Prognostic Genomic Alterations Research Articles

Prognostic genomic alterations in patients undergoing liver resection for hepatocellular carcinoma

IntroductionGenetic mutations and amplifications found in hepatocellular carcinoma (HCC) have a potentially prognostic impact. The aim of this study was to investigate the prognostic value of mutations and amplifications in HCC from patients that were liver resected.MethodsPatients liver resected for HCC at Copenhagen University Hospital Rigshospitalet between May 2014 and January 2018 were included. DNA from freshly frozen tumour tissue was investigated with TruSight Oncology 500. Mutations and amplifications were correlated with disease-free survival and overall survival using multivariate Cox regression to assess the effect on prognosis.ResultsOf the 51 patients included, 88% were male and the median age was 69 years. Most patients had a single tumour (84%) with no vascular invasion (67%) in a non-cirrhotic liver (76% with fibrosis, 24% with cirrhosis). The median follow-up was 37 months. Patients with a MYC amplification (8%) were significantly younger than the remaining patients. Furthermore, they had a significantly shorter overall survival (15 months (95% CI: 0.0–31.6) vs. 59 months (95% CI: 34.4–83.6), p = < 0.001) and disease-free survival (8 months (95% CI: 4.6–11.4) vs. 19 months (95% CI: 12.3–25.7), p = 0.03). However, only overall survival remained statistically significant in the adjusted analysis. Furthermore, all patients with an ARID1A mutation (6%) had microvascular invasion and significantly larger tumours than the patients without ARID1A mutation.ConclusionMYC amplifications had a prognostic influence on survival, whereas ARID1A gene mutations were correlated with microvascular invasion. These may serve as prognostic biomarkers and should be validated in large, independent cohort.

Genomic alterations predictive of poor clinical outcomes in pan-cancer.

Background: Genomic alterations are highly frequent across cancers, but their prognostic impact is not well characterized in pan-cancer cohorts. Here, we use pan-cancer cohorts from TCGA and MSK-IMPACT to evaluate the associations of common genomic alterations with poor clinical outcome.Materials and Methods: Genomic alterations in commonly altered genes were extracted from Pan-Cancer TCGA and MSK-IMPACT cohorts. Multivariable Cox regression analyses stratified by cancer type defined adjusted hazard ratios (AHRs) for disease-specific survival (DSS), progression-free survival (PFS) and overall survival (OS).Results: Using TCGA we identified 32 mutated genes, and 15 copy number (CN) genes with frequency >= 4% in 9,104 patients across 28 cancers. On UVA, having a TP53-mutations or any mutation in the 31 genes (mut31) were associated with worse PFS (HR: 1.22, p < 0.0001 and HR: 1.1, p = 0.04, respectively) and DSS (HR: 1.38, p < 0.0001, and HR: 1.16, p = 0.03, respectively). CDKN2A, PTEN deletions, and MYC-amplifications were associated with PFS and DSS (p < 0.05 for all).On MVA, including TP53-mutations, mut31, CDKN2A-deletion, PTEN-deletion, and MYC-amplification, all five alterations were independently prognostic of poor PFS and DSS.Similar results were observed in an independent cohort from MSK-IMPACT (n = 7,051) where TP53 was associated with poor OS independent of mut31 and CN alterations in CDKN2A, PTEN, and MYC in primary tumors (p < 0.0001).Conclusions: TP53-mutations, CDKN2A-deletion, PTEN-deletion, and MYC-amplification are independent pan-cancer prognostic genomic alterations.

Narrative review of the emerging role of molecular biomarkers in guiding the definitive management of unresectable non-small cell lung cancer.

The addition of PD-L1 targeting consolidation therapy to previously standard of care concurrent chemoradiation for locally advanced, unresectable non-small cell lung cancer resulted in dramatic improvements in clinical outcomes. However, in contrast to patients with metastatic disease, the application of immunotherapies is not currently guided by molecular characteristics of patient tumors. Furthermore, despite increasing awareness of predictive and/or prognostic genomic alterations in patients with locally advanced disease, the utility of targeted therapies, such as those aimed at alterations in EGFR or ALK, remains unclear in this subset of patients. As a result, patients with unresectable, locally advanced non-small cell lung cancer are treated uniformly according to histology, regardless of other molecular features despite the potential for treatment-associated risks without a clear benefit. Here, we first discuss the advantages of utilizing molecular biomarkers to guide treatment of non-small cell lung cancer based on treatment outcomes in the metastatic setting. Next, we review preclinical and retrospective clinical data that supports potential further personalization of these treatment strategies in earlier stages of disease. Finally, we discuss some of the ongoing clinical trials attempting to address these hypotheses prospectively.

Abstract 6468: Prognostic genomic alterations associated with recurrence after primary therapy for patients with luminal B breast cancer

Abstract Purpose: Luminal type breast cancers account for the most common subtypes of breast cancers, among which luminal B subtype is relatively faster tumor growing and confers substantial risk of recurrence after primary treatment despite adjuvant endocrine therapy. Understanding the molecular alterations underlying the poorer survival outcome for luminal B tumors represents an unmet medical need. Experimental design: The archival samples of 16 recurrences within 5 years, 3 recurrences between 5-10 years and 24 non-recurrence tumor tissues from luminal B breast cancer patients were retrieved. Genomic alterations of these 43 breast cancer samples were detected using deep next-generation sequencing of a 440-gene panel. The mRNA levels of candidate genes in breast cancer patients were analyzed from The Cancer Genome Atlas (TCGA) database. Results: Overall, genomic alterations were found in 340 genes, including single nucleotide variants and copy number variation. Comparing to the non-recurrence tumors, NUP98 (31.3%), MAPK4 (18.8%), PTEN (18.8%), PER1 (18.8%) and TRIP11 (18.8%) showed higher population frequency in the recurrence tumors, and IGF2R (50.0%), PIM1 (45.8%) and ROS1 (37.5%) were dominate in the non-recurrence tumors. After a validation with the public clinical dataset, we identified three potential prognostic biomarkers, including NUP98, PER1, and TRIP11. We observed missense mutation or copy number deletion of NUP98, PER1 and TRIP11 in early recurrence tumors. Data from TCGA database exhibited patients with breast cancer harbored lower NUP98, PER1 and TRIP11 transcripts levels. Notably, lower NUP98, PER1 and TRIP11 expression levels correlated with worse recurrence-free survival in luminal B breast cancer. Interestingly, based on algorithm for visualization of protein interaction network, we found these 3 genes were all involved in androgen receptor signaling network. Conclusion: Our study identified NUP98, PER1, and TRIP11 which potentially served as biomarkers to predict recurrence in luminal B breast cancer. Further research is required to understand the association between genomic alterations and androgen receptor signaling as well as its clinical impact. Citation Format: Chun-Yu Liu, Ji-Lin Chen, Yi-Ting Yang, Yi-Fang Tsai, Ta-Chung Chao, Kien Thiam Tan, Wan-Lun Wang, Pei-Ju Lien, Shu-Jen Chen, Ling-Ming Tseng. Prognostic genomic alterations associated with recurrence after primary therapy for patients with luminal B breast cancer [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 6468.

NIMG-09. NONINVASIVE PERFUSION IMAGING BIOMARKER OF MALIGNANT GENOTYPE IN ISOCITRATE DEHYDROGENASE MUTANT GLIOMAS

Abstract OBJECTIVE A small subset of IDHmut astrocytomas behave aggressively, similarly to IDHwt glioblastoma. Genomic correlates of poor prognosis IDHmut astrocytomas include global relative DNA hypomethylation, MYCN amplification copy number variation (CNV) abundance, and CDKN2A/B homozygous deletion. We sought to identify a non-invasive imaging correlate of poor prognosis IDHmut astrocytomas. METHODS 30 IDHmut astrocytomas (NYU=18, TCGA=12) were included. Relative cerebral blood volume was obtained from 4 regions of interest within the highest perfusion areas. Genomic CNV analysis and CDKN2A/B copy number status was obtained using Illumina Infinium 450k or Illumina EPIC methylation array data. Associations between rCBV, survival, and genomic alterations were evaluated. An additional 22 IDHmut astrocytomas were obtained from another institution for validation. RESULTS CNV stable (CNV-S, n=14) astrocytomas demonstrated significantly lower mean rCBV than and CNV unstable (CNV-U, n=16) (P=0.0.0155) ones. IDHmut astrocytomas with CDKN2A/B homozygous deletion (n=7) had higher rCBV (3.9 ± 2.3, mean ± SD) compared to those without this alteration (n=22; 1.8 ± 1.9, mean ± SD; P=0.0489). In the validation set, there was no significant evidence in rCBV between CNV-S and CNV-U tumors (P=0.3976). These results were sensitive to a single outlier in the CNV-S group. Excluding this case with rCBV=7.15, the CNV-S tumors demonstrated significantly lower mean rCBV (P=0.0279). IDHmut astrocytomas with CDKN2A/B homozygous deletion (n=9) tended to have higher rCBV (4.2 ± 1.8, mean ± SD) compared to those without this alteration (n=16; 2.5 ± 1.5, mean ± SD; P=0.0757, t-test). This led to significant discrimination (P=0.0328, Wilcoxon). CONCLUSION Our study is the first to identify a non-invasive imaging biomarker for prognostic genomic alterations in IDHmut astrocytomas. Greater CNV abundance and/or CDKN2A/B homozygous deletion have higher rCBV and worse prognosis. Our methods can be applied to standard clinical practice and may enhance informed treatment decisions in the preoperative and immediate postoperative settings.

Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy.

Liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor DNA (ctDNA) to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of a sequenced tissue sample obtained from the same tumor. The clinical utility study (CUS) for the FoundationACT™ ctDNA assay (Foundation Medicine, Cambridge, MA, USA; NCT02620527) is a multi-center prospective clinical study for multiple solid tumor types to compare genomic profiling of paired tissue and blood samples from the same patient. In this subset of the study, paired specimens from 96 patients with colorectal cancer (CRC) were analyzed with comprehensive genomic profiling (CGP) of the tumor tissue sample (FoundationOne®) and blood sample (FoundationACT™). Both samples underwent CGP using the hybrid capture-based Illumina Hi-Seq technology. Maximum somatic allele frequency (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both tumor and liquid were compared for each subject. Among these patients, 61% were male; 74% had clinical stage IV disease, 19% had clinical stage III disease, and 7% had clinical stage II disease. Time between the tissue biopsy and liquid biopsy (range, 0-709 days) had a significant impact on the positive percent agreement (PPA) between the two assays. Eighty percent of cases had evidence of ctDNA in the blood (MSAF >0). For all cases with MSAF >0, 171 base substitutions and insertions/deletions (indels) were identified in the tumor, and 79% (PPA) of these identical alterations were also identified in matched ctDNA samples; PPA increased to 87% for cases <270 days between the tissue and liquid biopsy, 95% for <90 days, and 100% PPA for <30 days. All known and likely short variants in KRAS, NRAS, and BRAF were analyzed independently as testing of these genes is recommended by the National Comprehensive Cancer Network (NCCN) for patients with CRC and have therapeutic implications. For NCCN genes, PPA was 80% for all time points for short variants; PPA increased to 90% for cases <270 days between the tissue and liquid biopsy. There was high concordance for KRAS G12X between tissue and liquid: overall percent agreement (97%), PPA (93%), negative percent agreement (NPA) (100%), positive predictive value (PPV) (100%), and negative predictive value (NPV) (96%) for the <270 day cohort. In cases where tumor tissue profiling is not possible, these results provide compelling evidence that genomic profiling of ctDNA in late stage CRC shows a high concordance with tumor tissue sequencing results and can be used to identify most clinically relevant alterations capable of guiding therapy for these patients.

Abstract 4607: G1/S transition-related gene mutations associated with survival of hepatocellular carcinoma patients

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common malignancies in China and has limited therapeutic options. Genomic alterations in HCC had been widely explored and some prognostic genomic alterations were identified. Different etiologic characteristics were discovered in Chinese HCC patients compared with Western population; however, the genomic profiles of Chinese patients had not been thoroughly elucidated. Methods: FFPE tumor samples of 94 Chinese HCC patients, including 79 males and 15 females with a median age of 56, were collected for next-generation sequencing (NGS)-based 450 genes panel assay. Genomic alterations including single base substitution, short and long insertions/deletions, copy number variations, and gene rearrangement and fusions were assessed. Gene Ontology (GO) analysis was conducted with the genes whose variation rates were higher than 5% (N = 22). The TCGA HCC dataset with 198 patients was used to assess the prognostic value of the significantly enriched GO terms. Results: The top 10 highly mutant genes in the 94 Chinese HCC cohort were TP53 (64.9%), TERT (31.9%), CTNNB1 (23.4%), AXIN1 (16.0%), STK24 (12.8%), RB1 (11.7%), CCND1 (9.6%), ARID1A (9.6%), LRPIB (8.5%) and ARID2 (8.5%). The Gene Ontology analysis revealed these gene alterations were significantly associated with pivotal signal pathways and cell proliferation including phosphatidylinositol phosphorylation, protein kinase B signaling, cell cycle arrest, and G1/S transition of mitotic cell cycle. The G1/S transition-related genes included TP53, TERT, RB1, CCND1 and CDKN2A. Moreover, the TCGA HCC patients with mutations of G1/S phase transition and mitotic cell cycle-related genes had a poor survival (p = 0.029). Conclusions: Our study showed that Chinese HCC patients had different genomic alteration profile compared with Western population. The most frequent mutant gene in Chinese HCC was TP53 in 65% of the HCC patients, compared to 31% in the TCGA dataset (PMID:28622513). Genomic alterations in G1/S transition of mitotic cell cycle-related genes in Chinese HCC patients might be a negative prognostic factor. Our preliminary result suggested that functional analysis of HCC genomic alteration profile could have prognostic utility. Citation Format: Bingyuan Zhang, Tianqiang Song, Pingzhou Yang, Songzhu Yang, Chao Guo, Lei Li, Shuang Ren, Maolin Yan, Weiyu Hu, Honglin Guo, Yongjian Zhang, Yanlin Li, Weifeng Wang, Kai Wang, Ming Yao. G1/S transition-related gene mutations associated with survival of hepatocellular carcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4607.

Comprehensive genomic profiling of ctDNA in patients with colon cancer and its fidelity to the genomics of the tumor biopsy.

569 Background: The liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor (ct) DNA to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of the tumor. The clinical utility study (CUS) for FoundationACT (Foundation Medicine, Cambridge, MA; NCT02620527) is a large multi-center prospective clinical study to validate this ctDNA assay for multiple solid tumor types. In this subset of the CUS study, paired specimens from 98 patients with colon cancer were analyzed with comprehensive genomic profiling of the tumor (FoundationOne) and a blood sample (FoundationACT). Methods: Maximum somatic allele fraction (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both FoundationOne and FoundationACT were compared for each subject. Results: 60% were male; 73 had stage IV, 17 had stage III, and 8 had stage II disease. 16% of cases had an MSAF value of 0, indicating that no ctDNA were in these samples. For the cases with MSAF &gt; 0, 153 insertion/deletions (indels)/substitutions were identified in the tumor, and 73% of these identical alterations were also identified in the ctDNA samples. As robust analytical performance for FoundationACT has been demonstrated at MSAF &gt; 0.5% for indel/subs, further analysis was conducted using this threshold. 83% of the alterations identified with FoundationOne were identified with FoundationACT. Further, 90% of NRAS/KRAS and 75% BRAF alterations (NCCN guideline genes) were concordant between the two assays. Lastly, there were 11 patients with tumor biopsy and blood draw taken within 30 days of each other, and in these there was 100% concordant. Association of the genomics results with other clinical variables will be presented for the available subset of patients. Conclusions: In cases where tumor profiling is not possible, these results provide compelling evidence that comprehensive molecular profiling of ctDNA in colon cancer can be used to identify most clinically relevant alterations and has fidelity to the genomics of the tumor. Clinical trial information: NCT02620527.

High Risk Myeloma Is Characterized By the Bi-Allelic Inactivation of CDKN2C and RB1

IntroductionGene expression and comprehensive genomic profiling (CGP) underscore the importance of multiple myeloma (MM) being driven by diverse genomic abnormalities and are increasingly being integrated into personalized treatment algorithms to optimize clinical outcomes, in particular that of high risk disease. Furthermore, CGP allow for ultra-deep sequencing of various clinically relevant and targetable genomic alterations using a single assay, with an advantage of detection of low frequency variants.MethodsSamples from 578 patients (monoclonal gammopathy of undetermined significance, MGUS, (n=19); smoldering multiple myeloma, SMM, (n=42); or multiple myeloma, MM, (n=517; 87 newly diagnosed (NDMM), 107after treatment (TRMM), and 323 at relapse (RLMM)) were analyzed using the FoundationOne® Heme (F1H) assay. 50 ng of DNA and RNA from CD138+ selected cells were analyzed for genomic alterations including base substitutions, indels, copy number alterations, and rearrangements. Sequencing was performed to a median depth of 468x in 405 genes, as well as selected introns of 31 genes involved in rearrangements. Additionally, matched Gene Expression Profiling (GEP) was performed using Affymetrix U133 Plus 2 array, and GEP70-defined risk status and molecular subgroups were calculated.ResultsResults of the F1H assay revealed the most common alterations in MM to be: KRAS (28.8%), NRAS (23.2%), TP53 (17.4%), BRAF (6.8%), CDKN2C (6.0%), RB1 (5.8%), TRAF3 (5.8%), DNMT3A (3.9%), TET2 (3.7%) and ATM (2.5%), including mutations, homozygous loss and rearrangements. When these frequencies were split across GEP70 risk groups, TP53, CDKN2C/FAF1, RB1, and the t(4;14) were significantly different (p<0.05). As the disease progressed from MGUS to relapse, the number of mutations showed an increasing trend. Likewise, there were significant differences in the number of mutations between CCND1/CCND3 (CD-1) and low bone disease, CD-1 and hyperdiploid, and hyperdiploid and proliferation groups.In order to identify independent prognostic genomic alterations, we performed a multivariate Cox regression analysis on all the gene alterations that were present in at least 5% of the patient cohort, resulting in identification of four significant alterations: the t(4;14), mutation/loss of TP53, CDKN2C/FAF1 or RB1. Alterations in CDKN2C and RB1 were associated with the PR group. When the MM samples were split according to type (NDMM, TRMM, RLMM) the effect on survival of each of these alteration was more pronounced at relapse, but still present at diagnosis for CDKN2C and t(4;14). Bi-allelic events in CDKN2C, TP53 and RB1 were examined, by both homozygous deletion and monosomy with accompanying mutation, showing the rate of inactivation increased from 9.2% in NDMM to 17.9% at relapse, indicating that bi-allelic inactivation of these genes are correlated with relapse. CDKN2C and TP53 are known prognostic markers but the prognostic significance of RB1 has been debated. Previous data have shown that the association of t(4;14) with del(13q) results in insignificance of del(13q) as a prognostic marker in multivariate analyses. Here, we confirmed that the prognostic effect of RB1 is not due to association with t(4;14), and show that patients with either the t(4;14) or alteration of RB1 have a poor prognosis, which is worse when both lesions are present.ConclusionsUsing the F1H assay, we establish the mutational spectrum in MM, identifying lesions associated with high risk. This is the first study in MM to identify and confirm the poor prognostic effect of RB1 driven by bi-allelic inactivation, which is more prevalent at relapse. Furthermore, we determined the gene alterations that are independent prognostic markers in relapsed MM, thereby identifying novel therapeutic targets. DisclosuresHe:Foundation Medicine, Inc: Employment, Equity Ownership. Bailey:Foundation Medicine, Inc: Employment, Equity Ownership. Ashby:University of Arkansas for Medical Sciences: Employment. Zhong:foundation medicine: Employment. Nahas:Foundation medicine: Employment. Ali:Foundation Medicine: Employment, Equity Ownership. Vergillo:Foundation Medicine, Inc: Employment. Ross:Foundation Medicine, Inc: Employment. Miller:Foundation Medicine: Employment, Equity Ownership. Stephens:Foundation Medicine: Employment, Equity Ownership. Barlogie:Signal Genetics: Patents & Royalties. Mughal:Foundation Medicine: Employment, Equity Ownership. Davies:Celgene: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Janssen: Consultancy, Honoraria. Morgan:Takeda: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Bristol Meyers: Consultancy, Honoraria; Janssen: Research Funding; Univ of AR for Medical Sciences: Employment.