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  • 1
    In: Genome Biology, Springer Science and Business Media LLC, Vol. 23, No. 1 ( 2022-12)
    Abstract: Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose CONET, a probabilistic model for joint inference of the evolutionary tree on copy number events and copy number calling. CONET employs an efficient, regularized MCMC procedure to search the space of possible model structures and parameters. We introduce a range of model priors and penalties for efficient regularization. CONET reveals copy number evolution in two breast cancer samples, and outperforms other methods in tree reconstruction, breakpoint identification and copy number calling.
    Type of Medium: Online Resource
    ISSN: 1474-760X
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 2
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. 3385-3385
    Abstract: Purpose: In the ongoing, single-arm, Phase 2 VISION study (NCT02864992), tepotinib (a highly selective MET inhibitor) has shown durable clinical activity in NSCLC patients (pts) with METex14 skipping. Here, we report the biomarker profile of pts screened with liquid biopsy (LBx) for inclusion in the study. Methods: Pts with advanced NSCLC and previously confirmed EGFR/ALK wild-type status were prospectively screened for MET alterations using plasma samples collected during pre-screening/screening. Plasma ctDNA sequencing was performed at a central laboratory using a 73-gene next-generation sequencing panel (Guardant360®). Results: Of 6,034 pts screened, 813 pts had results pending at data cut and of 5,221 pts tested, sequencing failed in 41 pts. The success rate of LBx testing was consistent across centers. Of 5,180 patients analyzed, 694 pts (13.4%) had no mutation detected. Despite the intent of screening EGFR/ALK wild-type pts, 327 pts (6.3%) had EGFR mutations and 49 (0.9%) had ALK/ROS fusions. 188 pts (3.6%) had METex14 skipping (Table) and 256 pts (4.9%) had MET amplification (amp) without METex14 skipping. The median age of METex14 pts was 72 years; 47% were male; 46% were never smokers and 65% had adenocarcinoma histology. In METex14 pts, the most frequently occurring driver co-alterations were amp in MET (13.3%), EGFR (7.4%), CDK4 (6.4%), BRAF (5.3%) and CDK6 (4.8%), and mutations in GNAS (5.3%). In METamp pts, the most frequently occurring driver co-alterations were CDK6 (60.5%), BRAF (43.4%), EGFR (28.9%), MYC (21.9%) and CCNE1 (19.9%) amps. Overall, TP53 mutations were detected in 55.9% of METex14 pts and 79.7% of METamp pts. Table:Characterization of METex14 skipping (n=188)n (%)Insertions/deletions (indels)93 (49.5)Indel at acceptor site54 (28.7)Indel at donor site36 (19.1)Whole exon 14 deletion3 (1.6)Single nucleotide variation (SNV)95 (50.5)SNV at donor site93 (49.5)SNV at acceptor site2 (1.1)SNVs and indelsSNV/indel at donor site129 (68.6)SNV/indel at acceptor site56 (29.8)SNV/indel whole exon 14 deletion3 (1.6) Conclusions: In this population, METex14 skipping can be successfully detected through non-invasive LBx analysis using a next-generation sequencing panel. The rate of METex14 skipping and the genomic profile and demographics of pts were similar to previously reported data. Citation Format: Xiuning Le, Dariusz Kowalski, Byoung Chul Cho, Pierfranco Conte, Enriqueta Felip, Marina Chiara Garassino, Santiago Viteri, Gee-Chen Chang, John Richart, Luiz Paz-Ares, Dilafruz Juraeva, Josef Straub, Christopher Stroh, Paul Paik. Liquid biopsy to detect MET exon 14 skipping (METex14) and MET amplification in patients with advanced NSCLC: Biomarker analysis from VISION study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3385.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 3
    Online Resource
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    Springer Science and Business Media LLC ; 2021
    In:  Scientific Reports Vol. 11, No. 1 ( 2021-08-06)
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 11, No. 1 ( 2021-08-06)
    Abstract: Computational models for drug sensitivity prediction have the potential to significantly improve personalized cancer medicine. Drug sensitivity assays, combined with profiling of cancer cell lines and drugs become increasingly available for training such models. Multiple methods were proposed for predicting drug sensitivity from cancer cell line features, some in a multi-task fashion. So far, no such model leveraged drug inhibition profiles. Importantly, multi-task models require a tailored approach to model interpretability. In this work, we develop DEERS, a neural network recommender system for kinase inhibitor sensitivity prediction. The model utilizes molecular features of the cancer cell lines and kinase inhibition profiles of the drugs. DEERS incorporates two autoencoders to project cell line and drug features into 10-dimensional hidden representations and a feed-forward neural network to combine them into response prediction. We propose a novel interpretability approach, which in addition to the set of modeled features considers also the genes and processes outside of this set. Our approach outperforms simpler matrix factorization models, achieving R  $$=$$ =  0.82 correlation between true and predicted response for the unseen cell lines. The interpretability analysis identifies 67 biological processes that drive the cell line sensitivity to particular compounds. Detailed case studies are shown for PHA-793887, XMD14-99 and Dabrafenib.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
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  • 4
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-05-10)
    Abstract: Primary lymphomas of the central nervous system (PCNSL) are mainly diffuse large B-cell lymphomas (DLBCLs) confined to the central nervous system (CNS). Molecular drivers of PCNSL have not been fully elucidated. Here, we profile and compare the whole-genome and transcriptome landscape of 51 CNS lymphomas (CNSL) to 39 follicular lymphoma and 36 DLBCL cases outside the CNS. We find recurrent mutations in JAK-STAT, NFkB, and B-cell receptor signaling pathways, including hallmark mutations in MYD88 L265P (67%) and CD79B (63%), and CDKN2A deletions (83%). PCNSLs exhibit significantly more focal deletions of HLA-D (6p21) locus as a potential mechanism of immune evasion. Mutational signatures correlating with DNA replication and mitosis are significantly enriched in PCNSL. TERT gene expression is significantly higher in PCNSL compared to activated B-cell (ABC)-DLBCL. Transcriptome analysis clearly distinguishes PCNSL and systemic DLBCL into distinct molecular subtypes. Epstein-Barr virus (EBV)+ CNSL cases lack recurrent mutational hotspots apart from IG and HLA-DRB loci. We show that PCNSL can be clearly distinguished from DLBCL, having distinct expression profiles, IG expression and translocation patterns, as well as specific combinations of genetic alterations.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 5
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 41, No. 16_suppl ( 2023-06-01), p. 3030-3030
    Abstract: 3030 Background: To determine whether changes in circulating tumor DNA (ctDNA) levels reflect treatment outcome, Friends of Cancer Research created the ctDNA to Monitor Treatment Response (ctMoniTR) Project with collaborators from industry, government, academia, and advocacy. A prior ctMoniTR effort analyzing 5 clinical trials (CT) showed an association between decreases in ctDNA levels and improved outcomes in patients with advanced non-small cell lung cancer (aNSCLC) treated with an anti-PD-(L)1. The current study expands that work and focuses on CT investigating tyrosine kinase inhibitors (TKI) treatment in oncogene-driven aNSCLC. Methods: We performed a retrospective analysis of patient-level clinical and ctDNA data across 8 CT representing 1,015 patients with aNSCLC treated with TKI (i.e., anti-EGFR, ALK, RET, or MET). Patients included in the analysis had a baseline ctDNA measurement (T0), an on treatment ctDNA measurement within 10 weeks of treatment initiation (for those with multiple ctDNA measurements within 10 weeks, we used the lowest measurement within 10 weeks) (T1), and overall survival (OS) data (n=749). CT used different ctDNA collection timepoints and assays. We randomly divided the dataset into training (2/3 of the data) and validation (1/3 of the data) datasets stratified by CT cohort (i.e., arm), age, tumor stage, and prior lines of therapy, then ran initial analyses on the training dataset (n=501; reported herein). ctDNA change was calculated as the percent change in maximum variant allele frequency (VAF) between T0 and T1 using tumor-derived variants provided by sponsors for each unique patient sample. CT used either ddPCR or an NGS assay. ctDNA limits of detection were assay specific and varied across CT. Multivariate analyses are ongoing and validation dataset analyses will be conducted. Results: At T0, 141 patients had non-detected (ND) ctDNA and 360 patients had detected (D) ctDNA. Of these, 27% (n=136) had ND ctDNA at both T0 and T1 (“ND/ND”), 52% (n=260) had changes from D at T0 to ND at T1 (“D/ND”), 12% (n=60) had at least a 50% decrease from T0 to T1 (“decrease”) and 9% (n=45) had an increase or a less pronounced decrease in ctDNA. In a univariate analysis, patients with ND/ND and D/ND were associated with improved OS compared to the decrease group. In addition to other characteristics, patients with max VAF ≤0.5% or ND at T0 (n=214, 43%) had improved OS (HR=0.44, P 〈 0.001) compared to those with max VAF 〉 0.5% at T0 (n=287, 57%). Conclusions: In a retrospective aggregate analysis of 8 CT, ND ctDNA at T1 was associated with improved OS in patients with aNSCLC treated with TKI. Changes in ctDNA levels, particularly from D to ND, may provide an early indication of treatment benefit and predict long-term outcomes in this population. Additional ctMoniTR analyses are ongoing to validate the potential use of ctDNA as an early endpoint.
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2023
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  • 6
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 39, No. 15_suppl ( 2021-05-20), p. 9012-9012
    Abstract: 9012 Background: In the VISION study, tepotinib in METex14 skipping NSCLC pts (Cohort A) had robust and durable clinical activity. Serial LBx samples were collected for biomarker analyses, presented herein. Methods: LBx samples taken at baseline (BL), Week 6, 12, & end of treatment (EOT) were analyzed using Guardant360 ® CDx (73 genes). Investigator (INV)-assessed clinical outcome was evaluated per BL biomarker profiles and by molecular response (MR; defined as 〉 75% depletion from BL in METex14 variant allele frequency [VAF] ctDNA confirmed in 2 consecutive samples) or molecular progression (MP; defined as VAF increase 〉 0 from BL). Acquired resistance was investigated in EOT samples, following progression per INV. Results: LBx pts (n = 99) had a median age of 72 yrs (range 49–88), 53% were male, 44% never smokers, 85% had adenocarcinoma. INV ORR was 53% (95% CI 42, 63); ORR in 1L (n = 44) was 59% (43, 74) & ≥2L (n = 55) was 47% (33, 61). 94 pts had BL biomarker profiles; these were similar in 1L and ≥2L pts, except EGFR amp: 1/43 1L [2%] vs 8/51 ≥2L [16%] . Outcomes were not impacted by location/type of METex14 alteration. 1 pt with concomitant MET M1250T mutation had a PFS of 17.3 months. A trend towards better efficacy was seen in pts with concomitant MET amp (6 responses in 8 pts). Response to tepotinib occurred both in pts with wt or mutant TP53; however, there was a trend for longer mDOR in pts with wt TP53 (18.3 [95% CI 9.7, ne] vs 7.1 [4.7, 10.9] months) and mPFS (9.5 [6.7, 19.7] vs 5.1 [2.8, 6.9] months). Concomitant oncogenic mutations were rare, with no responses in 3 pts with KRAS, NRAS alterations and 3 responses in 5 pts with PI3K/AKT alterations. 65 pts had 2 consecutive on-treatment samples: 46 (71%) had confirmed MR, 5 (8%) had confirmed MP, 14 (22%) had no change in VAF or lacked confirmation. MR was associated with clinical response and MP was associated with no response/short PFS (Table). 52 pts with progression had EOT LBx samples. Emerging MET resistance mutations (Y1230H/C & D1228H/N) occurred in 7 (13%) pts, all responders and 5/7 had PFS 〉 10 months. Analyses on non-MET-driven resistance mechanisms will be presented. Conclusions: LBx biomarker analysis from the largest on-treatment data set for a MET inhibitor in METex14 skipping NSCLC, showed that ctDNA depletion in METex14 VAF is associated with improved clinical response in pts treated with tepotinib. This suggests serial LBx could help us to monitor response/non-response, understand resistance, and guide trials that test escalation/de-escalation strategies to improve outcomes and maximize QOL. Clinical trial information: NCT02864992. [Table: see text]
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2021
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  • 7
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 40, No. 16_suppl ( 2022-06-01), p. 9121-9121
    Abstract: 9121 Background: Tepotinib, a potent, highly selective, oral, MET inhibitor, showed meaningful activity in patients (pts) with NSCLC with high-level METamp by LBx in VISION. Exploratory biomarker analyses are presented herein. Methods: Pts had 0–2 prior therapy lines, high-level METamp by LBx (Guardant360; MET copy number ≥2.5), and no MET exon 14 skipping or EGFR/ ALK alterations. Pts received tepotinib 500 mg once daily (450 mg active moiety). Primary endpoint was objective response by independent review; data cut-off: Aug 20, 2021. Exploratory biomarker analysis included LBx at baseline (BL), on treatment, and end of treatment (EOT). Early molecular response (eMR) was defined as undetectable METamp 6–8 weeks on treatment. Results: 24 pts were enrolled (median age: 63.4 years [yrs]; smokers: 88%; ECOG PS 1: 88%; adenocarcinoma: 67%). Treatment duration was ≥1 yr in five pts and ≥2 yrs in two pts (both ongoing). Overall, objective response rate (ORR) was 41.7% (95% CI: 22.1, 63.4). Treatment-naïve pts (n=7) had an ORR of 71.4% (29.0, 96.3), median (m) DOR was 14.3 months (2.8, not estimable [ne] ), and mPFS was 15.6 months (1.4, ne). BL biomarker analyses according to clinical benefit (CR/PR/SD [n=11] vs PD/NE [n=13] ) showed association with better outcomes in pts with focal METamp, or without MYCamp or RB1 mutation (Table). MYCamp/ RB1 mutation was detected in 4/7 pts with neuroendocrine/not otherwise specified histology; MYCamp in 2/3 pts with neuroendocrine histology. Low BL ctDNA mutant allele frequency (MAF) was associated with better outcomes. 14 pts had eMRs (ORR 71.4%); persistent METamp (n=4) was associated with lack of clinical response. 2/9 pts with EOT biomarker profiles had emerging resistance mechanisms (MET kinase domain mutations Y1230 and D1228); both had METamp re-emergence. Treatment-related adverse events included edema (composite term; any grade: 46%; Grade 3: 13%) and constipation (any grade: 17%; Grade ≥3: 0%). Conclusions: Tepotinib showed meaningful activity, especially in first line, in the first trial of a MET inhibitor in EGFR WT NSCLC with high-level METamp to enroll based on a convenient LBx assay. BL biomarker analyses indicated focal METamp, MYC/RB1 WT, and low ctDNA MAF were associated with improved outcomes. Serial LBx could monitor molecular response and evaluate resistance. Clinical trial information: NCT02864992. [Table: see text]
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2022
    detail.hit.zdb_id: 2005181-5
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  • 8
    In: JCO Precision Oncology, American Society of Clinical Oncology (ASCO), , No. 5 ( 2021-11), p. 1802-1812
    Abstract: MET exon 14 skipping alterations ( METex14) comprise a diverse set of actionable oncogene drivers in non–small-cell lung cancer (NSCLC). Recent studies have established the efficacy of tyrosine kinase inhibitors for this patient population. The landscape of co-occurring genetic alterations in METex14 NSCLC and their potential impact to therapeutic sensitivities has not yet been fully described. MATERIALS AND METHODS METex14 NSCLC cases were collected from three cohorts: the VISION trial, and data sets from Guardant360 and GenePlus. Clinicopathologic characteristics and METex14 mutation sites were analyzed and compared across data sets. Co-occurring genetic alterations and the clonality relationships to METex14 were evaluated. RESULTS Of 40,824 NSCLCs, 692 METex14 cases (1.7%) were identified, including 332 in Guardant360, 188 in VISION, and 172 in GenePlus. The demographics and mutation type and/or sites were similar in the Asian versus Western cohorts. MET amplification, which were found to be associated with sensitivity to MET kinase inhibitors, co-occurs in 7.6%-13.8% of cases, whereas kinase domain secondary mutation of MET co-occurs in 5%-6%. When co-occurring with METex14, EGFR mutations were often identified as the dominant clone (78%, 7 of 9), whereas when co-occurring, METex14 (39%, 7 of 18) and KRAS (44%, 8 of 18) had similar rates of clonal dominance. PIK3CA and PTEN mutations were almost always subclones (89%, 16 of 18) to METex14. Moreover, RET-CCDC6 fusion and EGFR mutation were detected following crizotinib treatment in two patients, suggesting novel mechanisms of resistance. CONCLUSION METex14 mutations frequently co-occur with other potential driver oncogenes with differing patterns of clonal dominance observed among the drivers. This cellular context can provide insights into whether METex14 is acting as a primary oncogenic driver or resistance mechanism and help guide treatment choices.
    Type of Medium: Online Resource
    ISSN: 2473-4284
    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2021
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  • 9
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 38, No. 15_suppl ( 2020-05-20), p. 9556-9556
    Abstract: 9556 Background: Preliminary tepotinib data showed durable activity in pts with NSCLC with METex14 skipping prospectively identified by liquid (L+) or tissue (T+) biopsy. Having met target enrollment of ≥60 L+ pts & ≥60 T+ pts, we report primary data. Methods: VISION Cohort A enrolled pts with advanced EGFR/ALK wt, METex14 skipping NSCLC (asymptomatic brain metastases [BM] allowed), who received oral tepotinib 500 mg QD. On-study treatment decisions were based on investigator assessment (INV) of response. Primary endpoint was objective response rate (ORR) by independent review committee (IRC) analyzed in 3 primary ITT sets: L+ and/or T+, L+, T+. 2ary endpoints included ORR by INV, duration of response (DOR), disease control rate (DCR), PFS, OS, & safety. Preplanned analyses were performed in pts with BM at baseline (BL). BL/on-treatment ctDNA plasma samples (L+) were analyzed using a 73-gene NGS panel (Guardant360). Deep molecular responses (MR), defined as 〉 75% depletion of METex14, were compared with objective responses (OR). Results: By data cut-off (1 Oct 19) 151 pts received tepotinib (safety set); 99 L+/T+, 66 L+, 60 T+ pts comprised the 3 ITT sets with ≥6-month [m] follow-up. Across treatment lines (n = 44 1L, n = 55 ≥2L), primary ORR & mPFS [95% CI] in 99 L+/T+ pts were 43% [34–54] & 8.6 m [6.9–11.0] by IRC and 56% [45–66] & 9.5 m [6.7–13.5] by INV. ORR was similar in L+ or T+ pts (table) or in T+L− pts (n = 25): 40% [21–61] by IRC and 48% [28–69] by INV. Only 2 pts were T−L+. Outcomes were also comparable in pts with BM (n = 11): IRC ORR 55% [23–83] & mPFS 10.9 m [8.0–ne]. 34/51 pts (67%) with matched BL/on-treatment L+ samples had deep MR strongly associated with clinical response: 32/34 pts (94%) with MR had disease control (INV), including 29/34 pts (85%) with OR; 2/34 pts had progressive disease. Further biomarker data will be presented. Grade ≥3 treatment-related adverse events (TRAEs) were reported by 37/151 pts (25%). 13 pts (9%) discontinued due to TRAEs. Conclusions: Tepotinib is a promising targeted therapy with durable clinical activity and manageable toxicity in pts with METex14 skipping NSCLC L+ or T+, including pts with BM. High ORR & DCR in pts with ctDNA molecular responses support that MET inhibition in METex14+ tumor cells can lead to clinical benefit. Clinical trial information: NCT02864992 . [Table: see text]
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2020
    detail.hit.zdb_id: 2005181-5
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  • 10
    In: New England Journal of Medicine, Massachusetts Medical Society, Vol. 383, No. 10 ( 2020-09-03), p. 931-943
    Type of Medium: Online Resource
    ISSN: 0028-4793 , 1533-4406
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    Language: English
    Publisher: Massachusetts Medical Society
    Publication Date: 2020
    detail.hit.zdb_id: 1468837-2
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