EIT PACMAN Study preliminary results: OncoSignal pathway analysis identifies actionable cancer targets.

e15606 Background: Precision medicine refers to tailoring of treatment to each individual patient, although identifying tumor driving signaling pathways (SP) that are functionally active is still a challenge. OncoSignal pathway tests quantitatively measure activity of SP such as estrogen receptor (ER), androgen receptor (AR), PI3K, MAPK, Hedgehog (HH), TGF-β, Notch on fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissue samples. OncoSignal pathway analysis aimed at assessing clinically actionable SP and retrospectively predicting targeted drug response on a series of patients’ (pts) samples from the MOSCATO trial run at Gustave Roussy. Methods: OncoSignal pathway analysis (ER, AR, PI3K, MAPK, HH, Notch, TGF-β) was performed blinded by Molecular Pathway Dx (Philips, Eindhoven) on metastatic tumor tissue samples from breast cancer (BC), prostate (PC), and high grade serous ovarian cancers (OC). Using Affymetrix expression array data from public GEO datasets, SP activity was analyzed in healthy prostate, breast, and ovarian tissue to define abnormal SP activity thresholds for tumor tissue pathway analysis. For each individual sample, SP alterations were considered tumor driving SP if sample SP activity exceeded the 95th percentile of SP activity within healthy tissue. Results by OncoSignal were also combined with clinical characteristics and molecular alterations identified in the MOSCATO trial. Results: Identified tumor driving SP were ER, AR, MAPK-AP1, HH, PI3K pathway in BC (n = 5), AR in PC (n = 30); AP1, Notch, TGFβ in OC (n = 17). OncoSignal identified clinically actionable tumor driving pathways in all BC samples (median tumor cellularity [MTC]: 40%, range 15-80%); 30/31 PC samples (MTC: 62%, range 25-90%), 16/17 OC samples (MTC 62%, range 15-80%). Actionable mutations were previously identified in 4/5 BC; 13/31 PC; 6/17 OC. Seven pts with BC and PC were treated with targeted therapy. OncoSignal pathway analysis correctly predicted response/resistance in 4 of these pts (57%). Conclusions: OncoSignal pathway analysis correctly identified SP activity alterations and predicted targeted drug response in this series of patients. OncoSignal will be further validated prospectively in precision medicine studies at Gustave Roussy in which patients are stratified for targeted treatment by mutation analysis.

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Primary tumor (p-bx) versus metastatic tumor (m-bx) tissue versus liquid biopsy (lb) in intrahepatic cholangiocarcinoma (IHCC): A comparative comprehensive genomic profiling (CGP) study.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.4579 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 4579-4579

Author(s):

Jeffrey S. Ross ◽

Ethan Sokol ◽

Dean Pavlick ◽

Jo-Anne Vergilio ◽

Jonathan Keith Killian ◽

...

Keyword(s):

Drug Response ◽

Soft Tissues ◽

Metastatic Tumor ◽

Genomic Profiling ◽

Tissue Samples ◽

Upper Gi ◽

Metastatic Lesions ◽

Mutational Burden ◽

Comprehensive Genomic Profiling ◽

Tumor Mutational Burden

4579 Background: Genomic alterations (GA) characteristic of IHCC are well known. We queried whether GA from Pbx would differ from Mbx and Lbx in IHCC. Methods: Hybrid-capture based CGP was performed on 1,268 tissue samples of advanced stage IHCC using Pbx in 1,048 cases and Mbx from 220 cases and 364 Lbx cases (solid tissue: 318-327 genes, Lbx: 72 genes). Tumor mutational burden (TMB) was determined on 0.8-1.1 Mbp of sequenced DNA. PD-L1 expression in tumor cells (Dako 22C3) was measured by IHC. Results: Mbx sites included: lymph nodes (63), soft tissues (47), peritoneum (34), lung/pleura (27), omentum (15), bone (10), abdomen (7), GYN tract (5), liver (4), brain (2), Upper GI (2), colon (2), bladder (1), and adrenal (1). The GA/sample and biomarkers of immuno-oncology (IO) drug response were similarThe KRAS mutation frequency including G12C alterations was doubled in Mbx compared to Pbx and Lbx (p < 0.001). Frequencies of untargetable GA were similar overall. IDH1 (p < 0.001) and FGFR2 GA known to be enriched in IHCC were less frequent in Mbx than Pbx. Both IDH1 and FGFR2 were identified in Lbx. GA in STK11 (p < 0.001) and SMAD4 (p = 0.0016) were more frequently identified in Mbx. Conclusions: GA found in Pbx vs Mbx and Lbx in IHCC are significantly different; the Mbx cohort features greater KRAS and lower IDH1 and FGFR2 GA. Lbx detected more IDH1 GA than Mbx. This suggests that the Mbx group may contain non-IHCC cases whose metastatic lesions were actually derived from other primary sites and incorrectly assigned the diagnosis of IHCC. [Table: see text]

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Concordance of DNA damage repair (DDR) gene mutations in paired primary and metastatic prostate cancer (PC) samples.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.5020 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 5020-5020

Author(s):

Michael Thomas Schweizer ◽

Smruthy Sivakumar ◽

Hanna Tukachinsky ◽

Ilsa Coleman ◽

Navonil De Sarkar ◽

...

Keyword(s):

Precision Medicine ◽

Tumor Tissue ◽

Final Analysis ◽

Molecular Testing ◽

Sequencing Data ◽

University Of Washington ◽

Tissue Samples ◽

Metastatic Tissue ◽

Mutational Status ◽

Primary Tissue

5020 Background: Mutations in DDR genes represent actionable alterations that can be used to guide precision medicine strategies in men with advanced PC. However, acquisition of contemporary tissue samples for advanced molecular testing can be a barrier to deploying precision medicine approaches. We hypothesized that most DDR alterations represent early truncal events in PC and that archival primary tissue would faithfully reflect mutations found in cell-free circulating tumor (ctDNA) and/or metastatic tissue. Methods: Patients were included in this study if a DDR pathway mutation was detected in metastatic tissue or ctDNA and primary tissue sequencing was available for comparison. Sequencing data from three cohorts were analyzed: 1) FoundationOne, 2) University of Washington (UW-OncoPlex or SU2C/PCF International Dream Team sequencing pipelines) and 3) University of Washington rapid autopsy series. Only pathogenic somatic mutations were included and we required ≥30 days between primary tumor tissue and ctDNA/tumor tissue acquisition. Clonal hematopoiesis of indeterminant potential (CHIP) and germline events were adjudicated by an expert molecular pathologist and excluded. Variants detected only in plasma were considered likely to be CHIP or low subclones if the variant fraction was <1% and/or >5-fold less than the estimate tumor content in plasma. Results: Paired primary and ctDNA/metastatic samples were sequenced from 72 individuals with known DDR alterations. After excluding ctDNA cases where only CHIP (N=13) and/or germline events (N=7) were observed, 51 subjects remained and were included in the final analysis. The median time from acquisition of primary tissue to acquisition of ctDNA or tumor tissue was 52 mos (range: 1 – 193 mos). Concordance in DDR genes across samples was 86% (95% CI: 74-93%). Rates of concordance between metastatic-primary and ctDNA-primary pairs were similar when CHIP cases were excluded (87% and 85%, respectively). BRCA2 reversion mutations associated with resistance to PARP inhibitors and platinum chemotherapy were detected in ctDNA from two subjects. Conclusions: These data provide evidence that primary prostate tissue accurately reflect the mutational status of actionable DDR genes in men with metastatic PC, supporting the hypothesis that DDR alterations are early truncal events. After excluding likely CHIP events, ctDNA profiling accurately captured these truncal DDR mutations, while also detecting reversion alterations that may suggest potential resistance mechanisms.[Table: see text]

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Towards Realizing the Vision of Precision Medicine: AI Based Prediction of Clinical Drug Response

SSRN Electronic Journal ◽

10.2139/ssrn.3729265 ◽

2020 ◽

Author(s):

Johann de Jong ◽

Ioana Cutcutache ◽

Matthew Page ◽

Sami Elmoufti ◽

Cynthia Dilley ◽

...

Keyword(s):

Precision Medicine ◽

Drug Response ◽

Clinical Drug

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A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

Current Bioinformatics ◽

10.2174/1574893615666200324133451 ◽

2020 ◽

Vol 15 ◽

Author(s):

Zheng Jiang ◽

Hui Liu ◽

Siwen Zhang ◽

Jia Liu ◽

Weitao Wang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Liquid Biopsy ◽

Tumor Tissue ◽

High Sensitivity ◽

Next Generation ◽

Tissue Samples ◽

Next Generation Sequencing Technology ◽

Medication Selection ◽

Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

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Combining tissue and circulating tumor DNA increases the detection rate of a CTNNB1 mutation in hepatocellular carcinoma

BMC Cancer ◽

10.1186/s12885-021-08103-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Stine Karlsen Oversoe ◽

Michelle Simone Clement ◽

Britta Weber ◽

Henning Grønbæk ◽

Stephen Jacques Hamilton-Dutoit ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Mutation Rate ◽

Detection Rate ◽

Tumor Tissue ◽

Circulating Tumor Dna ◽

Treatment Modalities ◽

Advanced Hepatocellular Carcinoma ◽

Tissue Samples ◽

The Impact ◽

Tumor Dna

Abstract Background and aims Studies suggest that mutations in the CTNNB1 gene are predictive of response to immunotherapy, an emerging therapy for advanced hepatocellular carcinoma (HCC). Analysis of circulating tumor DNA (ctDNA) offers the possibility of serial non-invasive mutational profiling of tumors. Combining tumor tissue and ctDNA analysis may increase the detection rate of mutations. This study aimed to evaluate the frequency of the CTNNB1 p.T41A mutation in ctDNA and tumor samples from HCC patients and to evaluate the concordance rates between plasma and tissue. We further evaluated changes in ctDNA after various HCC treatment modalities and the impact of the CTNNB1 p.T41A mutation on the clinical course of HCC. Methods We used droplet digital PCR to analyze plasma from 95 patients and the corresponding tumor samples from 37 patients during 3 years follow up. Results In tumor tissue samples, the mutation rate was 8.1% (3/37). In ctDNA from HCC patients, the CTNNB1 mutation rate was 9.5% (9/95) in the pre-treatment samples. Adding results from plasma analysis to the subgroup of patients with available tissue samples, the mutation detection rate increased to 13.5% (5/37). There was no difference in overall survival according to CTNNB1 mutational status. Serial testing of ctDNA suggested a possible clonal evolution of HCC or arising multicentric tumors with separate genetic profiles in individual patients. Conclusion Combining analysis of ctDNA and tumor tissue increased the detection rate of CTNNB1 mutation in HCC patients. A liquid biopsy approach may be useful in a tailored therapy of HCC.

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Personalizing Therapy for Metastatic Prostate Cancer: The Role of Solid and Liquid Tumor Biopsies

American Society of Clinical Oncology Educational Book ◽

10.1200/edbk_175510 ◽

2017 ◽

pp. 358-369 ◽

Cited By ~ 1

Author(s):

Terence W. Friedlander ◽

Colin C. Pritchard ◽

Himisha Beltran

Keyword(s):

Prostate Cancer ◽

Metastatic Prostate Cancer ◽

Tumor Tissue ◽

Neuroendocrine Differentiation ◽

Metastatic Tumor ◽

Metastatic Lesion ◽

Phenotypic Changes ◽

Tumor Biopsies ◽

Bioinformatic Approach

Although biopsies of metastatic prostate cancer are rarely undertaken in the clinical setting, there is increasing interest in developing personalized approaches to therapy by taking into account the genetic and phenotypic changes in an individual tumor. Indeed, analysis of metastatic prostate tumors can predict sensitivity to agents that inhibit DNA repair and resistance to novel hormonal agents, such as abiraterone and enzalutamide, and identify phenotypic changes, such as neuroendocrine differentiation, that have important clinical implications. Although obtaining metastatic tumor tissue is necessary for this genomic and molecular profiling, knowing when to biopsy, selecting the appropriate metastatic lesion, and interpreting the results are major challenges facing clinicians today. In this article, we discuss the rationale for obtaining metastatic tumor tissue, review the bioinformatic approach to analyzing these specimens, discuss the timing and approach to solid and liquid tumor biopsies, review the challenges associated with obtaining and acting on clinically relevant results, and discuss opportunities for the future.

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PATH-06. ASSESSMENT OF CIRCULATING TUMOR DNA IN CEREBROSPINAL FLUID BY WHOLE EXOME SEQUENCING TO DETECT GENOMIC ALTERATIONS OF GLIOBLASTOMA

Neuro-Oncology ◽

10.1093/neuonc/noaa215.688 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii165-ii165

Author(s):

Hao Duan ◽

Zhenqiang He ◽

Zhenghe Chen ◽

Yonggao Mou

Keyword(s):

Cerebrospinal Fluid ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Tumor Tissue ◽

Circulating Tumor Dna ◽

Genomic Alterations ◽

Tissue Samples ◽

Whole Exome ◽

Resected Tumor ◽

Tumor Dna

Abstract Cerebrospinal fluid (CSF) has been demonstrated as a better source of circulating tumor DNA (ctDNA) than plasma for brain tumors. However, it is unclear whether whole exome sequencing (WES) is qualified for detection of ctDNA in CSF. The aim of this study was to determine if assessment of ctDNA in CSF by WES is a feasible approach to detect genomic alterations of glioblastoma. CSFs of ten glioblastoma patients were collected pre-operatively at the Department of Neurosurgery, Sun Yat-sen University Cancer Center. ctDNA in CSF and genome DNA in the resected tumor were extracted and subjected to WES. The identified glioblastoma-associated mutations from ctDNA in CSF and genome DNA in the resected tumor were compared. Due to the ctDNA in CSF was unqualified for exome sequencing for one patient, nine patients were included into the final analysis. More glioblastoma-associated mutations tended to be detected in CSF comparing with the corresponding tumor tissue samples (3.56±0.75 vs. 2.22±0.32, P=0.097), while the statistical significance was limited by the small sample size. The average mutation frequencies were similar in CSF and tumor tissue samples (74.12% ± 6.03% vs. 73.83% ± 5.95%, P = 0.924). The R132H mutation of isocitrate dehydrogenase 1 and the G34V mutation of H3F3A which had been reported in the pathological diagnoses were also detected from ctDNA in CSF by WES. Patients who received temozolomide chemotherapy previously or those whose tumor involved subventricular zone tended to harbor more mutations in their CSF. Assessment of ctDNA in CSF by WES is a feasible approach to detect genomic alterations of glioblastoma, which may provide useful information for the decision of treatment strategy.

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Precision medicine biomarkers in brain metastases: applications, discordances, and obstacles

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab105 ◽

2021 ◽

Vol 3 (Supplement_5) ◽

pp. v35-v42

Author(s):

Ariane Steindl ◽

Priscilla K Brastianos ◽

Matthias Preusser ◽

Anna S Berghoff

Keyword(s):

Brain Metastases ◽

Precision Medicine ◽

Tumor Tissue ◽

Metastatic Cancer ◽

Predictive Biomarkers ◽

Current Evidence ◽

Therapeutic Decision ◽

Molecular Alteration ◽

Mortality And Morbidity ◽

Therapeutic Decision Making

Abstract Brain metastases (BM) present a common cause of mortality and morbidity in several metastatic cancer entities. New therapeutic developments during the last decades, including targeted and immune-related therapies, have shown considerable extra- and intracranial response rates in specific subgroups of BM patients. However, differences in the molecular alteration in the BM tumor tissue compared to extracranial tumors leads to heterogeneous therapeutic responses. Therefore, an accurate molecular analyzation of BM tissue, if possible, has become an essential part in therapeutic decision making in BM patients. The concordance of predictive molecular biomarkers between multiple sites including extracranial and intracranial tumor tissue have been analyzed for some but not all biomarkers routinely applied in modern precision medicine approaches. In the present review, we summarize the current evidence of predictive biomarkers for personalized therapy approaches in the treatment of parenchymal BM.

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