Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a molecularly heterogeneous solid malignancy, and its fitness may be shaped by how its tumor cells evolve. However, ability to monitor tumor cell evolution is hampered by the presence of numerous passenger mutations that do not provide any biological consequences. Here we develop a strategy to determine the tumor clonality of three independent HCC cohorts of 524 patients with diverse etiologies and race/ethnicity by utilizing somatic mutations in cancer driver genes. We identify two main types of tumor evolution, i.e., linear, and non-linear models where non-linear type could be further divided into classes, which we call shallow branching and deep branching. We find that linear evolving HCC is less aggressive than other types. GTF2IRD2B mutations are enriched in HCC with linear evolution, while TP53 mutations are the most frequent genetic alterations in HCC with non-linear models. Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.

The Mutographs biorepository: A unique genomic resource to study cancer around the world

Large-scale biorepositories and databases are essential to generate equitable, effective, and sustainable advances in cancer prevention, early detection, cancer therapy, cancer care, and surveillance. The Mutographs project has created a large genomic dataset and biorepository of over 7,800 cancer cases from 30 countries across five continents with extensive demographic, lifestyle, environmental, and clinical information. Whole-genome sequencing is being finalized for over 4,000 cases, with the primary goal of understanding the causes of cancer at eight anatomic sites. Genomic, exposure, and clinical data will be publicly available through the International Cancer Genome Consortium Accelerating Research in Genomic Oncology platform. The Mutographs sample and metadata biorepository constitutes a legacy resource for new projects and collaborations aiming to increase our current research efforts in cancer genomic epidemiology globally.

Knowledge and Attitudes toward Colorectal Cancer among Healthcare Workers: A Pilot Cross-Sectional Survey in Thailand

BACKGROUND

Colorectal cancer is an important public health problem in Thailand. The health workforce is one of the key strategies to reduce the burden of cancer. They are not only involved in patient care, but they can improve public knowledge of cancer within their community. This study aimed to explore the knowledge and attitudes toward colorectal cancer among Thai healthcare workers.

METHODS

A cross-sectional pilot study was conducted from October 2021 to March 2022. Convenience sampling was used to recruit study participants who worked in selected primary healthcare units or hospitals located in different regions across the country. The data on demographics and health behavior, knowledge of using the Fecal Immunochemical Test (FIT), and knowledge and attitudes toward colorectal cancer were collected using self-administered questionnaires. Descriptive statistics were used for data analysis.

RESULTS

A total of 300 healthcare workers were recruited in the study. The majority of participants presented a healthy lifestyle: 74% were in the healthy weight range, 68% had never consumed alcohol, and 99.3% were never smokers. More than 70% of participants provided correct answers to questions about the use of a FIT kit. The mean score for knowledge of colorectal cancer was 12.16 + 2.16 (out of 14) and 240 (80%) participants were considered to have adequate knowledge. Also, colorectal cancer knowledge was associated with age of participants (p<0.05). Most of the participants (76.2-92.3%) had positive attitudes toward colorectal cancer screening, however about half of them thought that a colonoscopy could be painful, uncomfortable, and embarrassing.

CONCLUSIONS

Overall, the majority of participants had adequate knowledge of colorectal cancer and positive attitudes toward its screening. The present study provided overview information on practical guidance for undertaking a nationwide survey in the future.

Pan-viral serology uncovers distinct virome patterns as risk predictors of hepatocellular carcinoma and intrahepatic cholangiocarcinoma

This study evaluates the pan-serological profiles of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) compared to several diseased and non-diseased control populations to identify risk factors and biomarkers of liver cancer. We used phage immunoprecipitation sequencing, an anti-viral antibody screening method using a synthetic-phage-displayed human virome epitope library, to screen patient serum samples for exposure to over 1,280 strains of pathogenic and non-pathogenic viruses. Using machine learning methods to develop an HCC or iCCA viral score, we discovered that both viral scores were positively associated with several liver function markers in two separate at-risk populations independent of viral hepatitis status. The HCC score predicted all-cause mortality over 8 years in patients with chronic liver disease at risk of HCC, while the viral hepatitis status was not predictive of survival. These results suggest that non-hepatitis viral infections may contribute to HCC and iCCA development and could be biomarkers in at-risk populations.

REPCAN: Guideline for REporting Population-based CANcer Registry Data

Background: The objective of this study was to develop a guideline on how to report result of a population-based cancer registry. Methods: The guideline's development involved a core working committee and a scientific committee comprising experts from diverse domains. The process comprised three steps: 1) a comprehensive review of existing tools and guidelines and the development of the initial draft of the guideline based on a review of literature, 2) refinement items through several rounds of focus group discussion among the core group, and development initial draft, and 3) Evaluation of the initial draft by scientific committee members. Items in the guideline were organized to accommodate reports of population-based cancer registries as a scientific manuscript. Results: The core committee developed 47 items distributed in the major heading of a scientific manuscript presented as a checklist. The evaluation of the scientific committee led to a consensus on the majority of the items included in the checklist. Among 10 committee members, 7 provided unreserved approval, validating each item's necessity, applicability, and comprehensibility in the checklist. Feedback from the remaining 3 members was carefully analyzed and integrated to enhance the guideline's robustness. Incorporating feedback, a first final draft was presented in a meeting of scientific and core working committee members. Collaborative discussion ensured clarity of expression for each items and a final checklist was developed. Conclusion: The guideline abbreviated as REPCAN offers a standardized framework for reporting population-based cancer registry, fostering transparency, comparability, and comprehensive data presentation. The guideline encourages flexibility while promoting comprehensive and robust reporting practices.

Agreement between Self- and Physician‑Sampling for Detection of High‑Risk Human Papillomavirus Infections in Women Attending Cervical Screening at National Cancer Institute, Thailand

BACKGROUND

We determined testing of self-sampling vagina swabs for Human Papilloma Virus (HPV) can be used to screen for cervical disease in outpatient clinics.

METHODS

In this study, women attending cervical cancer screening clinic and gynecology clinic of the National Cancer Institute were invited to take a vaginal self-sampling and physician-collected cervical sampling.

RESULTS

Of 268 participants, 20 (7.5%) were HPV-positive on the physician-collected samples. Among these screen-positive women, only two (0.7%) had HPV 18 and/or 45 and none had HPV 16 infections. For the self-collected samples, 4 participants had invalid HPV test results. Of the remaining 264 women with valid test results on self-collected samples, 29 (11.0 %) were HPV-positive, of whom, two (0.8%) were infected with HPV 16 and one (0.4%) with HPV 18 and/or 45 infections. The agreement between self-sampling and physician-sampling HPV test results (when two HPV results categories were considered) was 92. 8% with a moderate Kappa value of 0.57.

CONCLUSION

Overall, self-sampling seems to be a reliable alternative to health-provider collection. However, instructions on proper procedures for sample collection to the women are important step before general roll out.

Quantification of impact of COVID-19 pandemic on cancer screening programmes - a case study from Argentina, Bangladesh, Colombia, Morocco, Sri Lanka, and Thailand

It is quite well documented that the COVID-19 pandemic disrupted cancer screening services in all countries, irrespective of their resources and healthcare settings. While quantitative estimates on reduction in volume of screening tests or diagnostic evaluation are readily available from the high-income countries, very little data are available from the low- and middle-income countries (LMICs). From the CanScreen5 global cancer screening data repository we identified six LMICs through purposive sampling based on the availability of cancer screening data at least for the years 2019 and 2020. These countries represented those in high human development index (HDI) categories (Argentina, Colombia, Sri Lanka, and Thailand) and medium HDI categories (Bangladesh and Morocco). No data were available from low HDI countries to perform similar analysis. The reduction in the volume of tests in 2020 compared to the previous year ranged from 14.1% in Bangladesh to 72.9% in Argentina (regional programme) for cervical screening, from 14.2% in Bangladesh to 49.4% in Morocco for breast cancer screening and 30.7% in Thailand for colorectal cancer screening. Number of colposcopies was reduced in 2020 compared to previous year by 88.9% in Argentina, 38.2% in Colombia, 27.4% in Bangladesh, and 52.2% in Morocco. The reduction in detection rates of CIN 2 or worse lesions ranged from 20.7% in Morocco to 45.4% in Argentina. Reduction of breast cancer detection by 19.1% was reported from Morocco. No association of the impact of pandemic could be seen with HDI categories. Quantifying the impact of service disruptions in screening and diagnostic tests will allow the programmes to strategize how to ramp up services to clear the backlogs in screening and more crucially in further evaluation of screen positives. The data can be used to estimate the impact on stage distribution and avoidable mortality from these common cancers.

Abstract 6057: Association of liver cancer and chronic liver disease with urinary glyphosate and its metabolites in Thailand

Background: Glyphosate, the primary weed-killing ingredient in Roundup®, is the most widely used herbicide worldwide. The World Health Organization’s International Agency for Research on Cancer (IARC) Monographs Program classified glyphosate is a probable human carcinogen (Group 2A), capable of causing human cancer under some circumstances.

Methods: We analyzed urine specimens from 848 sequential patients with liver cancer and matched non-cancer controls from five different regional hospitals in Thailand. Gas chromatography electrospray ionization mass spectrometry (GC-ESI/MS) technique was used to measure glyphosate and its metabolites aminomethylphosphonic acid (AMPA) and phosphoric acid (PPA) to study their levels in hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (CCA), and chronic liver disease (CLD) in comparison to matched population controls.

Findings: Significantly higher levels of glyphosate were found in CLD patients compared to cancer cases and population controls, while significantly elevated levels of both AMPA and PPA were observed in HCC and CLD patients. Glyphosate and its metabolites were also detected at low to moderately high levels in convenience samples of food products and drinking water.

Interpretation: These results raise concern about the potential role of glyphosate in chronic human liver disease and cancer.

Citation Format: Daxesh P. Patel, Benjarath Pupacdi, Siritida Rabibhadana, Leila Toulabi, Majda Haznadar, Bhavik Dalal, Mohammed Khan, Joshua Stone, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Anon Chotirosniramit, Chawalit Pairojkul, Chirayu U. Auewarakul, Thaniya Sricharunrat, Kannika Phornphutkul, Suleeporn Sangrajrang, Anuradha Budhu, Chulabhorn Mahidol, Xin W. Wang, Frank J. Gonzalez, Mathuros Ruchirawat, Christopher A. Loffredo, Curtis C. Harris, TIGER-LC Consortium . Association of liver cancer and chronic liver disease with urinary glyphosate and its metabolites in Thailand [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6057.

Global survival trends for brain tumors, by histology: analysis of individual records for 556,237 adults diagnosed in 59 countries during 2000-2014 (CONCORD-3)

BACKGROUND

Survival is a key metric of the effectiveness of a health system in managing cancer. We set out to provide a comprehensive examination of worldwide variation and trends in survival from brain tumors in adults, by histology.

METHODS

We analyzed individual data for adults (15-99 years) diagnosed with a brain tumor (ICD-O-3 topography code C71) during 2000-2014, regardless of tumor behavior. Data underwent a 3-phase quality control as part of CONCORD-3. We estimated net survival for 11 histology groups, using the unbiased nonparametric Pohar Perme estimator.

RESULTS

The study included 556,237 adults. In 2010-2014, the global range in age-standardized 5-year net survival for the most common sub-types was broad: in the range 20%-38% for diffuse and anaplastic astrocytoma, from 4% to 17% for glioblastoma, and between 32% and 69% for oligodendroglioma. For patients with glioblastoma, the largest gains in survival occurred between 2000-2004 and 2005-2009. These improvements were more noticeable among adults diagnosed aged 40-70 years than among younger adults.

CONCLUSIONS

To the best of our knowledge, this study provides the largest account to date of global trends in population-based survival for brain tumors by histology in adults. We have highlighted remarkable gains in 5-year survival from glioblastoma since 2005, providing large-scale empirical evidence on the uptake of chemoradiation at population level. Worldwide, survival improvements have been extensive, but some countries still lag behind. Our findings may help clinicians involved in national and international tumor pathway boards to promote initiatives aimed at more extensive implementation of clinical guidelines.

Acceptability and Preference for Human Papilloma Virus Self-Sampling among Thai Women Attending National Cancer Institute

BACKGROUND

Cervical cancer screening is an important public health strategy to reduce cervical cancer incidence and mortality. Human papillomavirus (HPV) self-sampling is the alternative method that can potentially increase participation in cervical cancer screening. This study aimed to evaluate the acceptability of HPV self-sampling as a primary cervical cancer screening among Thai women.

METHODS

A cross-sectional study was conducted at National Cancer Institute, Thailand, between March and September 2021. Eligible women were invited to collect their own samples with a vaginal cotton swab for cervical screening. The data on demographics, acceptability, and preference for HPV self-sampling were collected via a self-administered questionnaire. A Likert scale was used to assess the response of self-sampling acceptability. The multivariable logistic regression determined factors that influence preference for HPV self-sampling.

RESULTS

A total of 265 participants were recruited. Over 70% agreed that self-sampling was easy, less embarrassing, and not painful. They also felt confident in their ability to self-sample correctly and would recommend this method to a friend or relative. For their next screening round, 66.4% preferred self-sampling whereas 33.6% preferred clinician-collected samples as routine screening. The factors that influence preference for self-sampling were age, marital status, feeling less embarrassed, and confidence in performing the tests.

CONCLUSIONS

Most of the study participants accepted HPV self-sampling. This suggests that the self-sampling method will be an additional option to increase cervical cancer screening coverage which leads to improving the effectiveness of the national program.

Cancer survival in Thailand from 1997 to 2012: Assessing the impact of universal health coverage

BACKGROUND

In recent decades, many countries worldwide have implemented some form of Universal Health Coverage (UHC). We sought to evaluate incidence and survival trends of breast, cervical, and colorectal cancer before and after the implementation of UHC in Thailand.

METHODS

The age-standardized incidence rate and 1- and 5-year net survival (NS) were calculated for five Thai provinces, namely Bangkok, Chiang Mai, Khon Kaen, Lampang, and Songkhla for breast, cervix, and colorectal cancer in three study periods (1997-2012): before, during, and after the implementation of UHC.

RESULTS

The incidence of breast and colorectal cancer has increased over time, while the incidence of cervical cancer has decreased (17.9-29.9, 9.0-13.6, and 19.6-12.3 per 100,000, respectively). Larger proportion of breast cancer were diagnosed with localized stage after UHC implementation compared to the period prior to UHC (31.5 % vs 19.0 %). Overall, The improvement in survival by cancer site varied in magnitude with a 5-year NS increase from 61.3 % to 75.1 % for breast, 55.4-59.5 % for cervical, and 39.9-47.6 % for colorectal cancer. The amount of increase slightly differed across provinces.

CONCLUSION

Rising incidence for breast and colorectal, and declining cervical cancer may partly be attributable to improved awareness and early detection programs. Additionally, improvement in survival may partly be attributable to increased access to healthcare, availability of treatment, and increased access to cancer screening after UHC was implemented. Thus, continued expansion of UHC package on cancer could potentially contribute to further improvement of cancer control in Thailand.

POLICY SUMMARY

This study provides important evidence on the impact of UHC in cancer burden and survival for breast, cervical, and colorectal cancer in Thailand. This study serves as an example for other countries where UHC has been recently implemented and guide policymakers in allocating resources towards UHC and cancer control programs.

Antitumor Effects of Cannabinoids in Human Pancreatic Ductal Adenocarcinoma Cell Line (Capan-2)-Derived Xenograft Mouse Model

Background

Pancreatic cancer is considered a rare type of cancer, but the mortality rate is high. Cannabinoids extracted from the cannabis plant have been interested as an alternative treatment in cancer patients. Only a few studies are available on the antitumor effects of cannabinoids in pancreatic cancer. Therefore, this study aims to evaluate the antitumor effects of cannabinoids in pancreatic cancer xenografted mouse model.

Materials and Methods

Twenty-five nude mice were subcutaneously transplanted with a human pancreatic ductal adenocarcinoma cell line (Capan-2). All mice were randomly assigned into 5 groups including negative control (gavage with sesame oil), positive control (5 mg/kg 5-fluorouracil intraperitoneal administration), and cannabinoids groups that daily received THC:CBD, 1:6 at 1, 5, or 10 mg/kg body weight for 30 days, respectively. Xenograft tumors and internal organs were collected for histopathological examination and immunohistochemistry.

Results

The average tumor volume was increased in all groups with no significant difference. The average apoptotic cells and caspase-3 positive cells were significantly increased in cannabinoid groups compared with the negative control group. The expression score of proliferating cell nuclear antigen in positive control and cannabinoids groups was decreased compared with the negative control group.

Conclusions

Cannabinoids have an antitumor effect on the Capan-2-derived xenograft mouse model though induce apoptosis and inhibit proliferation of tumor cells in a dose-dependent manner.

Out-of-pocket payments for complementary medicine following cancer and the effect on financial outcomes in middle-income countries in southeast Asia: a prospective cohort study

BACKGROUND

Complementary medicine, which refers to therapies that are not part of conventional medicine, comprising both evidence-based and non-evidence-based interventions, is increasingly used following a diagnosis of cancer. We aimed to investigate out-of-pocket spending patterns on complementary medicine and its association with adverse financial outcomes following cancer in middle-income countries in southeast Asia.

METHODS

In this prospective cohort study, data on newly diagnosed patients with cancer were derived from the ASEAN Costs in Oncology (ACTION) cohort study, a prospective longitudinal study in 47 centres located in eight countries in southeast Asia. The ACTION study measured household expenditures on complementary medicine in the immediate year after cancer diagnosis. Participants were given cost diaries at baseline to record illness-related payments that were directly incurred and not reimbursed by insurance over the 12-month period after study recruitment. We assessed incidence of financial catastrophe (out-of-pocket cancer-related costs ≥30% of annual household income), medical impoverishment (reduction in annual household income to below poverty line following subtraction of out-of-pocket cancer-related costs), and economic hardship (inability to make necessary household payments) at 1 year.

FINDINGS

Between March, 2012, and September, 2013, 9513 participants were recruited into the ACTION cohort study, of whom 4754 (50·0%) participants were included in this analysis. Out-of-pocket expenditures on complementary medicine were reported by 1233 households. These payments constituted 8·6% of the annual total out-of-pocket health costs in lower-middle-income countries and 42·9% in upper-middle-income countries. Expenditures on complementary medicine significantly increased risks of financial catastrophe (adjusted odds ratio 1·52 [95% CI 1·23-1·88]) and medical impoverishment (1·75 [1·36-2·24]) at 12 months in upper-middle-income countries only. However, the risks were significantly higher for economically disadvantaged households, irrespective of country income group.

INTERPRETATION

Integration of evidence-supported complementary therapies into mainstream cancer care, along with interventions to address use of non-evidence-based complementary medicine, might help alleviate any associated adverse financial impacts.

FUNDING

None.

An analysis of the incidence and survival rates of bone sarcoma patients in thailand: reports from population-based cancer registries 2001-2015

BACKGROUND

Epidemiology data from population-based cancer registries (PBCR) can be very valuable in the development of health policy and for improving the quality of cancer control strategies.

METHODS

This study analyzed the incidence of bone sarcomas in Thailand during 2001 - 2015 by analyzing data obtained from 5 PBCRs across country. Incidence rates per million person-years by sex, histological subtype, primary site and 5-year age group were calculated. Age-standardized incidence rates (ASR) were adjusted using the WHO's World Standard Population and comparisons between populations were done using standardized rate ratios (SRR). Incidence trends were evaluated using Joinpoint Trend Analysis. Survival rates were analyzed using STATA.

RESULTS

The ASR of bone sarcomas in Thailand was 5.1/10⁶ person-years, with an estimated 328 newly diagnosed bone sarcomas per year for the country overall. Osteosarcoma (52.5%), chondrosarcoma (18%), Ewing's sarcoma (11.6%), giant cell tumor (4.8%) and chordoma (4.7%) were the most common malignant bone tumors, representing 91.5% of all bone sarcomas. Bone sarcoma has a predilection for males (1.29:1) and an age-specific bimodal rate pattern closely related to the major histological subtypes, osteosarcoma. One- and five-year survival rates of Thai patients with bone sarcoma were 74% and 52%, respectively. Survival rates of bone sarcomas, particularly osteosarcoma, were lower than the rates reported from the United States, Europe and Japan.

CONCLUSION

The lower overall survival rate of bone sarcoma represented the gap of bone sarcoma control program in Thailand. That indicates the need for improvement in health promotion, treatment process and chemotherapy for bone sarcoma patients in the future.

National Cervical Cancer Screening in Thailand

Background:

Cervical cancer is an important public health problem in Thailand. It was the most common cancer in Thai women with the incidence rate of 23.4 per 100,000 women in 1990.

Objective:

The aim of this study was to share the experiences and summary the outcome of cervical cancer screening program in Thailand. Methods: The Ministry of Public Health in cooperation with the National Health Security Office, launched the National Cervical Cancer Screening Program, covering 76 provinces nationwide under Universal Coverage Scheme in 2005. The screening method are Pap smear and Visual Inspection with Acetic acid (VIA) for women aged 30-60 and 35-45 respectively with a 5-year screening interval. Detecting cervical pre-cancerous lesions will follow by day care treatment such as cryotherapy, Loop Electrosurgical Excision Procedure, etc.

Results:

The first phase (2005-2009), was carried out on 3,124,855 women, the coverage reached 77.5%. For the second phase (2010-2014), 7,637,226 women were screened, reaching 53.9% coverage of target women. However, we have few data of follow up examination after abnormal screening. Therefore, we conducted new system to get more follow up data in 2019. Under the coordination of many related partners, 10,762,081 women have been screened during 2005-2014. The incidence rate declined to 11.7 per 100,000 women which is ranked as the third most common in women in 2014.

Conclusion:

This article briefly reviews the challenge of implementing an efficient cervical cancer screening in Thailand. In 2020, HPV testing has been introduced as a primary screening test for all Thai women attending public health sector instead of conventional Pap test.

Breast cancer in Thailand: policy and health system challenges to universal healthcare

Thailand has successfully implemented Universal Health Coverage (UHC) and embedded the 2030 Agenda for Sustainable Development into its Thailand 4.0 policy. Breast cancer is a growing challenge in Thailand, as it is globally. It serves as a perfect medium through which to interrogate UHC and demonstrate areas of the health system which require further strengthening if UHC is to be sustainable in the longer term. We conducted a situation analysis and used a Systemic Rapid Assessment (SYSRA) framework to examine the challenges posed to UHC through the lens of breast cancer. We identified a number of challenges facing UHC including (1) continued political commitment; (2) the need for coordinated scale-up of strategic investments involving increased financing and fine-tuning of the allocation of resources according to health needs; (3) reducing inequities between health insurance schemes; (4) investing in innovation of technologies, and more critically, in technology transfer and capacity building; (5) increasing capacity, quality and confidence in the whole primary healthcare team but especially family medicine doctors. This would subsequently increase both efficiency and effectiveness of the patient pathway, as well as allow patients wherever possible to be treated close to their homes, work and family; (6) developing and connecting information systems to facilitate understanding of what is working, where needs are and track trends to monitor improvements in patient care. Our findings add to an existing body of evidence which suggest, in light of changing disease burden and increasing costs of care, a need for broader health system reforms to create a more enabling platform for integrated healthcare as opposed to addressing individual challenging elements one vertical system at a time. As low- and middle-income countries look to realize the 2015 Sustainable Development Goals and sustainable UHC this analysis may provide input for policy discussion at national, regional and community levels and have applicability beyond breast cancer services alone and beyond Thailand.

Cancer incidence and cancer control in Bangkok, Thailand: Results from the cancer registry 2011-15 and projections to 2035

BACKGROUND

With considerable diversity in the patterns of cancer in different regions of Thailand and between urban vs. rural areas, this report focuses on cancer incidence burden in the Bangkok Metropolis 2011-15.

METHODS

Incidence rates in Bangkok were derived as the mean annual number of new cancer cases per 100,000 inhabitants for the period 2011-2015 stratified by 5-year age group and sex. Age-standardized incidence rates (ASR) were calculated using the world standard population.

RESULTS

The five most frequent cancers in Bangkok correspond to close to 60 % of the total burden in both males and females. In males, cancers of the lung, liver and colorectum each comprised 14-16 % of the burden, while breast cancer was responsible for three in 10 cancers in women (or 29.4 %), with colorectal and cervical cancer ranking second and third (10.0 % and 8.5 % respectively). respectively. Under three different scenarios of trends in all-cancer incidence rates, demographic changes mean that the incidence burden will rise over the next two decades.

CONCLUSIONS

The critical relevance of this information in the context of the planning and evaluation of national cancer control policies in Thailand is discussed. Evidently, the Bangkok and other Thai population-based cancer registries are essential in measuring the population-level impact of tobacco control, HBV and HPV vaccination, cervical and colorectal cancer screening, and via survival estimation, the effectiveness of cancer care.

National Cancer Control Program of Thailand

Since 2000 cancer has been the leading cause of death in Thailand. In response to this challenge, the National Cancer Institute of Thailand (NCI), in collaboration with other bodies, has developed and promoted the National Cancer Control Program (NCCP) to provide appropriate policies and practice for the prevention, early detection and treatment of cancer, with optimal supportive care. With plans strongly supported by the Ministry of Public Health, the NCCP envisages integration into the health care system in 6 strategic areas: (1) cancer informatics; (2) primary prevention; (3) early detection; (4) treatment; (5) palliative care; and (6) cancer control research. For this purpose 7 regional cancer hospitals have been established to aid the NCI in conducting the NCCP. Cancer registration is a high priority, with 31.2% of the population now covered by quality registries. In primary prevention, there is a focus on awareness, lifestyle improvement, anti-smoking and alcohol control programs, vaccination, and Opisthorchis viverrini (OV) control. Screening programs for cervical, breast and colorectal cancer are underway to increase early detection. Priority is being given to facilities for chemotherapy and radiotherapy, as well as palliative care. Cancer control research encompasses international cooperation and participation in training programs, especially for development of cancer registration and other aspects of cancer control programs in South-East Asia, not least as an IARC Collaborating Center.

Human papillomavirus (HPV) DNA and mRNA primary cervical cancer screening: Evaluation and triaging options for HPV-positive women

Objective

Cervical cancer is the second most common cancer in Thai women; human papillomavirus (HPV) is the main cause. This study aimed to determine the clinical performance of HPV mRNA compared with HPV DNA testing.

Methods

Cervical specimens were collected from women aged 35 to 60 who attended the routine organized screening programme. We compared accuracy parameters of standalone HPV mRNA and HPV DNA tests, and those of triaging with liquid-based cytology or HPV genotyping and liquid-based cytology for those positive only for the less oncogenic HPV types. Test accuracy parameters were estimated using latent class analysis using Bayesian models.

Results

Of the 5046 women enrolled, 174 (3.4%) were HPV DNA positive and 141 (2.8%) HPV mRNA positive. Colposcopy compliance was 95.4% ( n = 166) among HPV DNA-positive women and 94.3% ( n = 133) among those HPV mRNA positive. The estimated sensitivity, specificity, and positive predictive value for detection of CIN2 or worse were 67.4%, 97.1%, 12.1% for HPV DNA testing, and 73.1%, 97.8%, 16.3% for HPV mRNA testing. These estimates for triaging of HPV DNA-positive women with liquid-based cytology were 64.4%, 98.8%, and 19.0%, respectively, and slightly better for liquid-based cytology triage of HPV mRNA-positive women, at 71.8%, 98.9%, and 22.1%.

Conclusion

A triaging strategy based on HPV genotyping and liquid-based cytology for those positive only for the less oncogenic HPV types had test characteristics comparable with that of liquid-based cytology triage. The HPV mRNA detection-based strategies had non-significant advantages over the HPV DNA detection-based strategies.

The functional ALDH2 polymorphism is associated with breast cancer risk: A pooled analysis from the Breast Cancer Association Consortium

BACKGROUND

Epidemiological studies consistently indicate that alcohol consumption is an independent risk factor for female breast cancer (BC). Although the aldehyde dehydrogenase 2 (ALDH2) polymorphism (rs671: Glu>Lys) has a strong effect on acetaldehyde metabolism, the association of rs671 with BC risk and its interaction with alcohol intake have not been fully elucidated. We conducted a pooled analysis of 14 case-control studies, with individual data on Asian ancestry women participating in the Breast Cancer Association Consortium.

METHODS

We included 12,595 invasive BC cases and 12,884 controls for the analysis of rs671 and BC risk, and 2,849 invasive BC cases and 3,680 controls for the analysis of the gene-environment interaction between rs671 and alcohol intake for BC risk. The pooled odds ratios (OR) with 95% confidence intervals (CI) associated with rs671 and its interaction with alcohol intake for BC risk were estimated using logistic regression models.

RESULTS

The Lys/Lys genotype of rs671 was associated with increased BC risk (OR = 1.16, 95% CI 1.03-1.30, p = 0.014). According to tumor characteristics, the Lys/Lys genotype was associated with estrogen receptor (ER)-positive BC (OR = 1.19, 95% CI 1.05-1.36, p = 0.008), progesterone receptor (PR)-positive BC (OR = 1.19, 95% CI 1.03-1.36, p = 0.015), and human epidermal growth factor receptor 2 (HER2)-negative BC (OR = 1.25, 95% CI 1.05-1.48, p = 0.012). No evidence of a gene-environment interaction was observed between rs671 and alcohol intake (p = 0.537).

CONCLUSION

This study suggests that the Lys/Lys genotype confers susceptibility to BC risk among women of Asian ancestry, particularly for ER-positive, PR-positive, and HER2-negative tumor types.

Accounting for Immigrant Status when Calculating Cancer Incidence Rates for Bangkok

Objective: Cancer-registry data are crucial for definingcancer incidence rates for use in setting service priorities and monitoringservice effects. This applies in Thailand where cancer is the leading cause of death and service needs are high. The Bangkok Cancer Registry (population-based) was established in 1990to determine cancer incidence rates for Bangkok. This proved difficult, however, because the Bangkokpopulation (>8million) fluctuates with numbers of temporary visitors, many of whom visit Bangkok temporarily for services. If these visitors are mis-categorized as usual residents, cancer incidence rateswould be inflated. During 2013-2015, residential addresses on the Registry were cross-checked against official addresses on the National Civil Registration records of the Ministry of Interior. The effectsof this cross-checking on incidence rates are discussed. Methods: Residential addresses recorded on the Registry for cancer diagnoses in 2013-2015 were corrected using official Ministry data. Effects on numbers of recorded cancers and crude and directly age-standardized rates (World Population) were determined. Results: Of 44,813 cancer casesdiagnosed and recorded on the Registryduring 2013-2015, 36,327 (81.1%) had an official Bangkok address. When limiting analyses to these cases, the crude incidencefor all cancer sites combined reduced by 18.9% (19.7% for males and 18.3% for females). Corresponding reductions in age-standardized incidence rates were 20.0% for males and 18.8% for females. These reductions varied for common cancer sites:in males,from 14.8% for lung to 25.9% for colorectal cancer; and in females, from 12.9% for lung to 24.0% for cervical cancer. Conclusions: These differences are considered sufficient in magnitude to justifyroutine use of official residential data when calculating cancer incidence rates for Bangkok. If these rates are to be compared with comparable rates for other Asian citiesthat serve broader populations, equivalent methodologies for determining residential status would be needed for all cities.

Data Reliability and Coding Completeness of Cancer Registry Information Using Reabstracting Method in the National Cancer Institute: Thailand, 2012 to 2014

PURPOSE

Data quality is a core value of cancer registries, which bring about greater understanding of cancer distribution and determinants. Thailand established its cancer registry in 1986; however, studies focusing on data reliability have been limited. This study aimed to assess the coding completeness and reliability of the National Cancer Institute (NCI) hospital-based cancer registry, Thailand.

METHODS

This study was conducted using the reabstracting method. We focused on seven cancer sites-the colon, rectum, liver, lung, breast, cervix, and prostate-registered between 2012 and 2014 in the NCI hospital-based cancer registry. Missing data were identified for coding completeness calculation among important variables. The agreement rate and κ coefficient were computed to represent data reliability.

RESULTS

For reabstracting, we retrieved 957 medical records from a total of 5,462. These were selected using the probability proportional to size method, stratified by topology, sex, and registered year. The overall coding completeness of the registered and reabstracted data was 89.9% and 93.6%, respectively. In addition, the overall agreement rate among variables ranged from 84.7% to 99.6%, and κ coefficient ranged from 0.619 to 0.995. The misclassification among unilateral organs caused lower coding completeness and agreement rate of laterality coding. The completeness of current residency could be improved using the reabstracting method. The lowest agreement rate was found among various categories of diagnosis basis. Sex misclassification for male breast cancer was identified.

CONCLUSION

The coding completeness and data reliability of the NCI hospital-based cancer registry met the standard in most critical variables. However, some challenges remain to improve the data quality. The reabstracting method could identify the critical points affecting the quality of cancer registry data.

Cancer Incidence among Healthcare Workers in Cancer Centers: A 14-Year Retrospective Cohort Study in Thailand

Objective:

To identify the situation and possible work-related cancer risks among healthcare workers in cancer centers.

Methods:

This research was a 14-year retrospective cohort study of 2,331 healthcare workers at the National Cancer Institute and 7 regional cancer centers in Thailand. The study period consisted of a total of 18,939 person-years of observation. The demographic data, such as occupation and work area were collected by self-administered questionnaires or by use of a proxy. The cases were identified by the diagnoses of physicians. The incidence rates for each type of cancer, occupation and work area among the population of this study were compared with the general working population, based on national cancer statistics. The results were reported in terms of Standard Incidence Ratio (SIR) and a 95% confidence interval (CI), using Fisher’s exact method.

Findings:

There were 12 different types of cancer identified in 35 cases during the 14 years of the study and breast cancer was found to be at the highest number. The overall cancer incidence rates were 221.04 and 173.43 per 100,000 person-years, in males and females, respectively. Leukemia showed statistically significant levels of high SIR among the female healthcare staffs (SIR = 11.54; 95% CI = 2.38–33.72). With regard to occupation, only the male physicians showed significant SIR = 6.02; 95% CI = 1.41–19.93, while this study did not identify significant SIR levels in any of the work areas.

Conclusions:

This study found that the risk of leukemia was higher than expected among healthcare workers and that physicians may have an increased risk of cancer compared to the general working population, which may be a work-related reflex. However, interpretations should be made with caution due to the small number of cases.

Publisher Correction: Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation

This corrects the article DOI: 10.1038/ncomms5999.

Role of Glutathione S-Transferase Omega Gene Polymorphisms in Breast-Cancer Risk

Background/Aims

Genetically influenced variations in the levels of activity and/or expression of some members of the glutathione S-transferase (GST) family have been identified as risk factors for cancer. One, GST omega (GSTO), has been found in a very limited number of studies. The aim of the present study was to investigate the influence of GSTO1 and GSTO2 polymorphisms on breast cancer risk.

Methods

DNA isolated from the blood of 101 patients with breast cancer and 151 healthy controls was investigated for GSTO1 and GSTO2 polymorphisms by polymerase chain reaction-restriction-fragment length polymorphism.

Results

Univariate and multivariate analyses showed no association between GSTO1 and GSTO2 genotypes and the risk of breast cancer. A higher prevalence of wild-type GSTO1 (A140/A140) was significantly correlated with advanced-stage breast cancer (OR = 0.1, 95% CI, 0.01-0.77), but the presence of the genotype did not correlate with patient age at diagnosis, menopausal status, tumor size, lymph node metastasis, or estrogen-receptor status. No association was found between GSTO2 genotype and clinicopathological features.

Conclusions

The results of the study suggest that GSTO1 and GSTO2 variants are not associated with breast cancer risk, but that wild-type GSTO1 (A140/A140) is likely among cases at an advanced stage.

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.

Association analysis identifies 65 new breast cancer risk loci

Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P < 5 × 10-8. The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.

Cost-effectiveness analysis study of HPV testing as a primary cervical cancer screening in Thailand

Objectives

The aim of this study is to compare the cost and benefit of four different cervical cancer screening strategies involving primary HPV 16/18 genotyping, hrHPV testing alone and cytology for detecting CIN2 +.

Methods

Economical analysis using Markov modeling approach to combine the epidemiological data from current population-based study of The National Cancer Institute of Thailand. A cohort of 100,000 hypothetical female population age 30–65 years was simulated in each strategy. The compared strategies are HPV 16/18 genotyping with reflexed cytology, hrHPV testing alone followed by colposcopy, Papanicolaou standard cytology and liquid based cytology followed by colposcopy. The interval of screening was 5 years' interval. The main outcomes were defined as a number of CIN2 + cases and cost per 100,000 women screening over 35 years.

Results

Model predictions indicated that, the most cost-effectiveness strategy is hrHPV testing alone by reducing cost and also increase CIN2 + detection rate. It identify an additional 130 cases and decrease cost by 46,950,840 THB (1,394,441 USD) per 100,000 women screened when compared to HPV 16/18 genotyping. Compared with cytology, hrHPV testing decrease cost by 51,279,781 THB (1,523,011 USD) and detected more 506 cases of CIN2 +. From sensitivity analysis, the cost of HPV testing, cost of colposcopy, incidence of HPV infection and sensitivity of cytology may affect the results. (1 USD = 33.67 Baht).

Conclusion

The results of this cost-effectiveness analysis support the full scale implementation of HPV testing as a primary cervical cancer screening in Thailand.

•

This is the first economic study of HPV testing as a screening method in Thailand.

•

The primary HPV testing is more effective than cytology method.

•

The most cost-effectiveness strategy is HR-HPV testing alone.

Common Molecular Subtypes Among Asian Hepatocellular Carcinoma and Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) and hepatocellular carcinoma (HCC) are clinically disparate primary liver cancers with etiological and biological heterogeneity. We identified common molecular subtypes linked to similar prognosis among 199 Thai ICC and HCC patients through systems integration of genomics, transcriptomics, and metabolomics. While ICC and HCC share recurrently mutated genes, including TP53, ARID1A, and ARID2, mitotic checkpoint anomalies distinguish the C1 subtype with key drivers PLK1 and ECT2, whereas the C2 subtype is linked to obesity, T cell infiltration, and bile acid metabolism. These molecular subtypes are found in 582 Asian, but less so in 265 Caucasian patients. Thus, Asian ICC and HCC, while clinically treated as separate entities, share common molecular subtypes with similar actionable drivers to improve precision therapy.

Abstract 4390: The Thailand initiative in genomics and expression research in liver cancer: Race related common molecular subtypes among Asian hepatocellular carcinoma and cholangiocarcinoma identified by integrated genomics

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are two distinct histological liver cancers. They are clinically and biologically heterogeneous and highly resistant to treatment, making liver cancer the second most lethal malignancy in the world. In Thailand, liver cancer represents the primary cause of cancer-related death and is a major health problem. While HBV and HCV are major etiological factors for HCC globally, liver fluke infection (O. viverrini) is a major etiological factor for ICC in Thailand, especially in north-eastern Thailand where O. viverrini is endemic and approximately 70% of liver cancers are ICC. These unique risk factor patterns provide an opportunity to study cancer heterogeneity and unique liver tumor biology. The Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC) consortium was established to identify genomic and expression factors that may modify HCC and ICC susceptibility and progression. Here, we determined molecular subtypes and features of HCC and ICC through systems integration of genomic, transcriptomic and metabolic profiles.

We performed genome wide profiling of 398 surgical specimens derived from 199 Thai liver cancer patients. We employed the Affymetrix Human Transcriptome Array 2.0, the Affymetrix Genome-Wide Human SNP Array 6.0, Metabolon's DiscoveryHD4 platform and Exome Sequencing to examine transcriptome profiles, somatic copy number alterations (SCNA), cancer metabolic profiles and mutation patterns, respectively. The results were validated in 847 independent Asian or Caucasian HCC or ICC cases.

Transcriptomic analyses revealed that Thai HCC consisted of 3 stable subgroups (C1-C3), while Thai ICC contained 4 stable subgroups (C1-C4). Interestingly, HCC-C1 and ICC-C1 subtypes shared a similar gene expression matrix, as did HCC-C2 and ICC-C2, which correlated with patient survival. These prognostic subtypes were validated in independent Asian HCC and ICC cohorts, but not in Caucasian patients, and were associated with tumor biology rather than etiology. GSEA revealed that the C1 subtype is enriched for mitotic checkpoint anomalies, while the C2 subtype is related to cytokine and chemokine signaling. We found that the C1 subtype encompassed a higher degree of SCNA when compared to the C2 subtype, suggesting an association with a genomic instability phenotype. Further analysis showed that the C2 subtype is linked to an increased body mass index, inflammatory responses and unique tumor metabolic activities.

HCC and ICC from Asian populations, while clinically treated as separate entities, share common subtypes with similar actionable drivers which can be targeted to improve precision therapy.

Citation Format: Anuradha Budhu, Jittiporn Chaisaingmongkol, Hien Dang, Siritida Rabibhadana, Benjarath Pupacdi, So Mee Kwon, Marshonna Forgues, Yotsawat Pomyen, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Anon Chotirosniramit, Chawalit Pairojkul, Chirayu U. Auewarakul, Thaniya Sricharunrat, Kannika Phornphutkul, Suleeporn Sangrajrang, Maggie Cam, Ping He, Stephen M. Hewitt, Xiaolin Wu, Snorri S. Thorgeirsson, Joshua J. Waterfall, Yuelin J. Zhu, Jennifer Walling, Holly S. Stevenson, Daniel Edelman, Paul S. Meltzer, Christopher A. Loffredo, Robert H. Wiltrout, Curtis C. Harris, Chulabhorn Mahidol, Mathuros Ruchirawat, Xin W. Wang. The Thailand initiative in genomics and expression research in liver cancer: Race related common molecular subtypes among Asian hepatocellular carcinoma and cholangiocarcinoma identified by integrated genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4390. doi:10.1158/1538-7445.AM2017-4390

Comparative accuracy of Pap smear and HPV screening in Ubon Ratchathani in Thailand

We evaluate the potential for using high-risk human papillomavirus (hr-HPV) testing-based screening for cervical intraepithelial neoplasia (CIN) in routine health services in Thailand; its accuracy in comparison to that of conventional cytology (CC); and the utility of HPV16/18 positive results and liquid-based cytology (LBC) triage for HPV-positive women in the detection of high-grade CIN. Women aged 30-60 years in Ubon Ratchathani province, Thailand were screened with CC and hr-HPV testing and those abnormal on either tests were referred for colposcopy and/or directed biopsies. The final diagnosis using COBAS was based on histology or colposcopy when histology was not available. Estimation of test accuracy parameters was done using latent class analysis using Bayesian models. Of the 5004 women were enrolled, 20 (0.4%) had abnormal CC and 174 (3.5%) women were HPV-positive. Among 185 women abnormal on CC or HPV-positive, 176 (95.1%) underwent colposcopy, of whom 101 (57.4%) had abnormal colposcopy findings. Ninety-seven women with abnormal and 69 with normal colposcopy had biopsies performed. All 21 women with histological CIN2 or worse had hr-HPV and none were abnormal on CC. The estimated sensitivity, specificity and positive predictive value were respectively 71.8%, 97.0% and 13.0% of HPV testing; 53%, 98.7% and 20.3% for triage of HPV-positive women with LBC; and 70.4%, 98.2% and 16.9% when test positivity was taken as HPV16/18 irrespective of LBC result or positive for hr-HPV non 16/18 types and LBC triage. Our study findings indicate poor performance of cytology screening and demonstrate the potential and utility of using HPV testing in public health services in Thailand as well as the utility of primary HPV testing and LBC triage in screening for cervical neoplasia.

BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case-control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. Cancer Res; 77(11); 2789-99. ©2017 AACR.

Evaluating genetic variants associated with breast cancer risk in high and moderate-penetrance genes in Asians

Over the past 20 years, high-penetrance pathogenic mutations in genes BRCA1, BRCA2, TP53, PTEN, STK11 and CDH1 and moderate-penetrance mutations in genes CHEK2, ATM, BRIP1, PALB2, RAD51C, RAD50 and NBN have been identified for breast cancer. In this study, we investigated whether there are additional variants in these 13 genes associated with breast cancer among women of Asian ancestry. We analyzed up to 654 single nucleotide polymorphisms (SNPs) from 6269 cases and 6624 controls of Asian descent included in the Breast Cancer Association Consortium (BCAC), and up to 236 SNPs from 5794 cases and 5529 controls included in the Shanghai Breast Cancer Genetics Study (SBCGS). We found three missense variants with minor allele frequency (MAF) <0.05: rs80358978 (Gly2508Ser), rs80359065 (Lys2729Asn) and rs11571653 (Met784Val) in the BRCA2 gene, showing statistically significant associations with breast cancer risk, with P-values of 1.2 × 10-4, 1.0 × 10-3 and 5.0 × 10-3, respectively. In addition, we found four low-frequency variants (rs8176085, rs799923, rs8176173 and rs8176258) in the BRCA1 gene, one common variant in the CHEK2 gene (rs9620817), and one common variant in the PALB2 gene (rs13330119) associated with breast cancer risk at P < 0.01. Our study identified several new risk variants in BRCA1, BRCA2, CHEK2, and PALB2 genes in relation to breast cancer risk in Asian women. These results provide further insights that, in addition to the high/moderate penetrance mutations, other low-penetrance variants in these genes may also contribute to breast cancer risk.

Targeted deep sequencing of plasma circulating cell-free DNA reveals Vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the second most common cause of cancer death worldwide, but is still lacking sensitive and specific biomarkers for early diagnosis and prognosis. In this study, we applied targeted massively parallel semiconductor sequencing to assess methylation on a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) in plasma circulating cell-free DNA (cfDNA) and to evaluate the potential of these genes as HCC biomarkers in two different series, one from France (42 HCC cases and 42 controls) and one from Thailand (42 HCC cases, 26 chronic liver disease cases and 42 controls). We also analyzed a set of HCC and adjacent tissues and liver cell lines to further compare with 'The Cancer Genome Atlas' (TCGA) data. The methylation in cfDNA was detected for FBLN1, PSMA7, PXDN and VIM, with differences in methylation patterns between cases and controls for FBLN1 and VIM. The average methylation level across analyzed CpG-sites was associated with higher odds of HCC for VIM (1.48 [1.02, 2.16] for French cases and 2.18 [1.28, 3.72] for Thai cases), and lower odds of HCC for FBLN1 (0.89 [0.76, 1.03] for French cases and 0.75 [0.63, 0.88] for Thai cases). In conclusion, our study provides evidence that changes in VIM and FBLN1 methylation levels in cfDNA are associated with HCC and could represent useful plasma-based biomarkers. Also, the potential to investigate methylation patterns in cfDNA could bring new strategies for HCC detection and monitoring high-risk groups and response to treatment.

Prediction of breast cancer risk based on common genetic variants in women of East Asian ancestry

BACKGROUND

Approximately 100 common breast cancer susceptibility alleles have been identified in genome-wide association studies (GWAS). The utility of these variants in breast cancer risk prediction models has not been evaluated adequately in women of Asian ancestry.

METHODS

We evaluated 88 breast cancer risk variants that were identified previously by GWAS in 11,760 cases and 11,612 controls of Asian ancestry. SNPs confirmed to be associated with breast cancer risk in Asian women were used to construct a polygenic risk score (PRS). The relative and absolute risks of breast cancer by the PRS percentiles were estimated based on the PRS distribution, and were used to stratify women into different levels of breast cancer risk.

RESULTS

We confirmed significant associations with breast cancer risk for SNPs in 44 of the 78 previously reported loci at P < 0.05. Compared with women in the middle quintile of the PRS, women in the top 1% group had a 2.70-fold elevated risk of breast cancer (95% CI: 2.15-3.40). The risk prediction model with the PRS had an area under the receiver operating characteristic curve of 0.606. The lifetime risk of breast cancer for Shanghai Chinese women in the lowest and highest 1% of the PRS was 1.35% and 10.06%, respectively.

CONCLUSION

Approximately one-half of GWAS-identified breast cancer risk variants can be directly replicated in East Asian women. Collectively, common genetic variants are important predictors for breast cancer risk. Using common genetic variants for breast cancer could help identify women at high risk of breast cancer.

rs2735383, located at a microRNA binding site in the 3'UTR of NBS1, is not associated with breast cancer risk

NBS1, also known as NBN, plays an important role in maintaining genomic stability. Interestingly, rs2735383 G > C, located in a microRNA binding site in the 3'-untranslated region (UTR) of NBS1, was shown to be associated with increased susceptibility to lung and colorectal cancer. However, the relation between rs2735383 and susceptibility to breast cancer is not yet clear. Therefore, we genotyped rs2735383 in 1,170 familial non-BRCA1/2 breast cancer cases and 1,077 controls using PCR-based restriction fragment length polymorphism (RFLP-PCR) analysis, but found no association between rs2735383CC and breast cancer risk (OR = 1.214, 95% CI = 0.936-1.574, P = 0.144). Because we could not exclude a small effect size due to a limited sample size, we further analyzed imputed rs2735383 genotypes (r2 > 0.999) of 47,640 breast cancer cases and 46,656 controls from the Breast Cancer Association Consortium (BCAC). However, rs2735383CC was not associated with overall breast cancer risk in European (OR = 1.014, 95% CI = 0.969-1.060, P = 0.556) nor in Asian women (OR = 0.998, 95% CI = 0.905-1.100, P = 0.961). Subgroup analyses by age, age at menarche, age at menopause, menopausal status, number of pregnancies, breast feeding, family history and receptor status also did not reveal a significant association. This study therefore does not support the involvement of the genotype at NBS1 rs2735383 in breast cancer susceptibility.

Evidence that the 5p12 Variant rs10941679 Confers Susceptibility to Estrogen-Receptor-Positive Breast Cancer through FGF10 and MRPS30 Regulation

Genome-wide association studies (GWASs) have revealed increased breast cancer risk associated with multiple genetic variants at 5p12. Here, we report the fine mapping of this locus using data from 104,660 subjects from 50 case-control studies in the Breast Cancer Association Consortium (BCAC). With data for 3,365 genotyped and imputed SNPs across a 1 Mb region (positions 44,394,495-45,364,167; NCBI build 37), we found evidence for at least three independent signals: the strongest signal, consisting of a single SNP rs10941679, was associated with risk of estrogen-receptor-positive (ER+) breast cancer (per-g allele OR ER+ = 1.15; 95% CI 1.13-1.18; p = 8.35 × 10-30). After adjustment for rs10941679, we detected signal 2, consisting of 38 SNPs more strongly associated with ER-negative (ER-) breast cancer (lead SNP rs6864776: per-a allele OR ER- = 1.10; 95% CI 1.05-1.14; p conditional = 1.44 × 10-12), and a single signal 3 SNP (rs200229088: per-t allele OR ER+ = 1.12; 95% CI 1.09-1.15; p conditional = 1.12 × 10-05). Expression quantitative trait locus analysis in normal breast tissues and breast tumors showed that the g (risk) allele of rs10941679 was associated with increased expression of FGF10 and MRPS30. Functional assays demonstrated that SNP rs10941679 maps to an enhancer element that physically interacts with the FGF10 and MRPS30 promoter regions in breast cancer cell lines. FGF10 is an oncogene that binds to FGFR2 and is overexpressed in ∼10% of human breast cancers, whereas MRPS30 plays a key role in apoptosis. These data suggest that the strongest signal of association at 5p12 is mediated through coordinated activation of FGF10 and MRPS30, two candidate genes for breast cancer pathogenesis.

Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2)  = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry.

Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)

Genome-wide association studies have found SNPs at 17q22 to be associated with breast cancer risk. To identify potential causal variants related to breast cancer risk, we performed a high resolution fine-mapping analysis that involved genotyping 517 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of genotypes for 3,134 SNPs in more than 89,000 participants of European ancestry from the Breast Cancer Association Consortium (BCAC). We identified 28 highly correlated common variants, in a 53 Kb region spanning two introns of the STXBP4 gene, that are strong candidates for driving breast cancer risk (lead SNP rs2787486 (OR = 0.92; CI 0.90-0.94; P = 8.96 × 10(-15))) and are correlated with two previously reported risk-associated variants at this locus, SNPs rs6504950 (OR = 0.94, P = 2.04 × 10(-09), r(2) = 0.73 with lead SNP) and rs1156287 (OR = 0.93, P = 3.41 × 10(-11), r(2) = 0.83 with lead SNP). Analyses indicate only one causal SNP in the region and several enhancer elements targeting STXBP4 are located within the 53 kb association signal. Expression studies in breast tumor tissues found SNP rs2787486 to be associated with increased STXBP4 expression, suggesting this may be a target gene of this locus.

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10(-20)), ER-negative BC (P=1.1 × 10(-13)), BRCA1-associated BC (P=7.7 × 10(-16)) and triple negative BC (P-diff=2 × 10(-5)). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10(-3)) and ABHD8 (P<2 × 10(-3)). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3'-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk.

An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression

Breast cancer is the most diagnosed malignancy and the second leading cause of cancer mortality in females. Previous association studies have identified variants on 2q35 associated with the risk of breast cancer. To identify functional susceptibility loci for breast cancer, we interrogated the 2q35 gene desert for chromatin architecture and functional variation correlated with gene expression. We report a novel intergenic breast cancer risk locus containing an enhancer copy number variation (enCNV; deletion) located approximately 400Kb upstream to IGFBP5, which overlaps an intergenic ERα-bound enhancer that loops to the IGFBP5 promoter. The enCNV is correlated with modified ERα binding and monoallelic-repression of IGFBP5 following oestrogen treatment. We investigated the association of enCNV genotype with breast cancer in 1,182 cases and 1,362 controls, and replicate our findings in an independent set of 62,533 cases and 60,966 controls from 41 case control studies and 11 GWAS. We report a dose-dependent inverse association of 2q35 enCNV genotype (percopy OR = 0.68 95%CI 0.55-0.83, P = 0.0002; replication OR = 0.77 95% CI 0.73-0.82, P = 2.1 × 10-19) and identify 13 additional linked variants (r2 > 0.8) in the 20Kb linkage block containing the enCNV (P = 3.2 × 10-15 - 5.6 × 10-17). These associations were independent of previously reported 2q35 variants, rs13387042/rs4442975 and rs16857609, and were stronger for ER-positive than ER-negative disease. Together, these results suggest that 2q35 breast cancer risk loci may be mediating their effect through IGFBP5.

Fine-Mapping of the 1p11.2 Breast Cancer Susceptibility Locus

The Cancer Genetic Markers of Susceptibility genome-wide association study (GWAS) originally identified a single nucleotide polymorphism (SNP) rs11249433 at 1p11.2 associated with breast cancer risk. To fine-map this locus, we genotyped 92 SNPs in a 900kb region (120,505,799-121,481,132) flanking rs11249433 in 45,276 breast cancer cases and 48,998 controls of European, Asian and African ancestry from 50 studies in the Breast Cancer Association Consortium. Genotyping was done using iCOGS, a custom-built array. Due to the complicated nature of the region on chr1p11.2: 120,300,000-120,505,798, that lies near the centromere and contains seven duplicated genomic segments, we restricted analyses to 429 SNPs excluding the duplicated regions (42 genotyped and 387 imputed). Per-allelic associations with breast cancer risk were estimated using logistic regression models adjusting for study and ancestry-specific principal components. The strongest association observed was with the original identified index SNP rs11249433 (minor allele frequency (MAF) 0.402; per-allele odds ratio (OR) = 1.10, 95% confidence interval (CI) 1.08-1.13, P = 1.49 x 10-21). The association for rs11249433 was limited to ER-positive breast cancers (test for heterogeneity P≤8.41 x 10-5). Additional analyses by other tumor characteristics showed stronger associations with moderately/well differentiated tumors and tumors of lobular histology. Although no significant eQTL associations were observed, in silico analyses showed that rs11249433 was located in a region that is likely a weak enhancer/promoter. Fine-mapping analysis of the 1p11.2 breast cancer susceptibility locus confirms this region to be limited to risk to cancers that are ER-positive.

Abstract 4468: Targeted deep sequencing of plasma circulating cell-free DNA shows VIM and FBLN1 methylation as potential biomarkers for hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the second most common cause of cancer death worldwide, but is still lacking sensitive and specific biomarkers for diagnosis and prognosis. HCC carcinogenesis is a multi-step process that usually arises in background chronic metabolic, inflammatory and/or infectious liver disease and it exhibits a wide range of epigenetic alterations that could potentially be used as biomarkers. In this study, we applied the targeted massively parallel semiconductor sequencing to assess in plasma circulating cell-free DNA (cfDNA) the methylation of a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) and to evaluate the potential of these genes as novel HCC biomarkers in two different series, one from France and one from Thailand. Methylation in cfDNA was detected for FBLN1, PSMA7, PXDN and VIM, with substantial differences in methylation patterns between cases and controls for FBLN1 and VIM. Further, the average methylation level across analyzed CpG-sites was associated with higher odds of HCC for VIM (1.48 [1.02, 2.16] for French cases, and 2.18 [1.28, 3.72] for Thai cases), and lower odds of HCC for FBLN1 (0.89 [0.76, 1.03] for French cases and 0.75 [0.63, 0.88] for Thai cases). We also analyzed a set of HCC and adjacent tissues as well as The Cancer Genome Atlas’ (TCGA) data to further investigate the origin of methylation pattern in cfDNA and noted that the analysis of VIM could be improved based on the methylation pattern detected in TCGA data. Overall, our study provides evidence that changes in methylation levels of cfDNA could be used as potential cancer biomarkers and that VIM and FBLN1 methylation in cfDNA are associated with HCC and may represent useful plasma-based biomarkers for improved detection and patient surveillance.

Citation Format: Reetta Holmila, Athena Sklias, David C. Muller, Davide Degli Esposti, Paule Guilloreau, James Mckay, Suleeporn Sangrajrang, Petcharin Srivatanakul, Pierre Hainaut, Philippe Merle, Andre Nogueira da Costa, Zdenko Herceg. Targeted deep sequencing of plasma circulating cell-free DNA shows VIM and FBLN1 methylation as potential biomarkers for hepatocellular carcinoma. [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 4468.

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

BACKGROUND

Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk.

METHOD

We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation.

RESULTS

Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05.

CONCLUSION

This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.

Assessing Cervical Cancer Screening Coverage Using a Population-Based Behavioral Risk Factor Survey--Thailand, 2010

Cervical cancer is the second most common cancer and fourth leading cause of cancer-related deaths among women in Thailand. In 2005, the Ministry of Public Health (MoPH) in Thailand initiated a phased national cervical cancer screening program. To monitor progress toward national screening targets--80% of women 30-60 years of age screened for cervical cancer once in the previous 5 years by 2013--the MoPH used the 2010 Thai Behavioral Risk Factor Surveillance System (BRFSS) to assess cervical cancer screening coverage. Results from the survey showed that 67.4% of women aged 30-60 years had been screened for cervical cancer in the past 5 years with varying screening coverage by region, residence, education, and marital status. Although the national cervical cancer screening program in Thailand appears to be close to reaching its national targets, the causes of lower coverage in some subpopulations need to be identified so that targeted interventions can be developed to increase coverage in these groups.

No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing

BACKGROUND

BRCA1 interacting protein C-terminal helicase 1 (BRIP1) is one of the Fanconi Anaemia Complementation (FANC) group family of DNA repair proteins. Biallelic mutations in BRIP1 are responsible for FANC group J, and previous studies have also suggested that rare protein truncating variants in BRIP1 are associated with an increased risk of breast cancer. These studies have led to inclusion of BRIP1 on targeted sequencing panels for breast cancer risk prediction.

METHODS

We evaluated a truncating variant, p.Arg798Ter (rs137852986), and 10 missense variants of BRIP1, in 48 144 cases and 43 607 controls of European origin, drawn from 41 studies participating in the Breast Cancer Association Consortium (BCAC). Additionally, we sequenced the coding regions of BRIP1 in 13 213 cases and 5242 controls from the UK, 1313 cases and 1123 controls from three population-based studies as part of the Breast Cancer Family Registry, and 1853 familial cases and 2001 controls from Australia.

RESULTS

The rare truncating allele of rs137852986 was observed in 23 cases and 18 controls in Europeans in BCAC (OR 1.09, 95% CI 0.58 to 2.03, p=0.79). Truncating variants were found in the sequencing studies in 34 cases (0.21%) and 19 controls (0.23%) (combined OR 0.90, 95% CI 0.48 to 1.70, p=0.75).

CONCLUSIONS

These results suggest that truncating variants in BRIP1, and in particular p.Arg798Ter, are not associated with a substantial increase in breast cancer risk. Such observations have important implications for the reporting of results from breast cancer screening panels.

Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor α) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER(+) or ER(-)) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER(-) tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.