The association of age at menarche and adult height with mammographic density in the International Consortium of Mammographic Density

BACKGROUND

Early age at menarche and tall stature are associated with increased breast cancer risk. We examined whether these associations were also positively associated with mammographic density, a strong marker of breast cancer risk.

METHODS

Participants were 10,681 breast-cancer-free women from 22 countries in the International Consortium of Mammographic Density, each with centrally assessed mammographic density and a common set of epidemiologic data. Study periods for the 27 studies ranged from 1987 to 2014. Multi-level linear regression models estimated changes in square-root per cent density (√PD) and dense area (√DA) associated with age at menarche and adult height in pooled analyses and population-specific meta-analyses. Models were adjusted for age at mammogram, body mass index, menopausal status, hormone therapy use, mammography view and type, mammographic density assessor, parity and height/age at menarche.

RESULTS

In pooled analyses, later age at menarche was associated with higher per cent density (β√PD = 0.023 SE = 0.008, P = 0.003) and larger dense area (β√DA = 0.032 SE = 0.010, P = 0.002). Taller women had larger dense area (β√DA = 0.069 SE = 0.028, P = 0.012) and higher per cent density (β√PD = 0.044, SE = 0.023, P = 0.054), although the observed effect on per cent density depended upon the adjustment used for body size. Similar overall effect estimates were observed in meta-analyses across population groups.

CONCLUSIONS

In one of the largest international studies to date, later age at menarche was positively associated with mammographic density. This is in contrast to its association with breast cancer risk, providing little evidence of mediation. Increased height was also positively associated with mammographic density, particularly dense area. These results suggest a complex relationship between growth and development, mammographic density and breast cancer risk. Future studies should evaluate the potential mediation of the breast cancer effects of taller stature through absolute breast density.

Parental perspectives towards sugar-sweetened beverages and polices: a qualitative study

PURPOSE

This qualitative study aimed to understand parental perception of (1) sugar-sweetened beverages (SSB) and implications of SSB on health; (2) their role in shaping their children's consumption of SSB; (3) the influences on SSB consumption of their children; and (4) potential government policies targeted at controlling SSB consumption.

METHODS

English-speaking parents of pre-schoolers aged 2-6 years were recruited. Semi-structured interviews based on the knowledge, attitude, practice framework were conducted, and transcripts were subjected to thematic analysis based on inductive approaches. Recruitment continued until data saturation was reached.

RESULTS

Twenty parents participated in the study and themes addressing the objectives identified. (1) There were misconceptions regarding the healthfulness of certain non-packaged SSB such as traditional remedies and juices. Some were unaware about the association between SSB and dental caries. (2) The need to reduce and restrict sugar consumption for overall and oral health reasons was well-recognised, but the extent of control varied. (3) Multiple stakeholders including pre-schools, grandparents and domestic helpers were involved in shaping children's diet. Children's sugar intake was also influenced by environmental factors, such as the ubiquitously available SSB, targeted marketing and high cost of healthy alternatives. (4) Participants were less accepting towards SSB taxation than the ban of SSB sales.

CONCLUSION

Despite the awareness of the types of SSBs and the general/oral health implications of sugar consumption, misconceptions exist. Although most parents possessed the knowledge and attitude, this did not translate into the practice of reducing sugar consumption in their children. There was no SSB reduction policy that had overwhelming acceptability.

The Long-Term Impact of Functional Disability on Hospitalization Spending in Singapore

Singapore is one of the fastest-aging populations due to increased life expectancy and lowered fertility. Lifestyle changes increase the burden of chronic diseases and disability. These have important implications for social protection systems. The goal of this paper is to model future functional disability and healthcare expenditures based on current trends. To project the health, disability and hospitalization spending of future elders, we adapted the Future Elderly Model (FEM) to Singapore. The FEM is a dynamic Markov microsimulation model developed in the US. Our main source of population data was the Singapore Chinese Health Study (SCHS) consisting of 63,000 respondents followed up over three waves from 1993 to 2010. The FEM model enables us to investigate the effects of disability compounded over the lifecycle and hospitalization spending, while adjusting for competing risk of multi-comorbidities. Results indicate that by 2050, 1 in 6 elders in Singapore will have at least one ADL disability and 1 in 3 elders will have at least one IADL disability, an increase from 1 in 12 elders and 1 in 5 elders respectively in 2014. The highest prevalence of functional disability will be in those aged 85 years and above. Lifetime hospitalization spending of elders aged 55 and above is US$24,400 (30.2%) higher among people with functional disability compared to those without disability. Policies that successfully tackle diabetes and promote healthy living may reduce or delay the onset of disability, leading to potential saving. In addition, further technological improvements may reduce the financial burden of disability.

Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study

The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups. Consistent patterns of correlations between lipid species also suggest the possibility of lipid tagging to simplify future lipidomics assays. The Singapore Integrative Omics Study is expected to allow the characterization of intra-omic and inter-omic correlations within and across all three ethnic groups through a systems biology approach.The Singapore Genome Variation projects characterized the genetics of Singapore's Chinese, Malay, and Indian populations. The Singapore Integrative Omics Study introduced here goes further in providing multi-omic measurements in individuals from these populations, including genetic, transcriptome, lipidome, and lifestyle data, and will facilitate the study of common diseases in Asian communities.

Mammographic density and ageing: A collaborative pooled analysis of cross-sectional data from 22 countries worldwide

BACKGROUND

Mammographic density (MD) is one of the strongest breast cancer risk factors. Its age-related characteristics have been studied in women in western countries, but whether these associations apply to women worldwide is not known.

METHODS AND FINDINGS

We examined cross-sectional differences in MD by age and menopausal status in over 11,000 breast-cancer-free women aged 35-85 years, from 40 ethnicity- and location-specific population groups across 22 countries in the International Consortium on Mammographic Density (ICMD). MD was read centrally using a quantitative method (Cumulus) and its square-root metrics were analysed using meta-analysis of group-level estimates and linear regression models of pooled data, adjusted for body mass index, reproductive factors, mammogram view, image type, and reader. In all, 4,534 women were premenopausal, and 6,481 postmenopausal, at the time of mammography. A large age-adjusted difference in percent MD (PD) between post- and premenopausal women was apparent (-0.46 cm [95% CI: -0.53, -0.39]) and appeared greater in women with lower breast cancer risk profiles; variation across population groups due to heterogeneity (I2) was 16.5%. Among premenopausal women, the √PD difference per 10-year increase in age was -0.24 cm (95% CI: -0.34, -0.14; I2 = 30%), reflecting a compositional change (lower dense area and higher non-dense area, with no difference in breast area). In postmenopausal women, the corresponding difference in √PD (-0.38 cm [95% CI: -0.44, -0.33]; I2 = 30%) was additionally driven by increasing breast area. The study is limited by different mammography systems and its cross-sectional rather than longitudinal nature.

CONCLUSIONS

Declines in MD with increasing age are present premenopausally, continue postmenopausally, and are most pronounced over the menopausal transition. These effects were highly consistent across diverse groups of women worldwide, suggesting that they result from an intrinsic biological, likely hormonal, mechanism common to women. If cumulative breast density is a key determinant of breast cancer risk, younger ages may be the more critical periods for lifestyle modifications aimed at breast density and breast cancer risk reduction.

Mammographic density assessed on paired raw and processed digital images and on paired screen-film and digital images across three mammography systems

BACKGROUND

Inter-women and intra-women comparisons of mammographic density (MD) are needed in research, clinical and screening applications; however, MD measurements are influenced by mammography modality (screen film/digital) and digital image format (raw/processed). We aimed to examine differences in MD assessed on these image types.

METHODS

We obtained 1294 pairs of images saved in both raw and processed formats from Hologic and General Electric (GE) direct digital systems and a Fuji computed radiography (CR) system, and 128 screen-film and processed CR-digital pairs from consecutive screening rounds. Four readers performed Cumulus-based MD measurements (n = 3441), with each image pair read by the same reader. Multi-level models of square-root percent MD were fitted, with a random intercept for woman, to estimate processed-raw MD differences.

RESULTS

Breast area did not differ in processed images compared with that in raw images, but the percent MD was higher, due to a larger dense area (median 28.5 and 25.4 cm2 respectively, mean √dense area difference 0.44 cm (95% CI: 0.36, 0.52)). This difference in √dense area was significant for direct digital systems (Hologic 0.50 cm (95% CI: 0.39, 0.61), GE 0.56 cm (95% CI: 0.42, 0.69)) but not for Fuji CR (0.06 cm (95% CI: -0.10, 0.23)). Additionally, within each system, reader-specific differences varied in magnitude and direction (p < 0.001). Conversion equations revealed differences converged to zero with increasing dense area. MD differences between screen-film and processed digital on the subsequent screening round were consistent with expected time-related MD declines.

CONCLUSIONS

MD was slightly higher when measured on processed than on raw direct digital mammograms. Comparisons of MD on these image formats should ideally control for this non-constant and reader-specific difference.

Ethnic disparities in risk of cardiovascular disease, end-stage renal disease and all-cause mortality: a prospective study among Asian people with Type 2 diabetes

AIM

To study prospectively the ethnic-specific risks of cardiovascular disease, end-stage renal disease and all-cause mortality in patients with Type 2 diabetes mellitus among native Asian subpopulations.

METHODS

A total of 2337 subjects with Type 2 diabetes (70% Chinese, 17% Malay and 13% Asian Indian) were followed for a median of 4.0 years. Time-to-event analysis was used to study the association of ethnicity with adverse outcomes.

RESULTS

Age- and gender-adjusted hazard ratios for cardiovascular disease in ethnic Malay and Asian Indian subjects were 2.01 (1.40-2.88; P<0.0001) and 1.60 (1.07-2.41; P=0.022) as compared with Chinese subjects. Adjustment for conventional cardiovascular disease risk factors, including HbA1c , blood pressure and lipid profile, slightly attenuated the hazards in Malay (1.82, 1.23-2.71; P=0.003) and Asian Indian subjects (1.47, 0.95-2.30; P=0.086); However, further adjustment for baseline renal function (estimated GFR) and albuminuria weakened the cardiovascular disease risks in Malay (1.48, 0.98-2.26; P=0.065) but strengthened that in Asian Indian subjects (1.81, 1.14-2.87; P=0.012). Competing-risk regression showed that the age- and gender-adjusted sub-distribution hazard ratio for end-stage renal disease was 1.87 (1.27-2.73; P=0.001) in Malay and 0.39 (0.18-0.83; P=0.015) in Asian Indian subjects. Notably, the difference in end-stage renal disease risk among the three ethnic groups was abolished after further adjustment for baseline estimated GFR and albuminuria. There was no significant difference in risk of all-cause mortality among the three ethnic groups.

CONCLUSIONS

Risks of cardiovascular and end-stage renal diseases in native Asian subjects with Type 2 diabetes vary substantially among different ethnic groups. Differences in prevalence of diabetic kidney disease may partially explain the ethnic disparities.

International Consortium on Mammographic Density: Methodology and population diversity captured across 22 countries

Mammographic density (MD) is a quantitative trait, measurable in all women, and is among the strongest markers of breast cancer risk. The population-based epidemiology of MD has revealed genetic, lifestyle and societal/environmental determinants, but studies have largely been conducted in women with similar westernized lifestyles living in countries with high breast cancer incidence rates. To benefit from the heterogeneity in risk factors and their combinations worldwide, we created an International Consortium on Mammographic Density (ICMD) to pool individual-level epidemiological and MD data from general population studies worldwide. ICMD aims to characterize determinants of MD more precisely, and to evaluate whether they are consistent across populations worldwide. We included 11755 women, from 27 studies in 22 countries, on whom individual-level risk factor data were pooled and original mammographic images were re-read for ICMD to obtain standardized comparable MD data. In the present article, we present (i) the rationale for this consortium; (ii) characteristics of the studies and women included; and (iii) study methodology to obtain comparable MD data from original re-read films. We also highlight the risk factor heterogeneity captured by such an effort and, thus, the unique insight the pooled study promises to offer through wider exposure ranges, different confounding structures and enhanced power for sub-group analyses.

Evaluation of transethnic fine mapping with population-specific and cosmopolitan imputation reference panels in diverse Asian populations

There has been limited success in identifying causal variants underlying association signals observed in genome-wide association studies (GWAS). The use of 1000 Genomes Project (1KGP) allows the imputation to estimate the genetic information at untyped variants. However, long stretches of high linkage disequilibrium within the genome prevent us from differentiating between causal variants and perfect surrogates, thus limiting our ability to identify causal variants. Transethnic strategies have been proposed as a possible solution to mitigate this. However, these studies generally rely on imputing genotypes from multiple ancestries from 1KGP but not against population-specific reference panels. Here, we perform the first transethnic fine-mapping study across three Asian cohorts from diverse ancestries at the loci implicated with eye and blood lipid traits, using population-specific reference panels that have been generated by whole-genome sequencing samples from the same ancestry groups. Our study outlines several challenges faced in a fine-mapping exercise where one simply aims to meta-analyse existing GWAS that have been imputed against reference haplotypes from the 1KGP.

Health-related quality of life of Asian patients with end-stage renal disease (ESRD) in Singapore

BACKGROUND

This study aimed to identify factors associated with the health-related quality of life (HRQOL) of multiethnic Asian end-stage renal disease (ESRD) patients treated with dialysis. The role of dialysis modality was also explored.

METHODS

Data used in this study were from two cross-sectional surveys of Singaporean ESRD patients on haemodialysis (HD) or peritoneal dialysis (PD). In both surveys, participants were assessed using the kidney disease quality of life (KDQOL) instrument and questions assessing socio-demographic characteristics. Clinical data including co-morbidity (measured by Charlson comorbidity index [CCI]), albumin level, haemoglobin level, and dialysis-related variables (e.g. dialysis vintage and dialysis adequacy) were retrieved from medical records. The 36-item KDQOL (KDQOL-36) was used to generate three summary scores (physical component summary [PCS], mental component summary [MCS] and kidney disease component summary [KDCS]) and two health utility scores (Short Form 6-dimension [SF-6D] and EuroQol 5-dimension [EQ-5D]). Linear regression analysis was performed to examine the association of factors with each of the HRQOL scale scores.

RESULTS

Five hundred and two patients were included in the study (mean age 57.1 years; male 52.4 %; HD 236, PD 266). Mean [standard deviation (SD)] PCS, MCS and KDCS scores were 37.9 (9.7), 46.4 (10.8) and 57.6 (18.1), respectively. Mean (SD) health utility score was 0.66 (0.12) for SF-6D and 0.60 (0.21) for EQ-5D. In multivariate regression analysis, factors found to be significantly associated with better HRQOL included: young (<45 years) or old age (>60 years), low CCI (<5), high albumin (≥37 g/l) and high haemoglobin (≥11 g/dl) with PCS; long dialysis vintage (≥3.5 years) with MCS; old age, Malay ethnicity and PD modality with KDCS; low CCI, high albumin and high haemoglobin with EQ-5D and high albumin with SF-6D.

CONCLUSIONS

Clinical characteristics are better predictors of HRQOL in ESRD patients than socio-demographics in Singapore. Dialysis modality has no impact on the health utility of those patients.

Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing

South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language–speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP). The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP). SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal) identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

Indians of South Asia has long been a population of interest to a wide audience, due to its unique diversity. We have deep-sequenced 38 individuals of Indian descent residing in Singapore (SSIP) in an effort to illustrate their diversity from a whole-genome standpoint. Indeed, among Asians in our population panel, SSIP was most diverse, followed by the Malays in Singapore (SSMP). Their diversity is further observed in the population's chromosome Y haplogroup and mitochondria haplogroup profiles; individuals with European-dominant haplogroups had greater proportion of European admixture. Among variants (single nucleotide polymorphism and small insertions/deletions) discovered in SSIP, 21.69% were novel with respect to previous sequencing projects. In addition, some 14 loss-of-function variants (LOFs) were associated to cancer, Type II diabetes, and cholesterol levels. Finally, D statistic test with ancient hominids concurred that there was gene flow to East Asians compared to South Asians.

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS) including 26,488 cases and 83,964 controls of European, East Asian, South Asian, and Mexican and Mexican American ancestry. We observed significant excess in directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven novel T2D susceptibility loci. Furthermore, we observed considerable improvements in fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterisation of complex trait loci, and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.

A study assessing the association of glycated hemoglobin A1C (HbA1C) associated variants with HbA1C, chronic kidney disease and diabetic retinopathy in populations of Asian ancestry

Glycated hemoglobin A1C (HbA1C) level is used as a diagnostic marker for diabetes mellitus and a predictor of diabetes associated complications. Genome-wide association studies have identified genetic variants associated with HbA1C level. Most of these studies have been conducted in populations of European ancestry. Here we report the findings from a meta-analysis of genome-wide association studies of HbA1C levels in 6,682 non-diabetic subjects of Chinese, Malay and South Asian ancestries. We also sought to examine the associations between HbA1C associated SNPs and microvascular complications associated with diabetes mellitus, namely chronic kidney disease and retinopathy. A cluster of 6 SNPs on chromosome 17 showed an association with HbA1C which achieved genome-wide significance in the Malays but not in Chinese and Asian Indians. No other variants achieved genome-wide significance in the individual studies or in the meta-analysis. When we investigated the reproducibility of the findings that emerged from the European studies, six loci out of fifteen were found to be associated with HbA1C with effect sizes similar to those reported in the populations of European ancestry and P-value ≤ 0.05. No convincing associations with chronic kidney disease and retinopathy were identified in this study.

Comparing methods for performing trans-ethnic meta-analysis of genome-wide association studies

Genome-wide association studies (GWASs) have discovered thousands of variants that are associated with human health and disease. Whilst early GWASs have primarily focused on genetically homogeneous populations of European, East Asian and South Asian ancestries, the next-generation genome-wide surveys are starting to pool studies from ethnically diverse populations within a single meta-analysis. However, classical epidemiological strategies for meta-analyses that assume fixed- or random-effects may not be the most suitable approaches to combine GWAS findings as these either confer low statistical power or identify mostly loci where the variants carry homogeneous effect sizes that are present in most of the studies. In a trans-ethnic meta-analysis, it is likely that some genetic loci will exhibit heterogeneous effect sizes across the populations. This may be due to differences in study designs, differences arising from the interactions with other genetic variants, or genuine biological differences attributed to environmental, dietary or lifestyle factors that modulate the influence of the genes. Here we compare different strategies for meta-analyzing GWAS across genetically diverse populations, where we intentionally vary the effect sizes present across the different populations. We subsequently applied the methods that yielded the highest statistical power to a trans-ethnic meta-analysis of seven GWAS in type 2 diabetes, and showed that these methods identified bona fide associations that would otherwise have been missed by the classical strategies.

Assessing risk of breast cancer in an ethnically South-East Asia population (results of a multiple ethnic groups study)

BACKGROUND

Gail and others developed a model (GAIL) using age-at-menarche, age-at-birth of first live child, number of previous benign breast biopsy examinations, and number of first-degree-relatives with breast cancer as well as baseline age-specific breast cancer risks for predicting the 5-year risk of invasive breast cancer for Caucasian women. However, the validity of the model for projecting risk in South-East Asian women is uncertain. We evaluated GAIL and attempted to improve its performance for Singapore women of Chinese, Malay and Indian origins.

METHODS

Data from the Singapore Breast Screening Programme (SBSP) are used. Motivated by lower breast cancer incidence in many Asian countries, we utilised race-specific invasive breast cancer and other cause mortality rates for Singapore women to produce GAIL-SBSP. By using risk factor information from a nested case-control study within SBSP, alternative models incorporating fewer then additional risk factors were determined. Their accuracy was assessed by comparing the expected cases (E) with the observed (O) by the ratio (E/O) and 95% confidence interval (CI) and the respective concordance statistics estimated.

RESULTS

From 28,883 women, GAIL-SBSP predicted 241.83 cases during the 5-year follow-up while 241 were reported (E/O=1.00, CI=0.88 to 1.14). Except for women who had two or more first-degree-relatives with breast cancer, satisfactory prediction was present in almost all risk categories. This agreement was reflected in Chinese and Malay, but not in Indian women. We also found that a simplified model (S-GAIL-SBSP) including only age-at-menarche, age-at-birth of first live child and number of first-degree-relatives performed similarly with associated concordance statistics of 0.5997. Taking account of body mass index and parity did not improve the calibration of S-GAIL-SBSP.

CONCLUSIONS

GAIL can be refined by using national race-specific invasive breast cancer rates and mortality rates for causes other than breast cancer. A revised model containing only three variables (S-GAIL-SBSP) provides a simpler approach for projecting absolute risk of invasive breast cancer in South-East Asia women. Nevertheless its role in counseling the individual women regarding their risk of breast cancer remains problematical and needs to be validated in independent data.

Genome-wide meta-analysis of five Asian cohorts identifies PDGFRA as a susceptibility locus for corneal astigmatism

Corneal astigmatism refers to refractive abnormalities and irregularities in the curvature of the cornea, and this interferes with light being accurately focused at a single point in the eye. This ametropic condition is highly prevalent, influences visual acuity, and is a highly heritable trait. There is currently a paucity of research in the genetic etiology of corneal astigmatism. Here we report the results from five genome-wide association studies of corneal astigmatism across three Asian populations, with an initial discovery set of 4,254 Chinese and Malay individuals consisting of 2,249 cases and 2,005 controls. Replication was obtained from three surveys comprising of 2,139 Indians, an additional 929 Chinese children, and an independent 397 Chinese family trios. Variants in PDGFRA on chromosome 4q12 (lead SNP: rs7677751, allelic odds ratio = 1.26 (95% CI: 1.16–1.36), P_meta = 7.87×10⁻⁹) were identified to be significantly associated with corneal astigmatism, exhibiting consistent effect sizes across all five cohorts. This highlights the potential role of variants in PDGFRA in the genetic etiology of corneal astigmatism across diverse Asian populations.

Corneal astigmatism is associated with reduced visual acuity and an increased risk of developing refractive amblyopia. Although it is highly heritable, there is no prior study on the genetic etiology of corneal astigmatism. Our genome-wide meta-analysis across 8,513 individuals in five genome-wide surveys from three genetically diverse populations in Asia reveals that genetic variants in the PDGFRA gene on chromosome 4q12 is significantly associated with corneal astigmatism. These polymorphisms in the PDGFRA gene exhibit strong and consistent effects over all five Asian cohorts. PDGFRA is a receptor for platelet-derived growth factor, which is expressed in many retinal tissues in the eyes and appears to contribute to ocular development. Results from our study further suggest the potential role of PDGFRA in the regulation of corneal biometrics.

Regions of homozygosity in three Southeast Asian populations

The genomes of outbred populations were first shown in 2006 to contain regions of homozygosity (ROHs) of several megabases. Further studies have also investigated the characteristics of ROHs in healthy individuals in various populations but there are no studies on Singapore populations to date. This study aims to identify and investigate the characteristics of ROHs in three Singapore populations. A total of 268 samples (96 Chinese, 89 Malays and 83 Indians) are genotyped on Illumina Human 1 M Beadchip and Affymetrix Genome-Wide Human SNP Array 6.0. We use the PennCNV algorithm to detect ROHs. We report an abundance of ROHs (≥500 kb), with an average of more than one hundred regions per individual. On average, the Indian population has the lowest number of ROHs and smallest total length of ROHs per individual compared with the Chinese and Malay populations. We further investigate the relationship between the occurrence of ROHs and haplotype frequency, regional linkage disequilibrium (LD) and positive selection. Based on the results of this data set, we find that the frequency of occurrence of ROHs is positively associated with haplotype frequency and regional LD. The majority of regions detected for recent positive selection and regions with differential LD between populations overlap with the ROH loci. When we consider both the location of the ROHs and the allelic form of the ROHs, we are able to separate the populations by principal component analysis, demonstrating that ROHs contain information on population structure and the demographic history of a population.

A statistical method for region-based meta-analysis of genome-wide association studies in genetically diverse populations

Genome-wide association studies (GWAS) have become the preferred experimental design in exploring the genetic etiology of complex human traits and diseases. Standard SNP-based meta-analytic approaches have been utilized to integrate the results from multiple experiments. This fundamentally assumes that the patterns of linkage disequilibrium (LD) between the underlying causal variants and the directly genotyped SNPs are similar across the populations for the same SNPs to emerge with surrogate evidence of disease association. We introduce a novel strategy for assessing regional evidence of phenotypic association that explicitly incorporates the extent of LD in the region. This provides a natural framework for combining evidence from multi-ethnic studies of both dichotomous and quantitative traits that (i) accommodates different patterns of LD, (ii) integrates different genotyping platforms and (iii) allows for the presence of allelic heterogeneity between the populations. Our method can also be generalized to perform gene-based or pathway-based analyses. Applying this method on real GWAS data in type 2 diabetes (T2D) boosted the association evidence in regions well-established for T2D etiology in three diverse South-East Asian populations, as well as identified two novel gene regions and a biologically convincing pathway that are subsequently validated with data from the Wellcome Trust Case Control Consortium.

Incidence and Outcome of Male Breast Cancer: An International Population-Based Study

Purpose

Male breast cancer is a rare disease with an incidence rate less than 1% of that of female breast cancer. Given its low incidence, few studies have assessed risk and prognosis.

Methods

This population-based study, including 459,846 women and 2,665 men diagnosed with breast cancer in Denmark, Finland, Geneva, Norway, Singapore, and Sweden over the last 40 years, compares trends in incidence, relative survival, and relative excess mortality between the sexes.

Results

World standardized incidence rates of breast cancer were 66.7 per 105 person-years in women and 0.40 per 105 person-years in men. Women were diagnosed at a younger median age (61.7 years) than men (69.6 years). Male patients had a poorer 5-year relative survival ratio than women (0.72 [95% CI, 0.70 to 0.75] v 0.78 [95% CI, 0.78 to 0.78], respectively), corresponding to a relative excess risk (RER) of 1.27 (95% CI, 1.13 to 1.42). However, after adjustment for age and year of diagnosis, stage, and treatment, male patients had a significantly better relative survival from breast cancer than female patients (RER, 0.78; 95% CI, 0.62 to 0.97).

Conclusion

Male patients with breast cancer have later onset of disease and more advanced disease than female patients. Male patients with breast cancer have lower risk of death from breast cancer than comparable female patients.

Identification of four novel variants that influence central corneal thickness in multi-ethnic Asian populations

Central corneal thickness (CCT) is a highly heritable trait. Genes that significantly influence CCT can be candidate genes for common disorders in which CCT has been implicated, such as primary open-angle glaucoma (POAG) and keratoconus. Because the genetic factors controlling CCT in different Asian populations are unclear, we have built on previous work conducted on Singaporean Indians and Malays and extended our hypothesis to individuals of Chinese descent. We have followed up on all suggestive signals of association with CCT (P < 10(-4)) from the previously reported meta-analysis comprising Indians and Malays in a sample of Chinese individuals (n= 2681). In the combined sample (n= 7711), strong evidence of association was observed at four novel loci: IBTK on chromosome 6q14.1; CHSY1 on chromosome 15q26.3; and intergenic regions on chromosomes 7q11.2 and 9p23 (8.01 × 10(-11) < λ(GC) corrected P(meta) < 8.72 × 10(-8)). These four new loci explain an additional 4.3% of the total CCT variance across the sample cohorts over and above that of previously identified loci. We also extend on a previous finding at a fifth locus (AKAP13) where a new single-nucleotide polymorphism (rs1821481, P(meta) = 9.99 × 10(-9)) was found to be significantly more informative compared with the previously reported rs6496932 (P(meta) = 3.64 × 10(-5)). Performing association analysis in Asians may lead to the discovery of ethnic-specific genes that control CCT, offering further mechanistic insights into the regulation of CCT. In addition, it may also provide several candidate genes for interrogation for POAG, keratoconus and possible racial/ethnic variations.

SgD-CNV, a database for common and rare copy number variants in three Asian populations

Copy number variants (CNVs) extend our understanding of the genetic diversity in humans. However, the distribution and characteristics of CNVs in Asian populations remain largely unexplored, especially for rare CNVs that have emerged as important genetic factors for complex traits. In the present study, we performed an in-depth investigation of common and rare CNVs across 8,148 individuals from the three major Asian ethnic groups: Chinese (n = 1,945), Malays (n = 2,399), and Indians (n = 2,217) in Singapore, making this investigation the most comprehensive genome-wide survey of CNVs outside the European-ancestry populations to date. We detected about 16 CNVs per individual and the ratio of loss to gain events is ∼2:1. The majority of the CNVs are of low frequency (<10%), and 40% are rare (<1%). In each population, ∼20% of the CNVs are not previously catalogued in the Database of Genomic Variants (DGV). Contrary to findings from European studies, the common CNVs (>5%) in our populations are not well tagged by SNPs in Illumina 1M and 610K arrays, and most disease-associated common CNVs previously reported in Caucasians are rare in our populations. We also report noticeable population differentiation in the CNV landscape of these Asian populations, with the greatest diversity seen between the Indians and the Chinese.

Natural positive selection and north-south genetic diversity in East Asia

Recent reports have identified a north-south cline in genetic variation in East and South-East Asia, but these studies have not formally explored the basis of these clinical differences. Understanding the origins of these variations may provide valuable insights in tracking down the functional variants in genomic regions identified by genetic association studies. Here we investigate the genetic basis of these differences with genome-wide data from the HapMap, the Human Genome Diversity Project and the Singapore Genome Variation Project. We implemented four bioinformatic measures to discover genomic regions that are considerably differentiated either between two Han Chinese populations in the north and south of China, or across 22 populations in East and South-East Asia. These measures prioritized genomic stretches with: (i) regional differences in the allelic spectrum for SNPs common to the two Han Chinese populations; (ii) differential evidence of positive selection between the two populations as quantified by integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH); (iii) significant correlation between allele frequencies and geographical latitudes of the 22 populations. We also explored the extent of linkage disequilibrium variations in these regions, which is important in combining genetic association studies from North and South Chinese. Two of the regions that emerged are found in HLA class I and II, suggesting that the HLA imputation panel from the HapMap may not be directly applicable to every Chinese sample. This has important implications to autoimmune studies that plan to impute the classical HLA alleles to fine map the SNP association signals.

High constant incidence rates of second primary cancers of the head and neck: a pooled analysis of 13 cancer registries

Scanty data are available on the incidence (i.e., the absolute risk) of second cancers of the head and neck (HN) and its pattern with age. We investigated this issue using data from a multicentric study of 13 population-based cancer registries from Europe, Canada, Australia and Singapore for the years 1943-2000. A total of 99,257 patients had a first primary HN cancer (15,985 tongue, 22,378 mouth, 20,758 pharyngeal, and 40,190 laryngeal cancer), contributing to 489,855 person-years of follow-up. A total of 1,294 of the patients (1.3%) were diagnosed with second HN cancers (342 tongue, 345 mouth, 418 pharynx and 189 larynx). Male incidence rates of first HN cancer steeply increased from 0.68/100,000 at age 30-34 to 46.2/100,000 at age 70-74, and leveled off at older age; female incidence increased from 0.50/100,000 at age 30-34 to 16.5/100,000 at age 80-84. However, age-specific incidence of second HN cancers after a first HN cancer in men was around 200-300/100,000 between age 40-44 and age 70-74 and tended to decline at subsequent ages (150/100,000 at age 80-84); in women, incidence of second HN cancers was around 200-300/100,000 between age 45-49 and 80-84. The patterns of age-specific incidence were consistent for different subsites of second HN cancer and sexes; moreover, they were similar for age-specific incidence of first primary HN cancer in patients who subsequently developed a second HN cancer. The incidence of second HN cancers does not increase with age, but remains constant, or if anything, decreases with advancing age.

Association of variants in FRAP1 and PDGFRA with corneal curvature in Asian populations from Singapore

Corneal curvature (CC) is a key determinant of major eye diseases, such as keratoconus, myopia and corneal astigmatism. No prior studies have discovered the genes for CC. Here we report the findings from four genome-wide association studies of CC in 10 008 samples from three population groups in Singapore. Our discovery phase surveyed 2867 Chinese and 3072 Malays, allowing us to identify two loci that were associated with CC variation: FRAP1 on chromosome 1p36.2 and PDGFRA on chromosome 4q12. These findings were subsequently replicated in a validation study involving an additional 2953 Asian Indians and a further collection of 1116 Chinese children. The effect sizes of the identified variants were consistent across all four cohorts, with seven single nucleotide polymorphisms (SNPs) in FRAP1 (lead SNP: rs17036350, meta P-value = 4.06 × 10(-13)) and six SNPs in PDGFRA (lead SNP: rs2114039, meta P-value = 1.33 × 10(-9)) attaining genome-wide significance in the SNP-based meta-analysis of the four studies. This is the first genome-wide survey of CC variation and we have identified two implicated loci in three genetically diverse Asian populations, suggesting the presence of common genetic etiology across multiple populations.

A population-based study of copy number variants and regions of homozygosity in healthy Swedish individuals

The abundance of copy number variants (CNVs) and regions of homozygosity (ROHs) have been well documented in previous studies. In addition, their roles in complex diseases and traits have since been increasingly appreciated. However, only a limited amount of CNV and ROH data is currently available for the Swedish population. We conducted a population-based study to detect and characterize CNVs and ROHs in 87 randomly selected healthy Swedish individuals using the Affymetrix SNP Array 6.0. More than 600 CNV loci were detected in the population using two different CNV-detection algorithms (PennCNV and Birdsuite). A total of 196 loci were consistently identified by both algorithms, suggesting their reliability. Numerous disease-associated and pharmacogenetics-related genes were found to be overlapping with common CNV loci such as CFHR1/R3, LCE3B/3C, UGT2B17 and GSTT1. Correlation analysis between copy number polymorphisms (CNPs) and genome-wide association studies-identified single-nucleotide polymorphisms also indicates the potential roles of several CNPs as causal variants for diseases and traits such as body mass index, Crohn's disease and multiple sclerosis. In addition, we also identified a total of 14 815 ROHs 500 kb or 2814 ROHs 1M in the Swedish individuals with an average of 170 and 32 regions detected per individual respectively. Approximately 141 Mb or 4.92% of the genome is homozygous in each individual of the Swedish population. This is the first population-based study to investigate the population characteristics of CNVs and ROHs in the Swedish population. This study found many CNV loci that warrant further investigation, and also highlighted the abundance and importance of investigating ROHs for their associations with complex diseases and traits.

Transferability of type 2 diabetes implicated loci in multi-ethnic cohorts from Southeast Asia

Recent large genome-wide association studies (GWAS) have identified multiple loci which harbor genetic variants associated with type 2 diabetes mellitus (T2D), many of which encode proteins not previously suspected to be involved in the pathogenesis of T2D. Most GWAS for T2D have focused on populations of European descent, and GWAS conducted in other populations with different ancestry offer a unique opportunity to study the genetic architecture of T2D. We performed genome-wide association scans for T2D in 3,955 Chinese (2,010 cases, 1,945 controls), 2,034 Malays (794 cases, 1,240 controls), and 2,146 Asian Indians (977 cases, 1,169 controls). In addition to the search for novel variants implicated in T2D, these multi-ethnic cohorts serve to assess the transferability and relevance of the previous findings from European descent populations in the three major ethnic populations of Asia, comprising half of the world's population. Of the SNPs associated with T2D in previous GWAS, only variants at CDKAL1 and HHEX/IDE/KIF11 showed the strongest association with T2D in the meta-analysis including all three ethnic groups. However, consistent direction of effect was observed for many of the other SNPs in our study and in those carried out in European populations. Close examination of the associations at both the CDKAL1 and HHEX/IDE/KIF11 loci provided some evidence of locus and allelic heterogeneity in relation to the associations with T2D. We also detected variation in linkage disequilibrium between populations for most of these loci that have been previously identified. These factors, combined with limited statistical power, may contribute to the failure to detect associations across populations of diverse ethnicity. These findings highlight the value of surveying across diverse racial/ethnic groups towards the fine-mapping efforts for the casual variants and also of the search for variants, which may be population-specific.

Type 2 diabetes mellitus (T2D) is a chronic disease which can lead to complications such as heart disease, stroke, hypertension, blindness due to diabetic retinopathy, amputations from peripheral vascular diseases, and kidney disease from diabetic nephropathy. The increasing prevalence and complications of T2D are likely to increase the health and economic burden of individuals, families, health systems, and countries. Our study carried out in three major Asian ethnic groups (Chinese, Malays, and Indians) in Singapore suggests that the findings of studies carried out in populations of European ancestry (which represents most studies to date) may be relevant to populations in Asia. However, our study also raises the possibility that different genes, and within the genes different variants, may confer susceptibility to T2D in these populations. These findings are particularly relevant in Asia, where the greatest growth of T2D is expected in the coming years, and emphasize the importance of studying diverse populations when trying to localize the regions of the genome associated with T2D. In addition, we may need to consider novel methods for combining data across populations.

Mammographic density and its interaction with other breast cancer risk factors in an Asian population

BACKGROUND

Joint effects of mammographic density and other risk factors on breast cancer risk remain unclear.

METHODS

From The Singapore Breast Screening Project, we selected 491 cases and 982 controls. Mammographic density was measured quantitatively. Data analysis was by conditional logistic regression.

RESULTS

Density was a significant risk factor, adjusting for other factors. Density of 76-100% had an odds ratio of 5.54 (95% CI 2.38-12.90) compared with 0-10%. Density had significant interactions with body mass index and oral contraceptive use (P=0.02).

CONCLUSIONS

Percent density increases breast cancer risk in addition to effects of other risk factors, and modifies the effects of BMI and OCs.

Genome-wide association studies in Asians confirm the involvement of ATOH7 and TGFBR3, and further identify CARD10 as a novel locus influencing optic disc area

Damage to the optic nerve (e.g. from glaucoma) has an adverse and often irreversible impact on vision. Earlier studies have suggested that the size of the optic nerve head could be governed by hereditary factors. We conducted a genome-wide association study (GWAS) on 4445 Singaporean individuals (n = 2132 of Indian and n = 2313 of Malay ancestry, respectively), with replication in Rotterdam, the Netherlands (n = 9326 individuals of Caucasian ancestry) using the most widely reported parameter for optic disc traits, the optic disc area. We identified a novel locus on chromosome 22q13.1, CARD10, which strongly associates with optic disc area in both Singaporean cohorts as well as in the Rotterdam Study (RS; rs9607469, per-allele change in optic disc area = 0.051 mm(2); P(meta) = 2.73×10(-12)) and confirmed the association between CDC7/TGFBR3 (lead single nucleotide polymorphism (SNP) rs1192415, P(meta) = 7.57×10(-17)) and ATOH7 (lead SNP rs7916697, P(meta) = 2.00 × 10(-15)) and optic disc area in Asians. This is the first Asian-based GWAS on optic disc area, identifying a novel locus for the optic disc area, but also confirming the results found in Caucasian persons suggesting that there are general genetic determinants applicable to the size of the optic disc across different ethnicities.

Identifying candidate causal variants via trans-population fine-mapping

Genome-wide association studies have discovered and confirmed a large number of loci that are implicated with disease susceptibility and severity. Polymorphisms that emerged from these studies are mostly indirectly associated to the phenotype, and the natural progression is to identify the causal variants that are functionally responsible for these association signals. Long stretches of high linkage disequilibrium (LD) benefitted the initial discovery phase in a genome-wide scan, allowing commercial genotyping products with imperfect coverage to detect genomic regions genuinely associated with the phenotype. However, regions of high LD confound the fine-mapping phase, as markers that are perfectly correlated to the causal variants display similar evidence of phenotypic association, hampering the process of differentiating the functional polymorphisms from neighboring surrogates. Here, we explore the potential of integrating information across different populations for narrowing the candidate region that a causal variant resides in, and compare the efficacy of this process of trans-population fine-mapping with the extent of variation in patterns of LD between the populations. In addition, we explore two different strategies for pooling data across multiple populations for the purpose of prioritizing the rankings of the causal variants. Our results clearly establish the benefits of trans-population analysis in reducing the number of possible candidates for the causal variants, particularly in genomic regions displaying strong evidence of inter-population LD variation. Directly integrating the statistical evidence by summing the test statistics outperforms the standard meta-analytic procedure. These findings have direct relevance to the design and analysis of ongoing fine-mapping studies.

A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies

MOTIVATION

Methods for detecting positive selection relied on finding evidence of long haplotypes to identify candidate regions under selection. However, these methods generally do not identify the length and form of the selected haplotype.

RESULTS

We present HapFinder, a method which can find the common longest haplotype under three different settings from a database, which is relevant in the analysis of positive selection in population genetics and also in medical genetics for finding the likely haplotype form carrying the causal allele at the functional polymorphism.

AVAILABILITY

A java program, implementing the methods described in HapFinder, together with R scripts and datasets for producing the figures presented in this article are publicly available at http://www.nus-cme.org.sg/sgvp/software/hapfinder.html. The site also hosts an online browser for finding haplotypes from the International HapMap Project and the Singapore Genome Variation Project.

Cancer survival in Singapore, 1993-1997

The Singapore cancer registry is a national registry established in 1968. Cancer registration is done by passive methods. The registry contributed survival data on 45 cancer sites or types registered during 1993-1997. Data on 34 cancers registered during 1968-1997 were utilized for survival trend by period and cohort approaches. Follow-up was done by passive methods, with median follow-up ranging between 2-72 months for different cancers. The proportion with histologically verified diagnosis for various cancers ranged between 27-100%; death certificates only (DCOs) comprised 0-7%; 76-100% of total registered cases were included for the survival analysis. The top-ranking cancers on 5-year age-standardized relative survival rates were nonmelanoma skin (96%), thyroid (90%), testis (88%), corpus uteri (77%), breast (74%), Hodgkin lymphoma (73%) and penis (70%). Five-year relative survival by age group showed either a decreasing trend with increasing age groups or was fluctuating. Localized stage of disease ranged between 18-65% for various cancers and survival decreased with increasing extent of disease. Period survival closely predicted survival experience of cancers diagnosed in that period, and an increasing trend in period survival over different periods indicated an improved prognosis for cancers diagnosed in those calendar periods.

Nephrinuria associates with multiple renal traits in type 2 diabetes

BACKGROUND

The involvement of nephrin in controlling renal function is unclear with the literature only emphasizing its role in albuminuria. We therefore investigated the potential association between nephrinuria as evidenced by the appearance of urinary immunopositive nephrin fragments, with multiple renal traits.

METHODS

Western blot analysis of the urine samples from a cross-sectional study of 381 Chinese type 2 diabetic patients revealed four distinct protein fragments, indicative of nephrinuria. Albuminuria was measured in random spot urine samples using the albumin/creatinine ratio (ACR), while estimated glomerular filtration rate (eGFR) was calculated using the creatinine-based Modification of Diet in Renal Disease formula.

RESULTS

Each nephrin fragment was associated with a decline in eGFR (smallest P = 0.001). Even with the inclusion of logarithmic form of ACR (ln ACR) in the multivariate model, nephrinuria still remained significantly associated with lower eGFR (smallest P < 0.05). Nephrinuria was also strongly associated with lnACR and this finding was independent of eGFR (smallest P < 0.001). Thus, nephrinuria was independently associated with both renal traits in the form of lnACR and eGFR. Furthermore, nephrinuria was significantly associated with lower eGFR even among normoalbuminuric patients (ACR ≤ 30 mg/g) (smallest P = 0.002), potentially implicating nephrinuria in the development of normoalbuminuric renal insufficiency. Apart from the renal traits under investigation, the presence of nephrinuria did not associate with other patient clinical characteristics.

CONCLUSIONS

Nephrinuria was associated with multiple renal traits in type 2 diabetes even in normoalbuminuric patients who are traditionally perceived as having a low risk of chronic kidney disease.

Abstract P3-11-08: Incidence and Outcome of Male and Female Breast Cancer: A Multinational Population Based Study

Background: Male breast cancer is a rare disease as its incidence rate is about 0.5% to 1% of that of female breast cancer. Given its scarcity, few studies have assessed the risk and prognosis.

Methods: We performed a multi-national population based study of 569,771 female breast cancer patients and 3,615 male breast cancer patients diagnosed in Denmark, Finland, Switzerland, Norway, Singapore and Sweden from 1943 to 2007. We calculated incidence and mortality as well as overall survival for both sexes. Life table analysis and Cox proportional hazard model were used to analyze the survival.

Results: The overall incidence rates, adjusted to the World Standard Population, of breast cancer were 60.2 per 100,000 in women and 0.4 per 100,000 in men. Women were diagnosed with breast cancer at a younger median age (61.4 years) than men (68.9 years). Among the 203,093 patients (35%) with information on TNM stage, 50% of the women and 47% of men were classified as stage I whilst stage III and stage IV cases accounted for 11% and 20% for women and men respectively. The 5-year cumulative survival was 66.2% for women and 53.0% for men. The adjusted relative risk of death was 24% higher in men [HR 1.24 (95% CI, 1.19-1.28)] as compared to women after controlling for age and time at diagnosis. Men had an 18% higher relative risk of death [HR 1.18 (95% CI, 1.09-1.27)] compared to women after further adjustment for TNM stage. Conclusion: Male breast cancer patients have later onset and worse prognosis than female patients. This may be due to the difference in tumour characteristics and treatment.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-11-08.

Modified least-variant set normalization for miRNA microarray

MicroRNAs (miRNAs) are short noncoding RNAs that are involved in post-transcriptional regulation of mRNAs. Microarrays have been employed to measure global miRNA expressions; however, because the number of miRNAs is much smaller than the number of mRNAs, it is not clear whether traditional normalization methods developed for mRNA arrays are suitable for miRNA. This is an important question, since normalization affects downstream analyses of the data. In this paper we develop a least-variant set (LVS) normalization method, which was previously shown to outperform other methods in mRNA analysis when standard assumptions are violated. The selection of the LVS miRNAs is based on a robust linear model fit of the probe-level data that takes into account the considerable differences in variances between probes. In a spike-in study, we show that the LVS has similar operating characteristics, in terms of sensitivity and specificity, compared with the ideal normalization, and it is better than no normalization, 75th percentile-shift, quantile, global median, VSN, and lowess normalization methods. We evaluate four expression-summary measures using a tissue data set; summarization from the robust model performs as well as the others. Finally, comparisons using expression data from two dissimilar tissues and two similar ones show that LVS normalization has better operating characteristics than other normalizations.

Genomic copy number variations in three Southeast Asian populations

Research on the role of copy number variations (CNVs) in the genetic risk of diseases in Asian populations has been hampered by a relative lack of reference CNV maps for Asian populations outside the East Asians. In this article, we report the population characteristics of CNVs in Chinese, Malay, and Asian Indian populations in Singapore. Using the Illumina Human 1M Beadchip array, we identify 1,174 CNV loci in these populations that corroborated with findings when the same samples were typed on the Affymetrix 6.0 platform. We identify 441 novel loci not previously reported in the Database of Genomic Variations (DGV). We observe a considerable number of loci that span all three populations and were previously unreported, as well as population-specific loci that are quite common in the respective populations. From this we observe the distribution of CNVs in the Asian Indian population to be considerably different from the Chinese and Malay populations. About half of the deletion loci and three-quarters of duplication loci overlap UCSC genes. Tens of loci show population differentiation and overlap with genes previously known to be associated with genetic risk of diseases. One of these loci is the CYP2A6 deletion, previously linked to reduced susceptibility to lung cancer.

Global health: challenges and opportunities for Singapore

Over the past decade, global health has evolved from a buzzword to a discipline, attracting interest from governments, academic institutions and funding organisations. Global health centres, institutes and initiatives in Western countries have increased in both size and number, aided primarily by institutional backing and supportive funding mechanisms. As the rise to prominence of global health on the public health agenda also coincides with shifts in global balances of power, Asia, as well as Singapore, has an expanded role to play in supporting global health teaching and research, both in the region and throughout the world. Foundations, universities, government agencies, statutory boards and the private sector all have an important role to play in moving the global health agenda forward in Singapore. Rigorous global health training and increased funding for global health research are now timely and essential in order for global health, as a discipline, to develop within Singapore and have an impact within the region.

Recent trends and patterns in breast cancer incidence among Eastern and Southeastern Asian women

BACKGROUND

Incidence of breast cancer is rising in Asian countries, and breast cancer is the most common cancer among Asian women. However, there are few recent descriptive reports on the epidemiology of breast cancer among Eastern and Southeastern Asian populations.

METHODS

We examined incidence trends for invasive breast cancer in women aged ≥20 years from 15 registries in Eastern (China, Japan, the Republic of Korea, Taiwan) and Southeastern Asia (the Philippines, Singapore, Thailand) for the period 1993-2002 mainly using data from Cancer Incidence in Five Continents, Volumes VIII and IX. We compared trends in annual incidence rates and age-specific incidence curves over a 10-year period. We also compared the incidence rates of Asian-Americans with the rates of their Asian counterparts.

RESULTS

Breast cancer incidence rates increased gradually over time in all study populations. Rates were relatively high in Southeastern Asia and became progressively lower along a south-to-north gradient, with a fourfold geographic variation within the study populations. Age-specific incidence curves showed patterns that gradually changed according to incidence rates. Breast cancer incidence among Asian women living in the United States was 1.5-4 times higher than the corresponding incidence rate in the women's respective countries of origin.

CONCLUSION

Breast cancer incidence is expected to continue to increase for the next 10 years in Asia and may approach rates reported among Asian-Americans. The number and mean age of breast cancer cases is expected to increase as the female Asian population ages, the prevalence of certain risk factors changes (early menarche, late menopause, low parity, late age at first live birth, and low prevalence of breastfeeding), and as Asian countries introduce mass screening programs.

Effect of childbirth after treatment on long-term survival from breast cancer

Background

This study quantified long-term absolute and relative mortality risks of survivors of breast cancer with subsequent childbirth.

Methods

The Singapore Birth Register (n = 319 437), Swedish Multi-Generation Register (n = 11 million) and population-based cancer registries were linked to identify 492 women with childbirth after breast cancer. For these women, cumulative mortality risks and standardized mortality ratios (SMRs) were calculated and compared with those of 8529 women aged less than 40 years with breast cancer without subsequent childbirth, and with those predicted by Adjuvant! Online.

Results

Women with subsequent childbirth had a lower 15-year cumulative overall mortality rate than other women with breast cancer (16·8 (95 per cent confidence interval (c.i.) 13·3 to 20·9) versus 40·7 (39·5 to 41·9) per cent), but a higher relative mortality risk than the background population (SMR 13·6, 95 per cent c.i. 10·6 to 17·3). Mortality risks decreased significantly with increasing interval between diagnosis and subsequent childbirth. Mean 10-year cumulative mortality risks of women with subsequent childbirth were within the range of 10-year mortality predicted by Adjuvant! Online for women with T1 N0 tumours in otherwise perfect health.

Conclusion

This study reinforced the view that pregnancy after breast cancer is not detrimental to survival. However, women who gave birth after this diagnosis had substantially higher mortality risks than young women in the general population. This information may be a valuable addition to routine mortality estimates.

Abstract 1832: Associations between ovarian cancer and other malignant neoplasms in an international population-based study

Recent studies have suggested that different histological types of ovarian cancer develop via different pathways. Large epidemiological studies of first and second malignant neoplasms associated with ovarian cancer can quantify such risk and may provide etiologic clues in understanding these complex pathways.

We analyzed ovarian cancer data from 13 different cancer registries in Europe, Australia, Canada and Singapore from 1943-2000. Cumulative risks were calculated using a competing risk model, and standardized incidence ratios (SIR) for 34 cancers were estimated based on the observed numbers of second malignancies and the expected numbers obtained from population-specific incidence rates.

We observed 5,052 second malignant neoplasms in 107,038 ovarian cancer patients and 5,804 second ovarian cancers in 3,722,434 patients with cancer of other sites. Within 20 years from diagnosis of ovarian cancer, the cumulative risk of second malignant neoplasms was 4.8% (95% CI 4.6%, 5.0%) before 1980 and 7.1% (6.1, 8.0) after 1980. After sex cord-stromal, mucinous or endometrioid tumors of the ovary, the cumulative risk of second malignant neoplasms was higher [12.7% (11.2, 14.3), 10.0% (9.0, 11.0), 9.3% (7.9, 10.7), respectively] than after germ-cell tumors, serous tumors or adenocarcinoma NOS [6.2% (3.7, 8.7), 5.9% (5.5, 6.3), 5.1% (4.9, 5.4), respectively] within 20 years from diagnosis at age 45+. We observed increased SIRs for cancer of stomach [SIR=1.5 (95% CI 1.1, 2.0)], small intestine [3.2 (1.3, 6.5)], colon [1.5 (1.2, 1.8)], rectum [1.9 (1.4, 2.4)], soft tissue sarcoma [3.2 (1.5, 5.8)], non-melanoma of skin [1.4 (1.0, 1.7)], breast [1.3 (1.2, 1.5)], other female genital organ [2.2 (1.3, 3.5)], bladder [2.3 (1.7, 3.1)], kidney [1.8 (1.3, 2.6)], myeloid leukemia [3.5 (2.2, 5.4)] and other leukemia [6.4 (3.7, 10.2)] after serous tumors of the ovary. There were increased SIRs for colon [2.2 (1.7, 2.7)], rectum [1.9 (1.3, 2.6)], lung [2.1 (1.6, 2.7)] and bladder cancer [1.8 (1.0, 2.8)] after mucinous tumors. After endometrioid tumors, we observed an excess risk for cancer of colon [2.1 (1.5, 2.9)], bone [12.1 (1.5, 43.6)], soft tissue sarcoma [5.2 (1.1, 15.3)], corpus uteri [3.3 (2.2, 4.7)] and kidney [2.3 (1.1, 4.4)]. There was an association with cancer of soft tissue sarcoma [3.2 (1.0, 7.4)], bladder [2.2 (1.2, 3.4)], kidney [2.1 (1.2, 3.3)], thyroid gland [3.1 (1.5, 5.6)] and myeloid leukemia [4.2 (1.5, 9.1)] after sex cord-stromal tumors. SIRs of second ovarian cancer were increased after stomach, small intestine, colon, gallbladder, pancreas, peritoneum, non-melanoma skin and breast cancer.

Women who survive ovarian cancer are at long-term risk of developing a second malignant neoplasm. The associations between specific types of ovarian cancer and other cancers may be attributed to late effects of radio- and chemotherapy, as well as to common genetic and environmental risk factors and pathways.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1832.

Simulating inadequate dialysis and its correction using an individualized patient-derived nomogram

Computerized kinetic modeling is a valuable automated peritoneal dialysis (APD) prescription tool for optimizing dialysis adequacy. However, non-compliance results in failure to achieve adequacy targets. The aim of this study was to determine if a nomogram could estimate dialysis compensations for shortfalls in simulated non-compliant patients, such that total weekly urea clearance (Kt/V(urea)) targets are met. Individualized nomograms comprising a series of curves were derived from PD Adequest (ver. 2.0)-predicted Kt/V(urea) data (r (2 ) > 0.99) for different APD prescriptions. The nomogram was then used to estimate the (Nomogram-computed) average of the daily Kt/V(urea) in 14 patients. The study comprised three 1-month phases. Patients were compliant to dialysis in phase I, where Adequest-predicted Kt/V(urea) showed good agreement with both measured (r (I) = 0.72), and Nomogram-computed values (r (I) > 0.99) (p < 0.001). Conversely, in non-compliant phase II, Nomogram-computed values were lower than Adequest-predicted values (p < 0.002). In phase III, the nomogram estimated prescription adjustments required to compensate for shortfalls, such that there was significantly less difference between Nomogram-computed and Adequest-predicted Kt/V(urea) than in phase II (p = 0.005). Thus, despite non-compliance, predicted Kt/V(urea) targets were attained using the nomogram to adjust the daily APD prescriptions. This concept is potentially useful for patients desiring to compensate for inadvertent shortfalls, rather than for 'truly non-compliant' patients.

Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.