Tumor Mutation Profiles Research Articles

24P Somatic tumor testing informs on mismatch repair deficiency (MMR-D) phenotype in patients with endometrial cancer

24P Somatic tumor testing informs on mismatch repair deficiency (MMR-D) phenotype in patients with endometrial cancer

Comparison of AYA versus non-AYA ovarian cancer genomic landscape in NCI-MATCH trial.

e17617 Background: NCI-MATCH, a signal-finding precision medicine trial, centrally screened tumors from ̃6000 patients age > 18 with refractory/relapsed cancer using Oncomine Comprehensive Assay (OCA) targeted gene panel. Screened cohort included a subset of patients with ovarian cancer age 18-39 yrs, overlapping adolescent and young adult (AYA) range (NCI consensus definition: 15-39 yrs). Objective of this study was to compare tumor genomic features of AYA to non-AYA ovarian cancers. Methods: Patient clinicopathologic, demographic, and tumor mutation (SNVs, Indels, CNVs by central OCA) data from NCI-MATCH were available. Analyses were restricted to mutation profiles generated by OCA version 2 (OCA v2), which assessed 143 genes and was used for most samples. Proportions of cases with mutations in each gene were compared for AYA and non-AYA groups by 2-sided Fisher’s exact tests. For each gene, association between age (continuous independent variable) and presence of mutation (binary dependent variable) was assessed using logistic regression. Benjamini-Hochberg adjusted p-values were computed; false discovery rate (FDR) was controlled at 10%. Results: Data from 455 ovarian cancers (437 epithelial, 18 stromal), including 21 AYA and 434 non-AYA cases, were included in this analysis. Among the 28 genes most frequently (in > 6 patient tumors) mutated and altered, CTNNB1 was mutated in 9.5% of AYA patients compared to 0.9% in non-AYA (unadj. p=0.027) but failed to meet 10% FDR criterion (FDR-adj. p=0.7). KRAS mutation was more frequent in AYA than non-AYA but not significantly after adjustment (FDR-adj. p=0.7). Logistic regression results showed TP53 mutation was significantly associated with older age (FDR-adj. p<0.0001), and ATM mutation was borderline associated with younger age (FDR-adj. p=0.052). No other differences, including in clinically actionable mutations ( BRCA1/2, MSH2), were observed. Table displays selected results. Conclusions: This preliminary study shows that no genes were mutated in significantly different proportion between AYA and non-AYA groups, but modeling age as a continuous variable highlighted known association of TP53 mutation with older age and a trend towards association of ATM mutation with younger age. More comprehensive tumor mutation profiling and analyses of additional tumor types may reveal further insights into rare AYA cancers. [Table: see text]

GATA6 amplification is associated with improved survival of TP53-mutated pancreatic cancer.

e16285 Background: Recent investigation in pancreatic adenocarcinoma (PDAC) demonstrates an association of molecular subtype with chemosensitivity and prognosis. TP53 and GATA6 are two genes independently associated with worse survival in PDAC. Here, we evaluated treatment outcome by genetic alterations of TP53 and GATA6 among patients with pancreatic cancer across New York’s largest health care system. Methods: This is a retrospective analysis of patients at Northwell Health diagnosed with PDAC between 2014 to 2021. Surgical status was used to segregate patients into two groups: resected and unresected. TP53 and GATA6 mutation status was compared for disease-free survival (DFS) (resected) or progression-free survival (PFS) (unresected), and for overall survival (OS). Additionally, patient survival by type of chemotherapy administered was evaluated. The Kaplan–Meier method was used to determine overall survival (OS), and the Wilcoxon test was used to compare survival curves. Results: Tumor mutational profiling data were available for 129 patients. TP53 mutations were found in 105 patients (81.4%), GATA6 amplifications were found in 18 patients (14.0%), and 16 patients had both mutations. TP53 mutations were associated with a worse OS compared to the wild-type TP53 population (n = 24) (median OS 22.7 months, 95% CI 12.5 to 41.1, vs. 44.3 months, 95% CI 24.5 to 80.3, HR 1.97, p = 0.048). Among patients with a TP53 mutation, a survival advantage was observed in those who had a GATA6 amplification compared to those who did not (median OS 25.5 months, 95% CI 10.9 to 44.6, vs. 22.1 months, 95% CI 12.6 to 51.5, HR 1.68, p = 0.038). In patients with unresected PDAC, the survival advantage of GATA6 amplification within TP53 mutated group was more prominent than the absence of the amplification (median OS 23.8 months, 95% CI 10.0 to 56.5, n = 12 vs. 10.5 months, 95% CI 4.4 to 24.8, n = 55, HR 0.52, p = 0.008). In the TP53 mutation group, among 33 patients who received Gem/NabP as the first-line chemotherapy, patients with GATA6 amplification (n = 8) had significantly improved survival compared to those without GATA6 amplification (n = 25) (mean OS 23.1 months, 95% CI 8.5 to 63.0, vs. 9.4 months, 95% CI 3.44 to 26.6, HR 0.51, p = 0.027). Conclusions: Genetic mutations in TP53 were associated with shorter OS than wild-type TP53. Contrary to our initial expectation that co-mutation would be associated with even worse survival, we found that GATA6 amplification appeared to attenuate poor prognosis observed in TP53-mutant patients. Additionally, GATA6 amplification may be a predictive marker for better responses to Gem/NabP chemotherapy.

The impact of African ancestry on colorectal cancer disparity.

3621 Background: Colorectal cancer is the second leading cause of cancer deaths in the world to affect both men and women. Racial disparities have been known to affect the disease diagnosis and progression, and proliferative genomic studies have been undertaken to elucidate their relationship. In this study, we investigate the tumor mutation profile in colorectal adenocarcinoma (COAD) based on genetic ancestry using The Cancer Genetic Ancestry Atlas (TCGAA). Methods: 59 AA (African American) individuals in TCGAA COAD dataset were identified. To account for and eliminate the biases introduced by self-identification of races, we utilized TCGAA genomic analysis to accurately estimate the ancestral genomic composition of each individual. For each individual, percentages of European (EA), West African (WA), East Asian (EAA), and Native American (NA) ancestry were identified based on Local Ancestry in adMixed Populations (LAMP). Individuals were screened for dominant WA ancestry (≥50% based on LAMP) and assigned to three groups, ≥90%, 80-89%, and 50-79%. Differences in gene mutation frequency and overall survival were compared among the three subgroups of individuals with WA ancestry. Results: Based on genomic ancestry analysis, 58 individuals with dominant WA ancestry (Range 53%-100%) were identified. We classified them into three groups based on percentage of WA ancestry: ≥90% (n = 17), 80-89% (n = 26), and 50-79% (n = 15). APC was the most frequently mutated gene in all groups except ≥90% WA ancestry, which had the most mutation frequency in TP53. ≥90% WA ancestry showed the highest rate of mutation of 81.3% in TP53 compared to 70.8% (80-90% WA ancestry) and 40.0% (50-79% WA ancestry). Interestingly, ≥90% WA ancestry had the highest average rate of mutation (33%) for 7 tumor suppressor genes ( AMER1, APC, ARID1, FBXW7, TCF7L2, TGFBR2, and TP53), compared to 29% and 22% in 80-89% WA ancestry and 50-79% WA ancestry, respectively. In addition, ≥90% WA ancestry had a lower rate (19%) of mutation in 6 oncogenes ( BRAF, NRAS, KRAS, PIK3CA, SMAD4, and SOX9) compared to 24% in both 80-89% and 50-79% WA ancestry. Although not statistically significant, a higher percentage of WA ancestry in an individual was correlated with a downward trend in the overall survival rate (median survival 56.3 months in ≥90% WA ancestry vs 61.8 months in 80-89% WA ancestry). Conclusions: In this study, we analyzed different gene mutations correlated with African ancestry and their potential relationship to the etiology, progression, and prognosis of COAD. The mutation profile of these genes will allow us to investigate altered pathways associated with African ancestry and draw insight into colon cancer pathogenesis in various ancestry groups. Further studies are warranted to elucidate the role of genetic ancestry in tumorigenesis and disease progression and to identify potential therapeutic targets specific to groups disproportionately affected by cancer.

Non-Iodine-Avid Disease Is Highly Prevalent in Distant Metastatic Differentiated Thyroid Cancer With Papillary Histology.

Patients with radioactive iodine (RAI) refractory metastatic differentiated thyroid cancer (DTC) have poor prognosis. Early identification of RAI refractoriness may improve care. This work aimed to characterize DTC patients with distant metastases (DM) at diagnosis who presented with non-iodine-avid disease. Retrospective analyses of DTC patients with DM at diagnosis who presented between 2012 and 2020 were performed. Iodine uptake in DM was correlated with tumor histology and mutational profile. The difference in uptake between BRAFV600E-like (BVL) and RAS-like (RL) cancers based on insights from The Cancer Genome Atlas was evaluated. Among 78 patients, 48.7% had negative uptake in DM on the first posttherapy scan. Negative scans were highly prevalent in papillary thyroid carcinoma (PTC) with papillary architecture, PTC with BRAFV600E mutation, and PTC with both BRAFV600E and TERT promoter mutations (71.1%, 80.9%, and 100%, respectively). BVL and RL tumors exhibited distinct uptake patterns with negative scan prevalence of 76.9% and 14.3% (P = .005). Multivariate logistical regression confirmed high odds of negative uptake in BVL tumors with either BVL mutations or papillary architecture, 19.8 (95% CI, 2.72-144), and low odds of negative uptake in RL tumors with either RL mutations or follicular architecture, 0.048 (95% CI, 0.006-0.344), after adjusting for age, sex, race, RAI preparation method, bone metastases, and RAI dose. Patients with negative scans were significantly older (62.4 vs 47.0 years, P = .03). Among DTC patients with DM at diagnosis, non-iodine-avid disease is highly prevalent in patients with BVL cancers, particularly with BRAFV600E and TERT promoter mutations, and is associated with an older age. Better strategies are needed to improve RAI treatment response for these patients.

Circulating Tumor DNA in Pediatric Cancer.

The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.

Prognostic impact of copy number alterations and tumor mutational burden in carcinoma of unknown primary.

Chromosomal aberrations are known to drive metastatic spread, but their profile is still elusive in carcinoma of unknown primary (CUP). Therefore, the aim of this study was to characterize the chromosomal aberration pattern in CUP depending on histological and clinical features and to assess its prognostic impact together with chromothripsis, tumor mutational burden (TMB), microsatellite instability (MSI), and mutational profiles as potential prognostic biomarkers. Chromosomal aberrations and chromothripsis were detected by methylation-based copy number variation (CNV) analysis, whereas TMB and MSI were calculated based on large next-generation sequencing (NGS) panels. Putative primaries were assigned by consensus between two independent oncologists. CNV losses varied depending on putative primaries and were more abundant in patients harboring TP53 mutations and/or deletions 17p. CNV loss was prognostically adverse in localized CUP treated with surgery and/or radiotherapy, but not in disseminated poor-risk CUP treated with palliative chemotherapy. CNV loss also worsened the prognosis in squamous cell CUP. Chromothripsis was detected in 18/59 (30.5%) patients without prognostic effect. TMB was highest in cases with MSI, squamous cell histology, and with lung, anal or cervical putative primaries. Overall, CNV, chromothripsis, TMB, and MSI profiles in CUP are reminiscent of biological characteristics known from other cancer entities without a unifying CUP-specific signature. Markedly, high-level CNV loss is an adverse predictive biomarker in localized but not disseminated chemotherapy-treated CUP. This implies that chromosomal losses drive CUP progression, but also increase susceptibility to chemotherapy, with both effects apparently leveling out in disseminated CUP.

Liquid Profiling for Cancer Patient Stratification in Precision Medicine-Current Status and Challenges for Successful Implementation in Standard Care.

Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.

Identification and verification of the ferroptosis- and pyroptosis-associated prognostic signature for low-grade glioma.

Accumulating evidence reveals that ferroptosis and pyroptosis play pivotal roles in tumorigenesis of low-grade glioma (LGG). In this research, we aimed to classify molecular subtypes and further identify and verify a novel multigene signature in LGG on the basis of ferroptosis- and pyroptosis-related genes (FPRGs). Raw sequencing data and corresponding clinical data of LGG samples retrieved from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases were obtained for the training and validation datasets. Non-negative matrix factorization (NMF) clustering defined by FPRGs associated with prognosis was performed to classify molecular subtypes of LGG patients. Least absolute shrinkage and selection operator-support vector machine-random forest analysis was carried out to develop a FPRG signature to predict the survival and benefit of immunotherapy of LGG patients. NMF clustering defined by FPRGs with prognostic values acted to categorize LGG patients into two molecular subtypes with different prognosis, clinical traits, and immune microenvironments. A six-FPRG prognostic signature was constructed, accompanied by the optimal p-value. The AUC values of our signature exhibited great prognostic performances. Our signature was superior to other four well-recognized signatures in predicting the survival probability of LGG patients. Immune characteristics, tumor mutation profile, tumor stemness indices, MGMT methylation, and immunotherapy response biomarkers showed significant differences between high- and low-risk populations. Finally, a nomogram was created for quantitative prediction of the survival probability of LGG patients, with the AUC values of the nomogram being 0.916, 0.888, and 0.836 for 1-, 3-, and 5-year survival, sequentially. Overall, the FPRG signature may function as an effective indicator for the prognosis prediction and immunotherapy response of LGG patients.

Abstract P1-18-05: Early changes in circulating tumor DNA and its effect on clinical outcomes in patients with advanced breast cancer receiving the CDK4/6 inhibitor palbociclib: Genotyping results from POLARIS

Abstract Background: POLARIS is a prospective, real-world study of palbociclib in patients with hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2–) advanced breast cancer (ABC) in the United States and Canada. These analyses evaluated the difference in tumor mutation profiles of patients receiving palbociclib in the first line versus second line or greater and examined the applicability of circulating tumor DNA (ctDNA) monitoring in a real-world setting. Methods: The clinical database cut-off date was March 16, 2021. Patients in the biomarker analysis group provided consent for serial blood sample collections, received ≥1 dose of initial palbociclib combination treatment, and had ≥1 ctDNA measurement available. The Guardant360 platform with somatic single-nucleotide variants in complete or critical exons of 73 genes was used. The association between early changes in ctDNA mutation allele fractions at Cycle 2 Day 1 (C2D1) and disease progression at Week 24 was evaluated using univariate and multivariable logistic regression analysis adjusting for line of therapy. Results: Among patients with HR+/HER2– ABC (N=347), 93.9% (n=326) had ctDNA measured at baseline, of which 85.9% (n=280) had ≥1 ctDNA alteration detected; 66.6% of patients received palbociclib treatment in the first line and 33.4% as second line or greater ABC setting. The frequencies of gene mutations at baseline were generally higher in patients receiving palbociclib as a second-line or greater therapy compared to those who received it as first-line therapy, particularly for ESR1 mutations (30% vs 15%) and FGFR1 mutations (13% vs 9%). With a median (range) follow-up duration of 18.5 (0.1-46.3) months, patients with total ctDNA increase at C2D1 (log ratio change >0) were 3.74 times more likely to have disease progression at Week 24 (odds ratio, 3.74 [95% CI, 1.71-8.17]; P=0.001) compared with those without change or with a decrease in ctDNA at C2D1 (log ratio change ≤0). The observed significant association remained after adjusting for line of therapy in the multivariable regression analysis (odds ratio, 2.62 [95% CI, 1.14-6.04]; P=0.023). Conclusions: Among patients with HR+/HER2- ABC receiving palbociclib, early changes in ctDNA mutations were significantly associated with disease progression. Further studies are needed to confirm these findings and to evaluate the clinical utility of ctDNA-guided “adaptive” early therapeutic interventions to improve outcomes in patients with metastatic breast cancer. Pfizer; NCT03280303 Citation Format: Debu Tripathy, Zhe Zhang, Joanne L. Blum, Meghan S. Karuturi, Steven L. McCune, Bijoy Telivala, Shailendra Lakhanpal, Kamal Patel, Richard C. Frank, Kit Lu, Chetan Deshpande, Yao Wang, Yuan Liu, Aditya Bardia. Early changes in circulating tumor DNA and its effect on clinical outcomes in patients with advanced breast cancer receiving the CDK4/6 inhibitor palbociclib: Genotyping results from POLARIS [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-18-05.

Abstract P4-07-05: Tumor mutational profiles of extreme long-term survivors with metastatic breast cancer

Abstract Background: Extreme population sampling can discover genomic characteristics with a high likelihood of functional significance. Here, we focus on people who live for many years or decades with metastatic breast cancer (MBC). Identification of genetic markers characteristic of this population may allow long-term survival to be predicted and enable de-escalation of treatment and improved care for this subgroup of breast cancer patients. . Methods: We identified women who have MBC and have lived greater than 10 years (HR+ breast cancer) or greater than 5 years (HR- breast cancer) from initial diagnosis. A total of 14 had archived FFPE metastatic tumor specimens and matched blood available for analysis. We performed whole-exome sequencing (WES) on FFPE tumor specimens (somatic) and blood samples (germline) pairs of 14 long term survivor patients. We used Illumina DRAGEN pipeline for the read alignment and base quality calibration and GATK MuTect2 pipeline for the somatic short variant identification. Common variants were filtered using 1000 Genomes Project, Exome Sequencing Project and gnomAD and annotated using Funcotator of the GATK pipeline. Results: A cohort of 53 patients, who met criteria, with biopsy proven MBC and long survival were identified in our institution. Among them, 14 patients had sufficient archived tumor for analysis, consisting of 7 HR+/HER2-, 5 HR+/HER2+, 1 HR+/HER2- and 1 TNBC specimens. Histological type was ductal in 9 patients and lobular in 4 patients. The median age of MBC diagnosis was 53 years with 11 patients diagnosed between ages 35-64 and 3 patients diagnosed after age 65. At the time of study, 13 of these 14 patients are still living. Median time to metastasis after diagnosis was 10.2 years with metastasis occurring in less than 1 year in 2 patients, less than 5 years in 10 patients and greater than 5 years in 2 patients. Metastases to bone were present in 9 patients, to visceral organs in 8 patients and to local and regional lymph nodes in 8 patients. The most common somatic variants identified were in PIK3CA, ARID1A, and TP53. When compared with prior analyses of MBC (INSERM, MBC Project), we found that ARID1A mutations were more commonly found, whereas PTEN and ESR1 mutations were never identified, suggesting a somatic mutational profile characteristic of extreme survivors. ARID1A mutations (2 nonsense - p.R1505* and p.Q944*, 1 missense - p.L1496V, 1 frameshift - p.P729fs) occurred in 4 patients, all with ER/PR+ and all HER2- breast cancer. Median survival to date since diagnosis was 30.1 years (range 21.4-39.0). Median survival to date after metastasis was 14.9 years (range 2.7-35.0). PIK3CA mutations (5 missense - p.H1047R x2, E545K, H1047L, E545K) occurred in 5 patients, all with ER/PR+ and 2 with HER2+ breast cancer. Median survival to date since diagnosis was 23.5 years (range 20.1-39.0). Median survival to date after metastasis was 15.97 years (range 3.4-35.0). TP53 mutations (1 nonsense - p.E285*, 1 missense - p.E285K, 1 frameshift - p.N200fs) occurred in 3 patients, all with ER/PR+ and 2 with HER2+ breast cancer. Median survival to date since diagnosis was 21.7 years (range 21.7-36.2). Median survival after metastasis was 16.0 years (range 2.7-21.4). Conclusions: ARID1A mutations are overrepresented and PTEN and ESR1 are underrepresented in metastatic tumors in extreme long-term survivors with MBC. Further analyses will determine if ARID1A mutations are present at tumor inception or are acquired in metastases in this cohort with indolent disease. Additionally, it is possible that germline genomic profiles may be relevant to long-term survival. Given the variability in this cohort, a larger sample of extreme survivors will be necessary to identify characteristic genetic profiles. Citation Format: Yang Hu, Junha Shin, Sushmita Roy, Mark E Burkard. Tumor mutational profiles of extreme long-term survivors with metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-07-05.

Association between tumor mutation profile and clinical outcomes among Hispanic-Latino patients with metastatic colorectal cancer.

17 Background: According to the World Health Organization GLOBOCAN database, in 2019, approximately 1.8 million new colorectal cancer cases were diagnosed, and almost 861,000 deaths were reported. In the United States, CRC is the third most frequent type of cancer and the second leading cause of cancer-related death. Although the overall incidence of CRC among the Hispanic population has been declining over the last decades, recently, a dramatic increase in CRC incidents among Hispanics younger than 50 years of age (early-onset CRC) has been reported. The increase in the incidence of early-onset CRC is markedly more significant in Hispanic-Latino (HL) patients population (45%) than in non-Hispanic Whites (NHW) (27%) and African-Americans (AA) (15%). Additionally, in contrast to NHW, Hispanics have a worse survival rate. The exact reason for these racial disparities and the biology of CRC in the HL population are not well understood. Therefore, we performed this study to better understand the biology of the disease in HL patients, which might help to identify new directions for targeted therapy. Methods: For the study, 52 formalin-fixed paraffin-embedded (FFPE) tumor tissue samples were collected and analyzed. We compared the results with individual patient clinical histories and outcomes. Of 52 patients with mCRC, 52 (100%) were identified as HL. We identified several commonly altered genes in HL patients ( APC, TP53, KRAS, GNAS, PICK3CA, and NOTCH). Compared to those in other studies. Results: Mutation frequencies in the APC gene were significantly higher among HL patients with mCRC. Moreover, the prevalence of the APC mutation was significantly higher among male HL patients compared to female patients. The combination of mutations in the APC, NOTCH, and KRAS genes in the same tumors was associated with a higher risk of progression after the first-line of chemotherapy and worse overall survival. In addition, mutations in the combination of GNAS and AURKA genes were associated with a significantly higher risk of progression after the first-line of chemotherapy. Conclusions: The data support the notion that the molecular drivers of colon cancer might be different in HL patients compared to other racial/ethnic groups.

Association Between Tumor Mutation Profile and Clinical Outcomes Among Hispanic-Latino Patients With Metastatic Colorectal Cancer.

In the United States, CRC is the third most common type of cancer and the second leading cause of cancer-related death. Although the incidence of CRC among the Hispanic population has been declining, recently, a dramatic increase in CRC incidents among HL younger than 50 years of age has been reported. The incidence of early-onset CRC is more significant in HL population (45%) than in non-Hispanic Whites (27%) and African-Americans (15%). The reason for these racial disparities and the biology of CRC in the HL are not well understood. We performed this study to understand the biology of the disease in HL patients. We analyzed formalin-fixed paraffin-embedded tumor tissue samples from 52 HL patients with mCRC. We compared the results with individual patient clinical histories and outcomes. We identified commonly altered genes in HL patients (APC, TP53, KRAS, GNAS, and NOTCH). Importantly, mutation frequencies in the APC gene were significantly higher among HL patients. The combination of mutations in the APC, NOTCH, and KRAS genes in the same tumors was associated with a higher risk of progression after first-line of chemotherapy and overall survival. Our data support the notion that the molecular drivers of CRC might be different in HL patients.

Role of predictive biomarkers and tumor mutational profile in selecting patients with platinum-refractory head-and-neck cancers for immune checkpoint inhibitor monotherapy: Where do we stand?

Role of predictive biomarkers and tumor mutational profile in selecting patients with platinum-refractory head-and-neck cancers for immune checkpoint inhibitor monotherapy: Where do we stand?

Advances in the diagnosis, evaluation, and management of leptomeningeal disease.

Leptomeningeal metastasis (LM) is a devastating complication of cancer with variable clinical presentation and limited benefit from existing treatment options. In this review, we discuss advances in LM diagnostics and therapeutics with the potential to reverse this grim course. Emerging cerebrospinal fluid circulating tumor cell and cell-free tumor DNA analysis technologies will improve diagnosis of LM, while providing crucial genetic information, capturing tumor heterogeneity, and quantifying disease burden. Circulating tumor cells and cell-free tumor DNA have utility as biomarkers to track disease progression and treatment response. Treatment options for LM include ventriculoperitoneal shunting for symptomatic relief, radiation therapy including whole-brain radiation and focal radiation for bulky leptomeningeal involvement, and systemic and intrathecal medical therapies, including targeted and immunotherapies based on tumor mutational profiling. While existing treatments for LM have limited efficacy, recent advances in liquid biopsy together with increasing availability of targeted treatments will lead to rational multimodal individualized treatments and improved patient outcomes.

Racial and Ethnic Differences in Clonal Hematopoiesis, Tumor Markers, and Clinical Outcomes of Patients with Multiple Myeloma

Racial and Ethnic Differences in Clonal Hematopoiesis, Tumor Markers, and Clinical Outcomes of Patients with Multiple Myeloma

Next generation sequencing identifies potential PARP inhibitor sensitive mutations

Abstract Introduction/Objective Poly ADP-ribose polymerase (PARP) inhibitors are a novel and important drug class targeting homologous recombination DNA repair defects (HRD) and have been approved for use in breast, pancreatic and ovarian cancers. Originally targeted for loss of function mutations in BRCA1 and BRCA2, many other genes are involved in the HRD pathway; Rimar et al detailed 19 DNA repair genes associated with homologous recombination and PARP inhibitor sensitivity. Our 214 gene NGS panel, Iowa Cancer Mutation Profile, includes BRCA1, BRCA2 and 15 other HRD pathway genes. We reviewed cases from the prior 12 months to determine the frequency of HRD7 pathway gene variants in various tumor types with potential PARP inhibitor sensitivity. Methods/Case Report Iowa Cancer Mutation Profile NGS test results from June 4, 2020 through May 7, 2021 were reviewed for variants involving ATM, ATR, BAP1, BLM, BRCA1, BRCA2, CDK12, CHEK1, CHEK2, FANCA, FANCC, FANCD2, MRE11A, NBN, PALB2, RAD51c and RAD51d, categorized as pathogenic, likely pathogenic or of unknown significance and had the tumor type identified. Additional chart review for PARP inhibitor therapy was performed in cases of breast, pancreatic, and ovarian cancer. Results (if a Case Study enter NA) A total of 599 cases were reviewed with 234 found to have variants in genes with possible PARP inhibitor sensitivity. Of these 2% (n=8) and 11% (n=43) of variants were categorized as pathogenic or likely pathogenic while most (n=334) were categorized as variants of unknown significance. The pathogenic and likely pathogenic variants included mutations in ATM (n=13), BRCA2 (n=12), BAP1 (n=8), FANCA (n=5), BRCA1 (n=4), NBM (n=3), FANCD2 (n=2), ATR (n=1), CDK12 (n=1), FANCC (n=1), and RAD51d (n=1), and frameshift (n=19) and nonsense (n=19) alterations were most common. Non-small cell lung cancer was the most frequent tumor type identified (n=78). At this time no PARP inhibitors were identified for use in cases of breast (n=9), pancreatic (n=3) and ovarian cancer (n=33). Conclusion Review of our institutional results for mutations in HRD pathway genes identified possible PARP inhibitor sensitivity in 8% (46 of 599) of cases during the period of review in a wide variety of tumor types. Our results suggest that variants with possible sensitivity to PARP inhibitor therapy are frequently identified from many tumor types and should be a component of solid tumor mutation profiling.

Genomic Predictors of Recurrence Patterns in Localized Soft Tissue Sarcoma Treated With Radiation Therapy

Soft tissue sarcomas (STSs) are diverse mesenchymal tumors that are primarily managed with surgery. Radiation therapy (RT) is frequently added pre- or post-operatively for localized disease but uncommonly used as definitive treatment because the majority of unresected tumors progress with RT alone. Advances in next-generation sequencing have led to the widespread use of clinical genomic profiling, but the genetic determinants of radiation response in STSs are unknown. We hypothesized that integrating patient outcome data and clinical tumor mutation profiling could identify genomic predictors of recurrence patterns after RT for localized STS.We retrospectively identified 31 patients treated at our institution with definitive RT with or without surgery for localized STS who underwent tumor genomic profiling using a sequencing platform. For genes altered in at least 10% of patients, the associations between genetic alterations and local failure or distant metastasis were analyzed with univariable and multivariable competing risk regression adjusted for the competing risk of death. Age, maximum tumor diameter, tumor grade, and extent of resection were included as co-variables, and P values were adjusted for multiple hypothesis testing.Median follow up was 24 months, and the median RT dose was 50.4 Gy in 28 fractions. The most common histologies were leiomyosarcoma (n = 4) and myxofibrosarcoma (n = 4). The majority of tumors were located in the trunk and extremities (68%) with the remaining tumors originating in the head and neck (16%) or abdomen and pelvis (16%). 48% of patients underwent margin-negative resection, 36% had microscopically positive margins, and 16% were unresected or had gross residual disease following surgery. Median age was 58, median tumor size was 7.5 cm, and 65% of tumors were high grade. On univariable analysis, younger age (P = 0.02) and extent of resection (P = 0.0002) were significantly associated with local recurrence, and there was a trend towards association between higher grade and distant metastasis (P = 0.09). On univariable analysis, amplification of FRS2 in isolation or in combination with MDM2 and CDK4 was associated with a significantly increased risk of local recurrence (n = 4, HR 4.3), and genetic alterations in FBXO11 were associated with a significantly increased risk of distant metastasis (n = 4, HR 3.9). On multivariable analysis, FBXO11 alterations continued to predict for distant metastasis (HR 5.7, P = 0.0002), but there were no significant predictors of local recurrence.Our results suggest that somatic tumor mutations may contribute to the risk of local recurrence and distant metastasis in patients treated with RT for localized STS. Additional analysis and validation in larger multi-institutional cohorts will be critical to identify molecular predictors of prognosis and patterns of recurrence.

Dynamic Tumor Mutational Profiling Using a Novel Non-Invasive Swab Technique for Serial Whole Exome Sequencing of Cervical Tumors During Chemoradiation Therapy

Clinically relevant genetic predictors of radiation response for cervical cancer are understudied due to the morbidity of repeat invasive biopsies required to obtain genetic material. We have developed a novel noninvasive cervical swab technique to collect tumor DNA with adequate throughput to perform whole exome sequencing (WES) at serial timepoints over the course of chemoradiation therapy (CRT). We hypothesize that characterization of dynamic changes in the mutational landscape of cervical tumors during the course of CRT will allow for identification of molecular signatures correlating with therapy response.A total of 69 patients with FIGO stage IB-IVA cervical cancer who underwent definitive CRT were prospectively enrolled on an IRB approved clinical trial. Cervical tumor DNA samples were collected by a noninvasive swab technique at baseline, and after 1, 3, and 5 weeks of CRT. Matched buccal DNA swabs were obtained to filter somatic mutations for each patient. An initial cohort included 24 patients (81 samples) and a second cohort included 45 patients (135 samples). WES was performed on the Illumina HiSeq 4000 series. Raw sequencing data were aligned to a human reference genome and MuTect was applied to detect somatic single nucleotide variants (SNV). Tumor purity (TP) was estimated from the distribution of variant allelic fractions of SNVs. In patients with pelvic MRIs at baseline and week 5 of CRT, 3D tumor volumes (TV) were generated (n = 6,8). Regression analysis was used to evaluate the goodness of fit between TP and TV.Estimated TP was highly correlated with TV in both cohorts (R2 = 0.969 and 0.858). Between the two cohorts, there was overlap in 4 of the top 5 genes (80%) containing the greatest number of exonic mutations across all timepoints (PIK3CA, MUC4, TPRXL, TTN). The number of altered genes present at baseline decreased over time in both cohorts. When normalized to TP, relative mutational burden decreased among standard and exceptional responders (< 20% TV remaining at week 5 of CRT) and increased among poor responders (> 20% TV remaining at week 5). The top ranked genes by magnitude of change at week 5 included MUC2, PARP10 and PIK3CA. Pathway analysis of these top ranked genes mapped to key radiation response pathways including regulation of the G1/S transition.We validated this method of performing serial WES over the course of CRT in 2 independent prospective patient cohorts, highlighting the robustness of our novel noninvasive technique. This allowed for the identification of a panel of potential genes involved in CRT resistance. Future directions include examination of dynamic changes in copy number variation, indels, and tumor mutational burden towards a comprehensive analysis of clinically relevant drivers of CRT resistance. This may allow future targeted treatment for patients with a radioresistant genetic profile, or concurrent targeted therapy for tumors with actionable mutations.

BRAF mutations may identify a clinically distinct subset of glioblastoma

Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. Prior studies examining the mutational landscape of GBM revealed recurrent alterations in genes that regulate the same growth control pathways. To this regard, ~ 40% of GBM harbor EGFR alterations, whereas BRAF variants are rare. Existing data suggests that gain-of-function mutations in these genes are mutually exclusive. This study was designed to explore the clinical, pathological, and molecular differences between EGFR- and BRAF-mutated GBM. We reviewed retrospective clinical data from 89 GBM patients referred for molecular testing between November 2012 and December 2015. Differences in tumor mutational profile, location, histology, and survival outcomes were compared in patients with EGFR- versus BRAF-mutated tumors, and microarray data from The Cancer Genome Atlas was used to assess differential gene expression between the groups. Individuals with BRAF-mutant tumors were typically younger and survived longer relative to those with EGFR-mutant tumors, even in the absence of targeted treatments. BRAF-mutant tumors lacked distinct histomorphology but exhibited unique localization in the brain, typically arising adjacent to the lateral ventricles. Compared to EGFR- and IDH1-mutant tumors, BRAF-mutant tumors showed increased expression of genes related to a trophoblast-like phenotype, specifically HLA-G and pregnancy specific glycoproteins, that have been implicated in invasion and immune evasion. Taken together, these observations suggest a distinct clinical presentation, brain location, and gene expression profile for BRAF-mutant tumors. Pending further study, this may prove useful in the stratification and management of GBM.