A time-course prediction model of global COVID-19 mortality

Introduction

The COVID-19 pandemic has caused over 6 million deaths worldwide and is a significant cause of mortality. Mortality dynamics vary significantly by country due to pathogen, host, social and environmental factors, in addition to vaccination and treatments. However, there is limited data on the relative contribution of different explanatory variables, which may explain changes in mortality over time. We, therefore, created a predictive model using orthogonal machine learning techniques to attempt to quantify the contribution of static and dynamic variables over time.

Methods

A model was created using Partial Least Squares Regression trained on data from 2020 to rank order the significance and effect size of static variables on mortality per country. This model enables the prediction of mortality levels for countries based on demographics alone. Partial Least Squares Regression was then used to quantify how dynamic variables, including weather and non-pharmaceutical interventions, contributed to the overall mortality in 2020. Finally, mortality levels for the first 60 days of 2021 were predicted using rolling-window Elastic Net regression.

Results

This model allowed prediction of deaths per day and quantification of the degree of influence of included variables, accounting for timing of occurrence or implementation. We found that the most parsimonious model could be reduced to six variables; three policy-related variables - COVID-19 testing policy, canceled public events policy, workplace closing policy; in addition to three environmental variables - maximum temperature per day, minimum temperature per day, and the dewpoint temperature per day.

Conclusion

Country and population-level static and dynamic variables can be used to predict COVID-19 mortality, providing an example of how broad temporal data can inform a preparation and mitigation strategy for both COVID-19 and future pandemics and assist decision-makers by identifying population-level contributors, including interventions, that have the greatest influence in mitigating mortality, and optimizing the health and safety of populations.

Genomic Landscapes and Hallmarks of Mutant RAS in Human Cancers

The RAS family of small GTPases represents the most commonly activated oncogenes in human cancers. To better understand the prevalence of somatic RAS mutations and the compendium of genes that are coaltered in RAS-mutant tumors, we analyzed targeted next-generation sequencing data of 607,863 mutations from 66,372 tumors in 51 cancer types in the AACR Project GENIE Registry. Bayesian hierarchical models were implemented to estimate the cancer-specific prevalence of RAS and non-RAS somatic mutations, to evaluate co-occurrence and mutual exclusivity, and to model the effects of tumor mutation burden and mutational signatures on comutation patterns. These analyses revealed differential RAS prevalence and comutations with non-RAS genes in a cancer lineage-dependent and context-dependent manner, with differences across age, sex, and ethnic groups. Allele-specific RAS co-mutational patterns included an enrichment in NTRK3 and chromatin-regulating gene mutations in KRAS G12C-mutant non-small cell lung cancer. Integrated multiomic analyses of 10,217 tumors from The Cancer Genome Atlas (TCGA) revealed distinct genotype-driven gene expression programs pointing to differential recruitment of cancer hallmarks as well as phenotypic differences and immune surveillance states in the tumor microenvironment of RAS-mutant tumors. The distinct genomic tracks discovered in RAS-mutant tumors reflected differential clinical outcomes in TCGA cohort and in an independent cohort of patients with KRAS G12C-mutant non-small cell lung cancer that received immunotherapy-containing regimens. The RAS genetic architecture points to cancer lineage-specific therapeutic vulnerabilities that can be leveraged for rationally combining RAS-mutant allele-directed therapies with targeted therapies and immunotherapy.

SIGNIFICANCE

The complex genomic landscape of RAS-mutant tumors is reflective of selection processes in a cancer lineage-specific and context-dependent manner, highlighting differential therapeutic vulnerabilities that can be clinically translated.

Real-world evidence on predictors of survival for hormone-positive and triple-negative advanced breast cancer by treatment and BRCA status in the United States

e18754

Background: Factors that affect overall survival (OS) for women with metastatic or recurrent breast cancer (BC) and BRCA1 or BRCA2 mutations (BRCA+) are a matter of debate. We analyzed electronic health records (EHR) from centers across the US to examine the effect of bilateral salpingo oophorectomy (BSO) and other factors on OS across treatment and molecular subtypes with emphasis on hormone-positive (HR+) and triple-negative BC (TNBC). Methods: A cohort of women diagnosed with stage 3 or 4 HR+ or TNBC from 1-Jan-2015 to 31-Dec-2019 was identified from EHR (Tempus Labs, Chicago, IL). BRCA+ was confirmed from medical notes and laboratory reports. A comparator group included HR+ and TNBC with no record of BRCA testing (Non-BRCA). Kaplan-Meier and Cox proportional hazards were used to evaluate predictors of OS from earliest diagnosis in multivariate models by BRCA status and molecular phenotype; treatment exposure (any time), mastectomy and BSO were treated as time-dependent variables. Results: We identified 1227 women with median age of 53 years (range 18-89) at BC diagnosis and median follow up of 26.1 months (max > 26 years) and 358 deaths. Two-thirds had distant visceral or bone metastases, almost 60% were recurrent after original stage 1-3 BC; 302 women were stage 3 and 296 stage 4 at BC. The BRCA+ cohort included 439 women (195 BRCA1, 220 BRCA2, 24 “BRCA” mutation; 265 HR+, 142 TNBC) and median age at BC was 46 years (44 BRCA1, 47 BRCA2). Non-BRCA cohort consisted of 788 women with a median age of 57 at BC (378 HR+, 341 TNBC). BRCA+ had longer OS than non-BRCA ( P= 0.0001); HR+ had longer OS than TNBC ( P= 0.0001). For 331 TNBC, chemotherapeutic regimens were most common first line treatment; few (17%) received third line and 31% had no evidence of receiving systemic therapy. Age ≤50, BRCA+, and mastectomy were associated with increased OS in HR+; BRCA+ status and mastectomy were predictors of increased OS whereas platinum-based chemotherapy was associated with decreased OS in TNBC (Table). Across molecular subtypes, BSO was not an independent predictor of OS and most women (92%) had BSO after BC diagnosis. Conclusions: Regardless of BRCA status, women with advanced TNBC were almost exclusively treated with chemotherapy, which highlights the remaining unmet need for effective treatment options. Taking timing of BSO and other interventions into account is critical to understanding their effects of BC mortality.[Table: see text]

Genetic architectures of proximal and distal colorectal cancer are partly distinct

OBJECTIVE

An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the colorectum suggest partly distinct mechanisms of carcinogenesis. The extent to which the contribution of inherited genetic risk factors for CRC differs by anatomical subsite of the primary tumor has not been examined.

DESIGN

To identify new anatomical subsite-specific risk loci, we performed genome-wide association study (GWAS) meta-analyses including data of 48 214 CRC cases and 64 159 controls of European ancestry. We characterised effect heterogeneity at CRC risk loci using multinomial modelling.

RESULTS

We identified 13 loci that reached genome-wide significance (p<5×10-8) and that were not reported by previous GWASs for overall CRC risk. Multiple lines of evidence support candidate genes at several of these loci. We detected substantial heterogeneity between anatomical subsites. Just over half (61) of 109 known and new risk variants showed no evidence for heterogeneity. In contrast, 22 variants showed association with distal CRC (including rectal cancer), but no evidence for association or an attenuated association with proximal CRC. For two loci, there was strong evidence for effects confined to proximal colon cancer.

CONCLUSION

Genetic architectures of proximal and distal CRC are partly distinct. Studies of risk factors and mechanisms of carcinogenesis, and precision prevention strategies should take into consideration the anatomical subsite of the tumour.

Coffee consumption and cancer risk in African Americans from the Southern Community Cohort Study

Coffee consumption has been associated with the risk of cancer at several anatomical sites, but the findings, mostly from studies of non-Hispanic whites and Asians, are inconsistent. The association between coffee consumption and the incidence of cancer has not been thoroughly examined in African Americans. We conducted a nested case-control study including 1801 cancer cases and 3337 controls among African Americans from the Southern Community Cohort Study (SCCS) to examine the association between coffee drinking, as assessed by a semi-quantitative food frequency questionnaire, and the risk of four common cancers (lung, prostate, breast, colorectal). We used logistic regression adjusted for age, sex and cancer-specific risk factors. Overall, only ≤ 9.5% of African American cases and controls from the SCCS drank regular or decaffeinated coffee ≥ 2 times/day. After adjustment for major cancer-specific risk factors, coffee consumption was not statistically significantly associated with the risk of lung, breast, colorectal, or prostate cancers (OR range 0.78-1.10; P ≥ 0.27 for ≥ 2 versus < 1 times/day) or overall cancer risk (OR 0.93; 95% CI 0.75-1.16; P = 0.52 for ≥ 2 versus < 1 times/day). Coffee consumption was not associated with the risk of cancer among African Americans in our study.

Variations in hospitalization and emergency department/observation stays using the oncology care model methodology in Medicare data

OBJECTIVE

To assess variations in hospitalizations, emergency department/observational (ED/OB) stays not resulting in hospitalization, reasons for hospitalization, and hospitalization discharge destinations after chemotherapy, information not provided as part of Oncology Care Model (OCM) baseline data.

METHODS

OCM methodology was applied to the Medicare 20% sample data to identify 6-month patient episodes triggered by chemotherapy in 2012-2015. Proportions of episodes with hospitalization or ED/OB stays, reasons for hospitalization, and discharge destinations were summarized.

RESULTS

Of 485,186 6-month episodes for 255,229 patients in 13,823 practices, 25% of episodes led to ≥1 hospitalization (from 14% in breast cancer to 56% in acute leukemia), and 23% to ED/OB stays (from 18% in breast cancer to 36% in liver cancer). In 2995 practices with ≥20 total episodes, practice-level proportions of episodes with hospitalization ranged from 14% to 31% (20th-80th percentile) and with ED/OB stays from 17% to 29%. For all cancers combined, the most frequent reasons for hospitalization were infection (13%), anemia (7%), dehydration (5%), and congestive heart failure (3%); the most common discharge destinations were home (71%) followed by a skilled nursing facility (13%), death (6%), and hospice (5%). Reasons for hospitalization and discharge destinations varied by cancer type; acute leukemia episodes led to the highest rates of infection and anemia, and central nervous system tumor episodes to the highest proportions of death or hospice discharge.

CONCLUSION

The variations in frequency of and reasons for hospitalization, ED/OB stays, and hospitalization discharge destinations across cancer types should be considered when evaluating OCM practice performance.

Abstract 1095: Comprehensive pan-cancer analyses of RAS genomic diversity

The RAS family of small GTPases represents the most commonly activated oncogenes and mutations in KRAS, NRAS and HRAS are found in approximately one third of all human cancers. To better understand the prevalence of somatic RAS mutations and the compendium of genes that have RAS-dependent co-mutation frequencies in an unbiased pan-cancer manner, we analyzed targeted next-generation sequence data from the AACR Project GENIE Registry (GENIE version 6.1-public). Our analyses utilized 644,757 mutations from 64,217 tumors in 97 cancer types. A Bayesian hierarchical model was implemented to estimate cancer-specific prevalence of RAS and non-RAS somatic mutations. To evaluate RAS co-mutations, we compared the observed co-mutation frequencies of RAS and non-RAS somatic mutations to posterior predictive distributions of their expected co-mutation frequencies under independence. The prevalence of RAS codon 12, 13 and 61 mutations varied among cancer types, ranging from 77.7% in pancreatic cancer-PAC, 44.8% in colorectal cancer-CRC, 31.2% in non-small cell lung cancer-NSCLC, 1.1% in breast cancer, and 0.5% in mesotheliomas. A cancer type-specific distribution was observed, such that KRAS was frequently mutated in &gt;25% of the tumors, NRAS was frequently mutated in melanoma, hematologic malignancies and thyroid cancer, while HRAS was overall less frequently mutated. KRAS codon 12 mutations predominated in pancreatic cancers (69.8%), GI cancers (30.9-48.5%), NSCLC (26.3%), endometrial cancer (14.7%) and germ cell tumors (11.6%). KRAS G12C mutations were predominantly seen in NSCLC (12.4%, 95% CI: 11.8-13.1%) with lower frequencies in GI cancers (3.2% in CRC). RAS mutations co-occurred with mutations in STK11, ATM, KEAP1, RBM10 and EPHA5 in NSCLC, TERT in melanoma and PIK3CA in CRC. Patterns of mutual exclusivity emerged between RAS mutations and BRAF in melanoma, thyroid and NSCLC, EGFR and RB1 in NSCLC, GNA11 and GNAQ in melanoma, FGFR3 in bladder cancer, MEN1 in PAC, RNF43 in CRC, BAP1 in melanoma and BAP1 and TERT2 in hepatobiliary carcinoma. A cancer type-specific co-occurrence pattern was noted for RAS and TP53 genomic alterations, with a significant enrichment in TP53 mutations in RAS-mutant PAC but a significant under-representation of TP53 mutations in RAS-mutant endometrial cancer, NSCLC, ovarian cancer and CRC. Analysis of codon specific RAS variants revealed additional co-mutation patterns, including an enrichment in NTRK3 mutations in KRAS G12C-mutant NSCLC and mutual exclusivity between KRAS G12C mutations and EGFR and BRAF in NSCLC. The tissue-distinct differential enrichment in RAS mutations and co-mutation patterns may be reflective of selection of oncogenic RAS signaling under the tumor type-specific modifying effect of other driver mutations. The RAS genetic architecture points to tissue-specific therapeutic vulnerabilities that may be translated to targeted treatment strategies.

Citation Format: Robert Scharpf, Gregory Riely, Mark Awad, Michele Lenoue-Newton, Biagio Ricciuti, Julia Rudolph, Leon Raskin, Andrew Park, Jocelyn Lee, Christine Lovly, Valsamo Anagnostou. Comprehensive pan-cancer analyses of RAS genomic diversity [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 1095.

Observational study of talimogene laherparepvec use in the anti-PD-1 era for melanoma in the US (COSMUS-2)

AIM

Talimogene laherparepvec (T-VEC) is an intralesional therapy for unresectable, metastatic melanoma. T-VEC real-world use in the context of anti-PD1-based therapy requires further characterization.

MATERIALS & METHODS

A retrospective review of T-VEC use from 1 January 2017 and 31 March 2018 for melanoma patients was conducted at seven US institutions.

RESULTS

Among 83 patients, three categories of T-VEC and anti-PD-1 therapy were identified: T-VEC used without anti-PD-1 (n = 29, 35%), T-VEC after anti-PD-1-based therapy (n = 22, 27%) and concurrent T-VEC and anti-PD-1-based therapy (n = 32, 39%). 25% of patients discontinued T-VEC therapy due to no remaining injectable lesions, 37% discontinued T-VEC due to progressive disease. Discontinuation of T-VEC did not differ by anti-PD-1-based therapy use or timing.

CONCLUSION

In real-world settings, T-VEC may be used concurrently with or after anti-PD-1-based therapy.

Treatment patterns of malignant melanoma in the United States from 2011 to 2016: a retrospective cohort study

Background: Since 2011, the approval of several new agents has improved treatment options for malignant melanoma. We describe treatment patterns for malignant melanoma in the United States from the MarketScan database from 2011 to 2016.Methods: Treatments used for patients aged >18 years diagnosed with malignant melanoma after January 1, 2011 and enrolled in the Truven MarketScan database were analyzed. Patient data were collected for the 12-month period from the date of the first melanoma diagnosis to either death, the pre-specified study end date (August 31, 2016), or date of termination of health insurance. Treatment patterns from 2011-2013 and 2014-2016 were analyzed according to agent, year of drug administration, and line of therapy.Results: From 2011 to 2016, use of cytokines (63.8; 13.3%) and chemotherapy (19.6; 12.9%) decreased, and use of checkpoint inhibitors increased (2.0; 49.9%). Checkpoint inhibitor use also increased across all lines of therapy from 2011-2013 and 2014-2016. Use of BRAF/MEK inhibitors remained relatively stable from 2011 to 2016 (6.5-12.5%); however, the use of vemurafenib monotherapy decreased (6.5; 0.8%), and treatment with combination regimens increased (0; 10.9%) from 2011-2016. BRAF/MEK inhibitor use only increased in the first line setting from 2011-2013 (9.7%) to 2014-2016 (11.2%).Conclusion: With the approval of immune checkpoint inhibitors, BRAF/MEK inhibitors, and targeted therapies, the therapeutic landscape for the treatment of metastatic melanoma has shifted dramatically away from cytokines and chemotherapy. Treatment patterns will likely continue to evolve as scientific advances are made.

Treatment patterns of melanoma by BRAF mutation status in the USA from 2011 to 2017: a retrospective cohort study

AIM

To describe treatment changes from 2011 to 2017 and demographic/clinical characteristics of patients with advanced melanoma who received systemic therapy by BRAF status.

PATIENTS & METHODS

Treatment patterns were evaluated in adults from the Oncology Services Comprehensive Electronic Records database who received antimelanoma systemic therapy.

RESULTS

Checkpoint inhibitors were prevailingly prescribed (66%); usage increased from 2011 (21%) to 2017 (84%). BRAF/MEK inhibitors were the second most common (21%); usage increased from 2011 (6%) to 2012 (18%) and stabilized until 2017 (22%). BRAF/MEK inhibitors (65%) and checkpoint inhibitors (57%) were predominantly used for BRAFMut melanoma.

CONCLUSION

Overall, checkpoint inhibitors have supplanted other therapies for advanced melanoma. Treatment shifts have occurred for BRAFMut melanoma, notably increased use of checkpoint inhibitors and BRAF/MEK combinations compared with monotherapies.

Publisher Correction: Shared heritability and functional enrichment across six solid cancers

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Observational study of talimogene laherparepvec use for melanoma in clinical practice in the United States (COSMUS-1)

Aim:

Talimogene laherparepvec (T-VEC) is an intralesional treatment for unresectable cutaneous, subcutaneous and nodal melanoma. COSMUS-1 was conducted to examine how T-VEC is used in US clinical practice.

Materials & methods:

A chart review was conducted at seven centers, with 78 patients screened and 76 eligible.

Results:

Patients began treatment with T-VEC between October 2015 and December 2016. Median follow-up was 9.4 months. Twenty percent of patients (n = 15) completed T-VEC treatment with no remaining injectable lesions or pathologic complete response. Flu-like symptoms were the most commonly reported adverse events (n = 8; 10.5%), followed by lesion ulceration (n = 4; 5.3%). No herpetic lesions or infections were reported.

Conclusion:

T-VEC was well tolerated and showed clinical utility.

Checkpoint inhibitor (CPI) experienced patients (pts) from COSMUS-1: A clinical observational study of talimogene laherparepvec (T-VEC) in United States practice

142

Background: T-VEC, a modified oncolytic herpes virus, is an intralesional therapy for unresectable advanced melanoma. COSMUS-1, a recently presented observational chart review study from 7 US academic sites, described metastatic melanoma treatment (tx) patterns and safety of T-VEC in the real-world setting (Perez et al, SMR 2018). In this analysis, we evaluated T-VEC use in pts after prior CPI use or with CPI from COSMUS-1. Methods: Of 76 pts treated with T-VEC (first dose 27Nov2015-15Dec2016), 33 pts had received pembrolizumab, nivolumab and/or ipilimumab (ie, CPI) prior to or with T-VEC and were analyzed for demographics, clinicopathologic characteristics, outcomes, and adverse events. Two groups were identified: Group A, CPI then T-VEC only and Group B, CPI with T-VEC. Results: There were 21 pts in A and 12 pts in B; in B, all received TVEC + CPI with (1) prior CPI, n = 5, (2) prior CPI and additional CPI after combination, n = 1, (3) as combination only, n = 4, or (4) as combination followed by CPI only, n = 2. In A and B, respectively, mean age was 72 yrs and 63 yrs; 12 (57%) and 9 (75%) were men; 17 (81%) and 9 (75%) had ECOG 0-1,10 (48%) and 4 (33%) had Stage IIIB-IVM1a, and 11 (52%) and 7 (58%) had Stage IVM1b/c. Two pts (both in B) remained on T-VEC by study end. 21 (100%) pts in A and 10 (83%) pts in B discontinued T-VEC (most common, respectively: 10 pts and 3 pts due to disease progression, 4 pts and 2 pts due to physician decision). 2 pts had no injectable lesions left (in A) and 1 pt (in A) had pathologic complete response (CR). Adverse events of interest were reported in 7 pts (33%) in A and 6 pts (50%) in B; most common events in A and B, respectively, were immune-mediated events (n = 3 and 6) which included flu-like symptoms (fever, chills, rigor; n = 2 and 5) and injection site complications (n = 5 and 2). No herpetic infections were reported in pts. Conclusions: These real-world data suggest that T-VEC is well tolerated and can be administered in pts previously treated with a CPI, both those who switched to T-VEC or those where T-VEC was added on. One pt achieved a pathologic CR.

Novel Common Genetic Susceptibility Loci for Colorectal Cancer

BACKGROUND

Previous genome-wide association studies (GWAS) have identified 42 loci (P < 5 × 10-8) associated with risk of colorectal cancer (CRC). Expanded consortium efforts facilitating the discovery of additional susceptibility loci may capture unexplained familial risk.

METHODS

We conducted a GWAS in European descent CRC cases and control subjects using a discovery-replication design, followed by examination of novel findings in a multiethnic sample (cumulative n = 163 315). In the discovery stage (36 948 case subjects/30 864 control subjects), we identified genetic variants with a minor allele frequency of 1% or greater associated with risk of CRC using logistic regression followed by a fixed-effects inverse variance weighted meta-analysis. All novel independent variants reaching genome-wide statistical significance (two-sided P < 5 × 10-8) were tested for replication in separate European ancestry samples (12 952 case subjects/48 383 control subjects). Next, we examined the generalizability of discovered variants in East Asians, African Americans, and Hispanics (12 085 case subjects/22 083 control subjects). Finally, we examined the contributions of novel risk variants to familial relative risk and examined the prediction capabilities of a polygenic risk score. All statistical tests were two-sided.

RESULTS

The discovery GWAS identified 11 variants associated with CRC at P < 5 × 10-8, of which nine (at 4q22.2/5p15.33/5p13.1/6p21.31/6p12.1/10q11.23/12q24.21/16q24.1/20q13.13) independently replicated at a P value of less than .05. Multiethnic follow-up supported the generalizability of discovery findings. These results demonstrated a 14.7% increase in familial relative risk explained by common risk alleles from 10.3% (95% confidence interval [CI] = 7.9% to 13.7%; known variants) to 11.9% (95% CI = 9.2% to 15.5%; known and novel variants). A polygenic risk score identified 4.3% of the population at an odds ratio for developing CRC of at least 2.0.

CONCLUSIONS

This study provides insight into the architecture of common genetic variation contributing to CRC etiology and improves risk prediction for individualized screening.

Shared heritability and functional enrichment across six solid cancers

Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, here we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (rg = 0.57, p = 4.6 × 10-8), breast and ovarian cancer (rg = 0.24, p = 7 × 10-5), breast and lung cancer (rg = 0.18, p =1.5 × 10-6) and breast and colorectal cancer (rg = 0.15, p = 1.1 × 10-4). We also found that multiple cancers are genetically correlated with non-cancer traits including smoking, psychiatric diseases and metabolic characteristics. Functional enrichment analysis revealed a significant excess contribution of conserved and regulatory regions to cancer heritability. Our comprehensive analysis of cross-cancer heritability suggests that solid tumors arising across tissues share in part a common germline genetic basis.

Discovery of common and rare genetic risk variants for colorectal cancer

To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10-8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.

Hospitalization and hospital discharge destinations after chemotherapy: Using the Oncology Care Model (OCM) methodology in 2012–2015 Medicare data

113

Background: The Medicare OCM gives financial incentives for efficient, high-quality care. Hospitalizations of cancer patients receiving chemotherapy substantially increases costs. We assessed reasons for hospitalization and hospitalization discharge destinations after chemotherapy in cancer patients. Methods: We applied OCM methodology in a Medicare fee-for-service 20% sample data to estimate 6-month patient episodes triggered by chemotherapy from 2012 to 2015. We summarized the most frequent reasons for hospitalization (using ICD-9-CM codes in the first 5 positions of hospital claims) and the discharge destinations among all episodes and by cancer type. Results: Of 485,186 6-month episodes in 255,229 patients, 121,886 (25%) episodes had ≥1 hospitalization. The most frequent reasons for hospitalization were infection (13%), anemia (7%), dehydration (5%), and congestive heart failure (CHF; 3%; Table). Most hospitalized patients were discharged to home (71%) or a skilled nursing facility (SNF; 13%); some died in the hospital (6%) or went to hospice (5%). Reasons for hospitalization and discharge destination varied by cancer type. Patients with lung cancer had the highest rates of infection and anemia and higher proportions of death and hospice discharge compared with other cancers. Conclusions: Among Medicare beneficiaries receiving chemotherapy, hospitalizations most often occurred as a result of infection or anemia. Patients were most often discharged to home or SNF. Variations across cancer types in the reasons for hospitalization, as well as discharge destinations, should be considered when evaluating OCM practice performance. [Table: see text]

Variations in hospitalization and emergency department or observation (ED/OB) stays using the oncology care model (OCM) methodology in Medicare data

112

Background: The Medicare OCM started in 2016 to improve oncology care and reduce costs. Two metrics for care evaluation are hospitalizations and ED/OB stays. Baseline data (2012−2015) on variations in all-cause hospitalization and ED/OB stays not resulting in hospitalization in the 21 reconciliation-eligible cancer types are not well characterized. Methods: We applied OCM methodology in Medicare fee-for-service 20% sample data to estimate 6-month patient (pt) episodes triggered by chemotherapy, as well as associated cancer type and practice, from 2012 to 2015. Proportions of episodes with hospitalization and ED/OBs stay were summarized overall and by cancer for all episodes and by practice in those with ≥20 pt-episodes. Results: In total, 485,186 pt-episodes at 13,823 practices were identified (mean episodes/practice, 35.1; median, 2; IQR, 1–15). The mean number of episodes/pt was 1.90 overall (from 1.17 in anal cancer to 2.32 in multiple myeloma [MM]). The proportion of episodes with hospitalization was 25% overall (from 14% in breast cancer [BC] to 56% in acute leukemia) and with ED/OB stays was 23% overall (from 18% in BC to 36% in liver cancer). In 2,995 practices with ≥20 total episodes, at practice-level, the proportion of episodes with hospitalization ranged (20th–80th percentile) from 14% to 31% and with ED/OB stays from 17% to 29%. For select cancers, the range of proportion of episodes with hospitalization and ED/OB stays were highest for lung cancer (LC) and lowest for BC (Table). Conclusions: The proportion of 6-month OCM episodes of care with hospitalization and ED/OB stays after chemotherapy varied by cancer and was higher for certain solid and hematological malignancies. Variations between practices and cancers are important factors when evaluating OCM performance. [Table: see text]

CDKN2A Germline Rare Coding Variants and Risk of Pancreatic Cancer in Minority Populations

Background: Pathogenic germline mutations in the CDKN2A tumor suppressor gene are rare and associated with highly penetrant familial melanoma and pancreatic cancer in non-Hispanic whites (NHW). To date, the prevalence and impact of CDKN2A rare coding variants (RCV) in racial minority groups remain poorly characterized. We examined the role of CDKN2A RCVs on the risk of pancreatic cancer among minority subjects.Methods: We sequenced CDKN2A in 220 African American (AA) pancreatic cancer cases, 900 noncancer AA controls, and 183 Nigerian controls. RCV frequencies were determined for each group and compared with that of 1,537 NHW patients with pancreatic cancer. Odds ratios (OR) and 95% confidence intervals (CI) were calculated for both a case-case comparison of RCV frequencies in AAs versus NHWs, and case-control comparison between AA cases versus noncancer AA controls plus Nigerian controls. Smaller sets of Hispanic and Native American cases and controls also were sequenced.Results: One novel missense RCV and one novel frameshift RCV were found among AA patients: 400G>A and 258_278del. RCV carrier status was associated with increased risk of pancreatic cancer among AA cases (11/220; OR, 3.3; 95% CI, 1.5-7.1; P = 0.004) compared with AA and Nigerian controls (17/1,083). Further, AA cases had higher frequency of RCVs: 5.0% (OR, 13.4; 95% CI, 4.9-36.7; P < 0.001) compared with NHW cases (0.4%).Conclusions: CDKN2A RCVs are more common in AA than in NHW patients with pancreatic cancer and associated with moderately increased pancreatic cancer risk among AAs.Impact: RCVs in CDKN2A are frequent in AAs and are associated with risk for pancreatic cancer. Cancer Epidemiol Biomarkers Prev; 27(11); 1364-70. ©2018 AACR.

A human MUTYH variant linking colonic polyposis to redox degradation of the [4Fe4S]2+ cluster

The human DNA repair enzyme MUTYH excises mispaired adenine residues in oxidized DNA. Homozygous MUTYH mutations underlie the autosomal, recessive cancer syndrome MUTYH-associated polyposis. We report a MUTYH variant, p.C306W (c.918C>G), with a tryptophan residue in place of native cysteine, that ligates the [4Fe4S] cluster in a patient with colonic polyposis and family history of early age colon cancer. In bacterial MutY, the [4Fe4S] cluster is redox active, allowing rapid localization to target lesions by long-range, DNA-mediated signalling. In the current study, using DNA electrochemistry, we determine that wild-type MUTYH is similarly redox-active, but MUTYH C306W undergoes rapid oxidative degradation of its cluster to [3Fe4S]⁺, with loss of redox signalling. In MUTYH C306W, oxidative cluster degradation leads to decreased DNA binding and enzyme function. This study confirms redox activity in eukaryotic DNA repair proteins and establishes MUTYH C306W as a pathogenic variant, highlighting the essential role of redox signalling by the [4Fe4S] cluster.

Activation of cancer-associated fibroblasts is required for tumor neovascularization in a murine model of melanoma

Metastatic melanoma is highly fatal. Within the tumor microenvironment, the role of cancer-associated fibroblasts (CAFs) in melanoma metastasis and progression is relatively understudied. The matricellular protein CCN2 (formerly termed connective tissue growth factor, CTGF) is overexpressed, in a fashion independent of BRAF mutational status, by CAFs in melanoma. Herein, we find, in human melanoma patients, that CCN2 expression negatively correlates with survival and positively correlates with expression of neovascularization markers. To assess the role of CAFs in melanoma progression, we used C57BL/6 mice expressing a tamoxifen-dependent cre recombinase expressed under the control of a fibroblast-specific promoter/enhancer (COL1A2) to delete CCN2 postnatally in fibroblasts. Mice deleted or not for CCN2 in fibroblasts were injected subcutaneously with B16-F10 melanoma cells. Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.

Abstract A17: Molecular and clinicopathological features of native Nigerian colorectal cancer

Colorectal cancer (CRC) needs no introduction in Africa; once a rare cancer type, it is now the 3rd or 4th most common cancer. However, there are significant differences in the incidence rates, tumor biology, and clinical behavior in comparison to other populations. While the total incidence rates are about one-tenth of those in the developed world, Nigerian CRC occurs at a younger age and rapidly metastasizes. Molecular pathology and genetics of African CRC have not been comprehensively studied. In addition to better understanding of the biology of African CRC, analysis of genetic and molecular biomarkers, including microsatellite instability (MSI), is aimed at improving CRC diagnosis, treatment, and prognosis in Africa. We obtained 83 CRC paraffin-embedded blocks from the University of Ibadan and private pathology laboratories in Ibadan collected in the period from 2007 to 2014. Median age of the cases was 56±14.6 years with equal number of males and females. More than 60% of the patients had stage III and IV CRC. The majority were adenocarcinomas (76%) with a relatively high prevalence of mucinous adenocarcinoma (10%) and signet ring carcinoma (4%). Of all patients, 66% had rectal cancer. Poorly differentiated tumors were observed in 34% of all cases. We found a high prevalence of MSI CRC (43%, 15/35) in the tested Nigerian samples. There were no significant differences in clinicopathological features, including tumor location, between MSI and microsatellite stable (MSS) CRC. Our results are in line with our previous report that found a high prevalence (41%) of MSI CRC in Ghanaian patients. These findings raise important questions about the role of genetic and environmental factors in CRC development in West Africa.

Citation Format: David O. Irabor, Marilena Melas, Stephen B. Gruber, Chanjuan Shi, Leon Raskin. Molecular and clinicopathological features of native Nigerian colorectal cancer [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr A17.

The effect of interactions between a bacterial strain isolated from drinking water and a pathogen surrogate on biofilms formation diverged under static vs flow conditions

AIMS

Interactions with water bacteria affect the incorporation of pathogens into biofilms and thus pathogen control in drinking water systems. This study was to examine the impact of static vs flow conditions on interactions between a pathogen and a water bacterium on pathogen biofilm formation under laboratory settings.

METHODS AND RESULTS

A pathogen surrogate Escherichia coli and a drinking water isolate Stenotrophomonas maltophilia was selected for this study. Biofilm growth was examined under two distinct conditions, in flow cells with continuous medium supply vs in static microtitre plates with batch culture. E. coli biofilm was greatly stimulated (c. 2-1000 times faster) with the presence of S. maltophilia in flow cells, but surprisingly inhibited (c. 65-95% less biomass) in microtitre plates. These divergent effects were explained through various aspects including surface attachment, cellular growth, extracellular signals and autoaggregation.

CONCLUSIONS

Interactions with the same water bacterium resulted in different effects on E. coli biofilm formation when culture conditions changed from static to flow.

SIGNIFICANCE AND IMPACT OF STUDY

This study highlights the complexity of species interactions on biofilm formation and suggests that environmental conditions such as the flow regime can be taken into consideration for the management of microbial contamination in drinking water systems.

Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort

The underlying genetic cause of colorectal cancer (CRC) can be identified for 5-10% of all cases, while at least 20% of CRC cases are thought to be due to inherited genetic factors. Screening for highly penetrant mutations in genes associated with Mendelian cancer syndromes using next-generation sequencing (NGS) can be prohibitively expensive for studies requiring large samples sizes. The aim of the study was to identify rare single nucleotide variants and small indels in 40 established or candidate CRC susceptibility genes in 1,046 familial CRC cases (including both MSS and MSI-H tumor subtypes) and 1,006 unrelated controls from the Colon Cancer Family Registry Cohort using a robust and cost-effective DNA pooling NGS strategy. We identified 264 variants in 38 genes that were observed only in cases, comprising either very rare (minor allele frequency <0.001) or not previously reported (n=90, 34%) in reference databases, including six stop-gain, three frameshift, and 255 non-synonymous variants predicted to be damaging. We found novel germline mutations in established CRC genes MLH1, APC, and POLE, and likely pathogenic variants in cancer susceptibility genes BAP1, CDH1, CHEK2, ENG, and MSH3. For the candidate CRC genes, we identified likely pathogenic variants in the helicase domain of POLQ and in the LRIG1, SH2B3, and NOS1 genes and present their clinicopathological characteristics. Using a DNA pooling NGS strategy, we identified novel germline mutations in established CRC susceptibility genes in familial CRC cases. Further studies are required to support the role of POLQ, LRIG1, SH2B3 and NOS1 as CRC susceptibility genes.

Microsatellite Instability Is Common in Colorectal Cancer in Native Nigerians

BACKGROUND

Colorectal cancer (CRC) is the fifth most common cancer in Africa, with significant differences in incidence, biology and clinical behavior from other populations.

MATERIALS AND METHODS

We studied prevalence and clinicopathological features of microsatellite instability (MSI) and young onset CRC in 83 archival samples from the University of Ibadan, Nigeria.

RESULTS

Nigerian cases of CRC were MSI-high in 43% and MSI-high CRC had significantly lower histological heterogeneity than microsatellite-stable CRC (20% vs. 55% respectively, p=0.046). Presence of signet ring cell differentiation (10-50% of tumor) was significantly higher in younger patients with CRC (<50 years) (odds ratio(OR)=5.93, 95% confidence interval(CI)=1.17-29.95, p=0.038). Poor differentiation (34%), invasive growth (96%), and high prevalence of mucinous (10%) and signet ring cell adenocarcinomas (4%) were among distinct features of Nigerian patients with CRC.

CONCLUSION

MSI-high CRC is more common in West Africa and more detailed molecular and genetic analysis is warranted as CRC incidence and mortality continue to increase in the Sub-Saharan Africa.

Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation

BACKGROUND

Melanoma is a heterogeneous malignancy. We set out to identify the molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes.

METHODS

We examined transcriptome changes from benign states to early-, intermediate-, and late-stage tumors using a set of 78 treatment-naive melanocytic tumors consisting of primary melanomas of the skin and benign melanocytic lesions. We utilized a next-generation sequencing platform that enabled a comprehensive analysis of protein-coding and -noncoding RNA transcripts.

RESULTS

Gene expression changes unequivocally discriminated between benign and malignant states, and a dual epigenetic and immune signature emerged defining this transition. To our knowledge, we discovered previously unrecognized melanoma subtypes. A high-risk primary melanoma subset was distinguished by a 122-epigenetic gene signature ("epigenetic" cluster) and TP53 family gene deregulation (TP53, TP63, and TP73). This subtype associated with poor overall survival and showed enrichment of cell cycle genes. Noncoding repetitive element transcripts (LINEs, SINEs, and ERVs) that can result in immunostimulatory signals recapitulating a state of "viral mimicry" were significantly repressed. The high-risk subtype and its poor predictive characteristics were validated in several independent cohorts. Additionally, primary melanomas distinguished by specific immune signatures ("immune" clusters) were identified.

CONCLUSION

The TP53 family of genes and genes regulating the epigenetic machinery demonstrate strong prognostic and biological relevance during progression of early disease. Gene expression profiling of protein-coding and -noncoding RNA transcripts may be a better predictor for disease course in melanoma. This study outlines the transcriptional interplay of the cancer cell's epigenome with the immune milieu with potential for future therapeutic targeting.

FUNDING

National Institutes of Health (CA154683, CA158557, CA177940, CA087497-13), Tisch Cancer Institute, Melanoma Research Foundation, the Dow Family Charitable Foundation, and the Icahn School of Medicine at Mount Sinai.

Fast detection of deletion breakpoints using quantitative PCR

The routine detection of large and medium copy number variants (CNVs) is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories.

Abstract LB-372: Robust targeted sequencing strategy identifies highly penetrant mutations in hereditary colorectal cancer cases from Colon Cancer Family Registry

Highly penetrant mutations responsible for Mendelian cancer syndromes have not been systematically identified in large populations. Historically, highly penetrant cancer mutations have been identified in large families with multiple cancer cases using linkage analysis. Next-generation sequencing (NGS) allows for efficient genomic screening of large numbers of familial cancer cases. Highly penetrant mutations such as those found in the APC or mismatch repair (MMR) genes for colorectal cancer (CRC) or BRCA1/2 genes for breast cancer, are rare and often population-specific. Therefore, to identify these rare, highly penetrant cancer-predisposing mutations using NGS requires a large sample size that can make this approach prohibitively expensive.

Here, we present a new, robust NGS pooling strategy for identification of rare, highly penetrant mutations. Our strategy is at least five times less expensive than traditional germline NGS of cancer patients. We screened 1,046 CRC cases and 1,006 unaffected controls from Colon Cancer Family Registry (Colon CFR), to identify highly penetrant CRC mutations in 40 known or candidate CRC genes. Cases were patients with familial CRC and controls were spouses or unrelated healthy individuals.

DNA from 1,046 cases and 1,006 controls were combined into 480 pools (3 cases/pool and 8 controls/pool) for targeted sequencing of the 40 selected genes with mean depth of &gt;1000X in cases and &gt;700X in controls using Qiagen GeneRead Customized Targeted Panel. Following quality control, alignment of reads, and calculation of allele frequencies, we selected likely functional variants (nonsynonymous and nonsense) in cases that were not found in controls and absent or very rare (minor allele frequency &lt;0. 001) in other populations. We found 264 rare variants in 273 cases: six stopgain and 258 nonsynonymous variants. While, &gt;40% (n = 106) of the variants have never been reported, almost all the variants identified in the MMR genes (MLH1, MSH2, MSH6, and PMS2) were reported in dbSNP. However, only 11 of 39 MMR variants have sufficient evidence to be considered pathogenic in ClinVar. In addition to known mutations, we found novel, deleterious variants in ABCC1, APC (including stopgain), AXIN2, BMPR1A, CHEK2, CTNNB1, ENG, MUTYH, POLD1, POLE, PTCH1, SH2B3, TGFBR2, and TP53 among other genes. Previously observed variants of unknown significance (VUS) were found in BMPR1A, EPCAM, and SMAD4. Deleterious variants were selected for Sanger sequencing to identify individual genotypes and validate NGS results.

Our study identified a large proportion of previously unreported, likely deleterious variants in known or candidate CRC susceptibility genes. The targeted NGS pooling strategy used in this study proved to be a robust and cost-effective alternative for screening a large cohort of familial CRC cases and controls for mutations in CRC susceptibility genes, making it applicable for screening other cancer types and complex diseases with dominant mode of inheritance.

Citation Format: Leon Raskin, Yan Guo, Stephen B. Gruber, Daniel D. Buchanan. Robust targeted sequencing strategy identifies highly penetrant mutations in hereditary colorectal cancer cases from Colon Cancer Family Registry. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-372.

A Germline Variant on Chromosome 4q31.1 Associates with Susceptibility to Developing Colon Cancer Metastasis

We tested for germline variants showing association to colon cancer metastasis using a genome-wide association study that compared Ashkenazi Jewish individuals with stage IV metastatic colon cancers versus those with stage I or II non-metastatic colon cancers. In a two-stage study design, we demonstrated significant association to developing metastatic disease for rs60745952, that in Ashkenazi discovery and validation cohorts, respectively, showed an odds ratio (OR) = 2.3 (P = 2.73E-06) and OR = 1.89 (P = 8.05E-04) (exceeding validation threshold of 0.0044). Significant association to metastatic colon cancer was further confirmed by a meta-analysis of rs60745952 in these datasets plus an additional Ashkenazi validation cohort (OR = 1.92; 95% CI: 1.28–2.87), and by a permutation test that demonstrated a significantly longer haplotype surrounding rs60745952 in the stage IV samples. rs60745952, located in an intergenic region on chromosome 4q31.1, and not previously associated with cancer, is, thus, a germline genetic marker for susceptibility to developing colon cancer metastases among Ashkenazi Jews.

Blood BDNF level is gender specific in severe depression

Though the role of brain derived neurotrophic factor (BDNF) as a marker for major depressive disorder (MDD) and antidepressant efficacy has been widely studied, the role of BDNF in distinct groups of patients remains unclear. We evaluated the diagnostic value of BDNF as a marker of disease severity measured by HAM-D scores and antidepressants efficacy among MDD patients. Fifty-one patients who met DSM-IV criteria for MDD and were prescribed antidepressants and 38 controls participated in this study. BDNF in serum was measured at baseline, 1st, 2nd and 8th treatment weeks. Depression severity was evaluated using the Hamilton Rating Scale for Depression (HAM-D). BDNF polymorphism rs6265 (val66met) was genotyped. We found a positive correlation between blood BDNF levels and severity of depression only among untreated women with severe MDD (HAM-D>24). Serum BDNF levels were lower in untreated MDD patients compared to control group. Antidepressants increased serum BDNF levels and reduced between-group differences after two weeks of treatment. No correlations were observed between BDNF polymorphism, depression severity, duration of illness, age and BDNF serum levels. Further supporting the role of BDNF in the pathology and treatment of MDD, we suggest that it should not be used as a universal biomarker for diagnosis of MDD in the general population. However, it has diagnostic value for the assessment of disease progression and treatment efficacy in individual patients.

A novel colorectal cancer risk locus at 4q32.2 identified from an international genome-wide association study

Only a fraction of colorectal cancer heritability is explained by known risk-conferring genetic variation. This study was designed to identify novel risk alleles in Europeans. We conducted a genome-wide association study (GWAS) meta-analysis of colorectal cancer in participants from a population-based case-control study in Israel (n = 1616 cases, 1329 controls) and a consortium study from the Colon Cancer Family Registry (n = 1977 cases, 999 controls). We used a two-stage (discovery-replication) GWAS design, followed by a joint meta-analysis. A combined analysis identified a novel susceptibility locus that reached genome-wide significance on chromosome 4q32.2 [rs35509282, risk allele = A (minor allele frequency = 0.09); odds ratio (OR) per risk allele = 1.53; P value = 8.2 × 10(-9); nearest gene = FSTL5]. The direction of the association was consistent across studies. In addition, we confirmed that 14 of 29 previously identified susceptibility variants were significantly associated with risk of colorectal cancer in this study. Genetic variation on chromosome 4q32.2 is significantly associated with risk of colorectal cancer in Ashkenazi Jews and Europeans in this study.

Genome measures used for quality control are dependent on gene function and ancestry

MOTIVATION

The transition/transversion (Ti/Tv) ratio and heterozygous/nonreference-homozygous (het/nonref-hom) ratio have been commonly computed in genetic studies as a quality control (QC) measurement. Additionally, these two ratios are helpful in our understanding of the patterns of DNA sequence evolution.

RESULTS

To thoroughly understand these two genomic measures, we performed a study using 1000 Genomes Project (1000G) released genotype data (N=1092). An additional two datasets (N=581 and N=6) were used to validate our findings from the 1000G dataset. We compared the two ratios among continental ancestry, genome regions and gene functionality. We found that the Ti/Tv ratio can be used as a quality indicator for single nucleotide polymorphisms inferred from high-throughput sequencing data. The Ti/Tv ratio varies greatly by genome region and functionality, but not by ancestry. The het/nonref-hom ratio varies greatly by ancestry, but not by genome regions and functionality. Furthermore, extreme guanine + cytosine content (either high or low) is negatively associated with the Ti/Tv ratio magnitude. Thus, when performing QC assessment using these two measures, care must be taken to apply the correct thresholds based on ancestry and genome region. Failure to take these considerations into account at the QC stage will bias any following analysis.

CONTACT

yan.guo@vanderbilt.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Distinct molecular features of colorectal cancer in Ghana

OBJECTIVES

While colorectal cancer (CRC) is common, its incidence significantly varies around the globe. The incidence of CRC in West Africa is relatively low, but it has a distinctive clinical pattern and its molecular characteristics have not been studied. This study is one of the first attempts to analyze molecular, genetic, and pathological characteristics of colorectal cancer in Ghana.

METHODS

DNA was extracted from microdissected tumor and adjacent normal tissue of 90 paraffin blocks of CRC cases (1997-2007) collected at the University of Ghana. Microsatellite instability (MSI) was determined using fragment analysis of ten microsatellite markers. We analyzed expression of mismatch repair (MMR) proteins by immunohistochemistry and sequenced exons 2 and 3 of KRAS and exon 15 of BRAF.

RESULTS

MSI analysis showed 41% (29/70) MSI-High, 20% (14/70) MSI-Low, and 39% (27/70) microsatellite-stable (MSS) tumors. Sequencing of KRAS exons 2 and 3 identified activating mutations in 32% (24/75) of tumors, and sequencing of BRAF exon 15, the location of the common activating mutation (V600), did not show mutations at codons 599 and 600 in 88 tumors.

CONCLUSIONS

Our study found a high frequency of MSI-High colorectal tumors (41%) in Ghana. While the frequency of KRAS mutations is comparable with other populations, absence of BRAF mutations is intriguing and would require further analysis of the molecular epidemiology of CRC in West Africa.

Abstract B92: Molecular characterization of colorectal cancer in Ghana

Colorectal cancer is the fourth most common cancer in men and the third most common cancer in women worldwide with significant variation between different parts of the globe. Although colorectal cancer incidence is relatively low in West Africa, the most recent publications from Nigeria and Ghana note significant increase of colorectal cancer incidence in these countries since 1970. These studies also show that colorectal cancer in West Africa has distinctive pattern with young age of onset and predominantly left-sided tumors, yet the spectrum of molecular changes in colorectal tumors has not been characterized in West African populations. The goal of this study was to investigate molecular characteristics of colorectal cancer in Ghana.

We retrieved 90 formalin-fixed paraffin embedded (FFPE) colorectal cancer blocks from the University of Ghana Medical School (Accra) diagnosed between 1997 and 2007. Ten 5 μm recuts and H&E slide were prepared for each block and reviewed by the pathologist to determine areas of at least 70% tumor cellularity and areas of adjacent normal tissue. DNA was extracted from the microdissected tumor and normal tissue. Only 71 samples had both tumor and normal tissue within the available specimen. Ten microsatellite marker loci (D10S197, BAT26, beta-catenin, D18S58, BAT40, D2S123, D17S250, BAT25, TGF-b-RIIF, and D5S346F) were used for microsatellite instability (MSI) testing using fluorescently labeled primers and fragment analysis. Tumors with at least one mononucleotide marker and a minimum of three available markers were considered for analysis. The tumors with instability in at least 30% of markers were called MSI-High, less than 30% classified as MSI-Low, and tumors with all stable markers were called microsatellite stable (MSS). Sequencing BRAF and KRAS was repeated twice from both directions and analyzed by two independent readers using Sequencher from GeneCodes (Ann Arbor, MI) and Mutation Surveyor from SoftGenetics (State College, PA) to avoid misinterpretation.

Out of 71 colorectal cancer pairs of normal and tumor tissue, MSI testing was informative for 70 pairs. An exceptionally large proportion of cancers were MSI-High (29/70, 41.4%), with 14/70 (20%) MSI-Low tumors, and 27/70 (38.6%) MSS tumors. Sequencing of exons 1 and 2 of KRAS in 75 tumors detected 24 (32%) activating mutations (G12D, G12V, G12C, G12S, G13D, Q61R, and Q61K). Surprisingly, the sequencing of exon 15 of BRAF, the location of frequent activating mutation (V600E), did not show any mutations at codons 599 and 600 in 88 tumor samples.

Our study showed a very high frequency of MSI-high colorectal tumors (41.4%), consistent with the higher rates of MSI-High cancers observed in some studies of colorectal cancer in African American patients. The frequency of KRAS mutations is comparable to one found in African Americans, but absence of BRAF mutations is intriguing and requires further analysis of the epidemiology and biology of colorectal cancer in West Africa.

Citation Format: Leon Raskin, Jonathan C.B. Dakubo, Nicole Palaski, Joel Greenson, Stephen Gruber. Molecular characterization of colorectal cancer in Ghana. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr B92.

Identification and functional characterization of a novel MUTYH gene mutation

e12026

Background: Biallelic germline mutations in MUTYH result in the autosomal recessive syndrome of MUTYH associated polyposis (MAP).Three well-known, common mutations account for the vast majority of identifiable germline mutations, and serve as the basis for current genetic testing strategies. Comprehensive sequencing of MUTYH often identifies variants of uncertain pathologic significance, and studies to determine the pathogenicity of newly identified variants may offer valuable clinical information and mechanistic insights. In the present study we seek to describe the base-excision repair function of a novel MUTYH (p.C306W) mutation identified in a patient with multiple colon polyps and a family history of colon cancers. Methods: A 50 year old patient with >50 adenomas underwent clinical and laboratory evaluation to assess for germline genetic mutations. We performed Sanger sequencing of tumor and germline DNA together with targeted restriction enzyme digest of germline DNA and fragment DNA sequencing of the alleles. We prepared MUTYH proteins with protein liquid chromatography and assessed their mismatched adenine excision repair capacity employing a glycosylase assay. Results: Analysis of the patient's germline DNA revealed an absence of APC mutations, and the presence of the previously well characterized p.G396D MUTYH mutation as well as a novel p.C306W mutation. Targeted restriction enzyme digest demonstrated trans configuration of the p.G396D and p.C306W MUTYH mutations. Mismatched adenine excision functionality of wildtype MUTYH, known mutant controls p.G396D and p.Y179C, and putative mutant p.C306W were assessed in the glycosylase assay. Consistent with previous experimental observations, relative to wildtype MUTYH, the p.G396D and p.Y179C MUTYH mutants demonstrated attenuated adenine excision activities of 43% and 0%, respectively. Comparable to the activity of the pY179C mutant, the novel p.C306D mutant demonstrated 0% adenine excision activity. Subsequent tumor analysis demonstrated G:C to T:A transversion in the APC gene in somatic DNA derived from an adenoma. Conclusions: Experimental and clinical data demonstrate that p.C306D MUTYH is a pathogenic mutation contributing to the phenotype of MAP.

Risk of non-melanoma cancers in first-degree relatives of CDKN2A mutation carriers

The purpose of this study was to quantify the risk of cancers other than melanoma among family members of CDKN2A mutation carriers using data from the Genes, Environment and Melanoma study. Relative risks (RRs) of all non-melanoma cancers among first-degree relatives (FDRs) of melanoma patients with CDKN2A mutations (n = 65) and FDRs of melanoma patients without mutations (n = 3537) were calculated as the ratio of estimated event rates (number of cancers/total person-years) in FDRs of carriers vs noncarriers with exact Clopper-Pearson-type tests and 95% confidence intervals (CIs). All statistical tests were two-sided. There were 56 (13.1%) non-melanoma cancers reported among 429 FDRs of mutation carriers and 2199 (9.4%) non-melanoma cancers in 23 452 FDRs of noncarriers. The FDRs of carriers had an increased risk of any cancer other than melanoma (56 cancers among 429 FDRs of carrier probands vs 2199 cancers among 23 452 FDRs of noncarrier probands; RR = 1.5, 95% CI = 1.2 to 2.0, P = .005), gastrointestinal cancer (20 cancers among 429 FDRs of carrier probands vs 506 cancers among 23 452 FDRs of noncarrier probands; RR = 2.4, 95% CI = 1.4 to 3.7, P = .001), and pancreatic cancer (five cancers among 429 FDRs of carrier probands vs 41 cancers among 23 452 FDRs of noncarrier probands; RR = 7.4, 95% CI = 2.3 to 18.7, P = .002). Wilms tumor was reported in two FDRs of carrier probands and three FDRs of noncarrier probands (RR = 40.4, 95% CI = 3.4 to 352.7, P = .005). The lifetime risk of any cancer other than melanoma among CDKN2A mutation carriers was estimated as 59.0% by age 85 years (95% CI = 39.0% to 75.4%) by the kin-cohort method, under the standard assumptions of Mendelian genetics on the genotype distribution of FDRs conditional on proband genotype.

Quantification of genes and gene transcripts for microbial perchlorate reduction in fixed-bed bioreactors

AIMS

Optimization of full-scale, biological perchlorate treatment processes for drinking water would benefit from knowledge of the location and quantity of perchlorate-reducing bacteria (PRB) and expression of perchlorate-related genes in bioreactors. The aim of this study was to quantify perchlorate removal and perchlorate-related genes (pcrA and cld) and their transcripts in bioreactors and to determine whether these genes or transcripts could serve as useful biomarkers for perchlorate treatment processes.

METHODS AND RESULTS

Quantitative PCR (qPCR) assays targeting pcrA and cld were applied to two pilot-scale, fixed-bed bioreactors treating perchlorate-contaminated groundwater. pcrA and cld genes per microgram of DNA were two- to threefold higher and three- to fourfold higher, respectively, in the bioreactor showing superior perchlorate-removal performance. In a laboratory-scale bioreactor, quantities of pcrA and cld genes and transcripts were compared under two distinct performance conditions (c.60 and 20% perchlorate removal) for a 5-min empty bed contact time. cld genes per microgram of DNA were approximately threefold higher and cld transcripts per microgram of RNA were approximately sixfold higher under the higher perchlorate-removal condition. No differences in pcrA genes or transcripts per microgram of DNA or RNA, respectively, were detected between the c.60 and 20% perchlorate-removal conditions, possibly because these assays did not accurately quantify pcrA genes and transcripts in the mixed culture present.

CONCLUSIONS

Quantities of cld genes and transcripts per microgram of DNA and RNA, respectively, were found to be higher when perchlorate removal was higher. However, quantities of pcrA and cld genes or transcripts were not found to directly correlate with perchlorate-removal rates.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this study represents the first application of qPCR assays to quantify perchlorate-related genes and transcripts in continuous-flow bioreactors. The results indicate that cld gene and transcript quantities can provide insights regarding the quantity, location and gene expression of PRB in bioreactors.

MRE11 deficiency increases sensitivity to poly(ADP-ribose) polymerase inhibition in microsatellite unstable colorectal cancers

Microsatellite instability (MSI) is displayed by approximately 15% of colorectal cancers (CRC). Defective DNA mismatch repair generates mutations at repetitive DNA sequences such as those located in the double strand break (DSB) repair gene MRE11. We assessed the mutational status of MRE11 in a panel of 17 CRC cell lines and 46 primary tumors and found a strong correlation with MSI status in both cell lines and tumors. Therefore, we hypothesized that deficiency in MRE11 may sensitize CRC cells to poly(ADP-ribose) polymerase (PARP-1) inhibition based on the concept of synthetic lethality. We further assessed the activity of the PARP-1 inhibitor, ABT-888, in CRC cell lines and observed preferential cytotoxicity in those MSI cell lines harboring mutations in MRE11 compared with both wild-type cell lines and microsatellite stable (MSS) cell lines. A significant correlation between MRE11 expression levels and cytotoxicity to ABT-888 at 10 μM was observed (R² = 0.915, P < 0.001). Using two experimental approaches, including short hairpin RNA knocking down MRE11 in the wild-type and MSS cell line SW-480 and a second cell line model transfected with mutant MRE11, we experimentally tried to confirm the role of MRE11 in conferring sensitivity to PARP-1 inhibition. Both models led to changes in proliferation in response to ABT-888 at different concentrations, and a drug-response effect was not observed, suggesting a possible contribution of additional genes. We conclude that MSI colorectal tumors deficient in DSB repair secondary to mutation in MRE11 show a higher sensitivity to PARP-1 inhibition. Further clinical investigation of PARP-1 inhibitors is warranted in MSI CRCs.

Disclosing individual CDKN2A research results to melanoma survivors: interest, impact, and demands on researchers

BACKGROUND

Whether to return individual research results from cancer genetics studies is widely debated, but little is known about how participants respond to results disclosure or about its time and cost burdens on investigators.

METHODS

We recontacted participants at one site of a multicenter genetic epidemiologic study regarding their CDKN2A gene test results and implications for melanoma risk. Interested participants were disclosed their results by telephone and followed for 3 months.

RESULTS

Among 39 patients approached, 27 were successfully contacted, and 19 (70% uptake) sought results, including three with mutations. Prior to disclosure, participants endorsed numerous benefits of receiving results (mean=7.7 of 9 posed), including gaining information relevant to their children's disease risk. Mean psychological well-being scores did not change from baseline, and no decreases to melanoma prevention behaviors were noted. Fifty-nine percent of participants reported that disclosure made participation in future research more likely. Preparation for disclosure required 40 minutes and $611 per recontact attempt. An additional 78 minutes and $68 was needed to disclose results.

CONCLUSION

Cancer epidemiology research participants who received their individual genetic research results showed no evidence of psychological harm or false reassurance from disclosure and expressed strong trust in the accuracy of results. Burdens to our investigators were high, but protocols may differ in their demands and disclosure may increase participants' willingness to enroll in future studies.

IMPACT

Providing individual study results to cancer genetics research participants poses potential challenges for investigators, but many participants desire and respond positively to this information.

Syntrophic acetate oxidation in two-phase (acid-methane) anaerobic digesters

The microbial processes involved in two-phase anaerobic digestion were investigated by operating a laboratory-scale acid-phase (AP) reactor and analyzing two full-scale, two-phase anaerobic digesters operated under mesophilic (35 °C) conditions. The digesters received a blend of primary sludge and waste activated sludge (WAS). Methane levels of 20% in the laboratory-scale reactor indicated the presence of methanogenic activity in the AP. A phylogenetic analysis of an archaeal 16S rRNA gene clone library of one of the full-scale AP digesters showed that 82% and 5% of the clones were affiliated with the orders Methanobacteriales and Methanosarcinales, respectively. These results indicate that substantial levels of aceticlastic methanogens (order Methanosarcinales) were not maintained at the low solids retention times and acidic conditions (pH 5.2-5.5) of the AP, and that methanogenesis was carried out by hydrogen-utilizing methanogens of the order Methanobacteriales. Approximately 43, 31, and 9% of the archaeal clones from the methanogenic phase (MP) digester were affiliated with the orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales, respectively. A phylogenetic analysis of a bacterial 16S rRNA gene clone library suggested the presence of acetate-oxidizing bacteria (close relatives of Thermacetogenium phaeum, 'Syntrophaceticus schinkii,' and Clostridium ultunense). The high abundance of hydrogen consuming methanogens and the presence of known acetate-oxidizing bacteria suggest that acetate utilization by acetate oxidizing bacteria in syntrophic interaction with hydrogen-utilizing methanogens was an important pathway in the second-stage of the two-phase digestion, which was operated at high ammonium-N concentrations (1.0 and 1.4 g/L). A modified version of the IWA Anaerobic Digestion Model No. 1 (ADM1) with extensions for syntrophic acetate oxidation and weak-acid inhibition adequately described the dynamic profiles of volatile acid production/degradation and methane generation observed in the laboratory-scale AP reactor. The model was validated with historical data from the full-scale digesters.

Characterization of two Ashkenazi Jewish founder mutations in MSH6 gene causing Lynch syndrome

Founder mutations are an important cause of Lynch syndrome and facilitate genetic testing in specific ethnic populations. Two putative founder mutations in MSH6 were analyzed in 2685 colorectal cancer (CRC) cases, 337 endometrial cancer (EnCa) cases and 3310 healthy controls of Ashkenazi Jewish (AJ) descent from population-based and hospital-based case–control studies in Israel, Canada and the United States. The carriers were haplotyped and the age of the mutations was estimated. MSH6*c.3984_3987dupGTCA was found in 8/2685 CRC cases, 2/337 EnCa cases, and 1/3310 controls, consistent with a high risk of CRC (odds ratio (OR) = 9.9, 95% confidence interval (CI) = 1.2–78.9, p = 0.0079) and a very high risk of EnCa (OR = 19.6, 95% CI = 1.8–217.2, p = 0.0006). MSH6*c.3959_3962delCAAG was identified in 3/2685 CRC cases, 2/337 EnCa cases and no controls. Each mutation was observed on separate conserved haplotypes. MSH6*c.3984_3987dupGTCA and MSH6*c.3959_3962delCAAG probably arose around 585 CE and 685 CE, respectively. No carriers were identified in Sephardi Jews (450 cases and 490 controls). Truncating mutations MSH6*c.3984_3987dupGTCA and MSH6*c.3959_3962delCAAG cause Lynch syndrome and are founder mutations in Ashkenazi Jews. Together with other AJ founder mutations, they contribute substantially to the incidence of CRC and EnCa and are important tools for the early diagnosis and appropriate management of AJ Lynch syndrome patients.