anti-her2 therapy. IGF1R X IGF1R expression can indicate resistance to HER2-targeted therapy in HER2-positive cancers. PIK3CA X expression PIK3CA could indicate resistance to HER2 and EGFR targeting drugs. PTEN X PTEN gene expression can be predictive for reduced responsiveness to HER2-inhibitors. HER2/ PI3K-downstream pathway inhibitors (e.g. everolimus, temsirolimus, vemurafenib, dabrafenib, sorafinib) BRAF X Very high expression of BRAF maybe indicates improved response to kinase inhibitors. KRAS X Very high expression of KRAS may indicate improved response to kinase inhibitors. MAP2K1 (MEK1) X expression of MAP2K1 is potentially linked to response to MEK1/2 inhibitors. MAP3K3 X MAP3K3 activates MEK1/2 which is linked to response to MEK1/2 inhibitors. MTOR X expression of MTOR may be linked to response to mtor inhibitors. PIK3CA X Very high expression of PIK3CA might be indicative for response to kinase inhibitors. PIK3R1 X expression of PIK3R1 might indicate a high activity of PI3-Kinase and better response to PI3-Kinase inhibitors. PTEN X PTEN gene expression can be predictive for increased responsiveness to AKT/mTOR inhibitors. BRAF variant analysis wt Patients with a p.val600 mutation might be eligible for clinical studies with BRAF-and MEK inhibitors. KRAS variant analysis wt MEK inhibitors are emerging as an important drug class to consider for KRAS Gly12 or Gly13 mutant patients. PIK3CA variant analysis wt Patients with PIK3CA activating mutations in exon 9 (p.glu542, p.glu545) or exon 20 (p.his1047) might have better response to PI3K/AKT/mTOR pathway inhibitors.
PAGE 6 OF 7 Other Kinase Inhibitors (e.g. aurora kinase inhibitor, foretinib) AURKA X expression of AURKA is likely to predict response to Aurora-A inhibitors. cmet (MET) X expression of MET has been linked to poor prognosis and better response to MET inhibitors. EPHA2 X expression of EPHA2 might be indicative for response to multikinase inhibitors like dasatinib. KIT X expression of KIT is a marker of basal-like breast cancer and may be linked to response to kinase inhibitors. LYN X expression of LYN is linked to response to Src kinase inhibitors, particularly in basal/ triple negative breast cancer. PDGFRA X expression of PDGFRA is linked to response to Tyrosine Kinase Inhibitors (TKI). SRC X SRC expression is a marker for triple negative subtype and might indicate improved response to SRC kinase inhibitors like dasatinib. Mismatch repair system modulators/ PARP Inhibitors (e.g. olaparib, veliparib, AG014699) BRCA1 X Patients with low expression of BRCA1 may benefit from PARP inhibitors. RAD51B X Rad51 expression is associated with increased resistance to DNA damaging agents. IGFR Inhibitor (e.g. figitumumab) IGF1R X expression of IGF1R is linked to response to IGFR inhibitors. Inhibitors of Apoptosis (e.g. YM155) BIRC5 X expression of BIRC5 (survin) are linked to therapy response to specific inhibitors like YM1555. BH3 Mimetic BCL2 X Patients with high expression of BCL2 might benefit from antisense therapy oblimersen sodium or specific inhibitors of Bcl-2, Bcl-xL and Bcl-w, like ABT-737. Proteosome Inhibitor (e.g. bortezomib) NFKB1 X NFKB1 is activated in HER2-positive breast cancer. Combining proteosome inhibitor with HER2 targeted therapy is linked to response. Demethylating Agents CDH1 X expression of E-Cadherin (CDH1) is a marker for lobular breast cancer and is linked to response to demethylating drug therapies. Bisphosphonates (or diphosphonates) PTHLH X expression of PTHLH is strongly linked to metastatic spread to bone and maybe indicative of poor response to bisphosphonates.
PAGE 7 OF 7 THERAPRINT ASSAY DETAILS GENE EXPRESSION Using DNA microarray technology, TheraPrint measures the mrna level of genes that are of potential interest in the context of cancer therapy. The expression of each gene is assessed in multifold to assure precise results. For most genes, there are no known absolute cut-offs to determine whether a given expression level is truly high/low or what exact level of expression determines sensitivity or resistance. To provide an indication of whether a gene expression is rather low or rather high, the patient s gene expression is compared to the gene expression of a reference population. The reference population was established using 2274 specimens from breast cancer patients untreated with chemotherapy. Each of the samples was hybridized onto the Agendia micro-array in the same fashion as the patient s sample. The reference distribution is different for each gene, but is translated to an expression range of 5% to 95% in order to standardize the results. The level of the patient s gene expression is compared to the reference distribution and indicated as X in the colored bars. to high expression is depicted from left to right. Drug sensitivity (green) and resistance (blue) are depicted as gradients with the deepest color indicating the highest likelihood of resistance or sensitivity. THERAPRINT ASSAY DETAILS VARIANT ANALYSIS This variant analysis assay qualitatively detects specific mutations in DNA of the KRAS, BRAF, PIK3CA and EGFR genes using mutation specific primers in combination with real time PCR. The detailed list of variants that can be detected are listed in the appendix. This highly sensitive PCR assay is capable of reproducibly detecting mutations in samples with as little as 1 to 5% mutated DNA. The variant analysis provides a binary result, wildtype or mutant. The result is linked to sensitivity (green) or resistance (blue) of specific drug classes. THERAPRINT ASSAY LEVEL OF EVIDENCE The level of evidence for each gene is assigned according to the literature level of evidence defined by the U.S. Preventive Services Task Force1 and indicated by circles with three empty circles for lowest level and three filled circles for highest evidence level. = Level 3 Late phase clinical trial evidence in humans and a strong association between gene expression or mutational variant and the responsiveness to therapy for the drug class under consideration = Level 2 Multiple studies in humans have shown moderate cause-effect relationship between the gene expression or mutational variant and the responsiveness to therapy for the drug class under consideration = Level 1 Preclinical evidence or evidence in other cancer types or cell lines indicate predictive value of marker = Level 0 No direct evidence to support the role of the gene in the activity of the drug class under consideration, but strong biological connection between the marker and drug response THERAPRINT ASSAY TUMOR PERCENTAGE Agendia requires specimens with a 30% tumor content or greater. The tumor percentage in this specimen was: 70% For more background information on all genes, drug classes and links to clinical studies, please see: www.agendia.com/theraprint/breastcancerinformation Jia-Perng Jennifer Wei, MD, PhD Laboratory Director Neil Barth, M.D., F.A.C.P. Chief Medical Officer For In Vitro Diagnostic Use Caution: Federal law restricts this device to sale by or on the order of a physician. Agendia is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) as qualified to perform high-complexity clinical testing. Decisions regarding care and treatment should not be based on a single test such as this test. Rather, decisions on care and treatment should be based on the independent medical judgment of the treating physician taking into consideration all available information concerning the patient s condition, including other pathological tests, in accordance with the standard of care in a given community. This test was performed at Agendia s Irvine, California laboratory (05D1089250) Reference: 1) Guirguis-Blake J, Calonge N, Miller T, Siu A, Teutsch S, Whitlock E (2007). Current processes of the U.S. Preventive Services Task Force: refining evidence-based recommendation development. Ann. Intern. Med. 147 (2): 117-122. PMID 17576998