In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR)= 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases.

Percent mammographic density adjusted for age and body mass index (BMI) is one of the strongest risk factors for breast cancer and has a heritable component that remains largely unidentified. We performed a three-stage genome-wide association study (GWAS) of percent mammographic density to identify novel genetic loci associated with this trait. In stage 1, we combined three GWAS of percent density comprised of 1,241 women from studies at the Mayo Clinic and identified the top 48 loci (99 SNPs). We attempted replication of these loci in 7,018 women from seven additional studies (stage 2). The meta-analysis of stage 1 and 2 data identified a novel locus, rs1265507 on 12q24, associated with percent density, adjusting for age and BMI (P = 4.43 x 10(-8)). We refined the 12q24 locus with 459 additional variants (stage 3) in a combined analysis of all three stages (n=10,377) and confirmed that rs1265507 has the strongest association in the 12q24 region (P = 1.03 x 10(-8)). Rs1265507 is located between the genes TBX5 and TBX3, which are members of the phylogenetically conserved T-box gene family and encode transcription factors involved in developmental regulation. Understanding the mechanism underlying this association will provide insight into the genetics of breast tissue composition.

Four loci have been associated with pancreatic cancer through genome-wide association studies (GWAS). Pathway-based analysis of GWAS data is a complementary approach to identify groups of genes or biological pathways enriched with disease associated SNPs whose individual effect sizes may be too small to be detected by standard single-locus methods. We used the adaptive rank truncated product method in a pathway-based analysis of GWAS data from 3,851 pancreatic cancer cases and 3,934 control participants pooled from 12 cohort studies and 8 case control studies (PanScan). We compiled 23 biological pathways hypothesized to be relevant to pancreatic cancer and observed a nominal association between pancreatic cancer and five pathways (P < 0.05), i.e. pancreatic development, Helicobacter pylori lacto/neolacto, hedgehog, Th1/Th2 immune response, and apoptosis (P = 2.0 × 10(-6), 1.6 × 10(-5), 0.0019, 0.019, and 0.023, respectively). After excluding previously identified genes from the original GWAS in three pathways (NR5A2, ABO, and SHH), the pancreatic development pathway remained significant (P = 8.3 × 10(-5)), while the others did not. The most significant genes (P < 0.01) in the five pathways were NR5A2, HNF1A, HNF4G, and PDX1 for pancreatic development; ABO for H. pylori lacto/neolacto; SHH for hedgehog; TGFBR2 and CCL18 for Th1/Th2 immune response; and MAPK8 and BCL2L11 for apoptosis. Our results provide a link between inherited variation in genes important for pancreatic development and cancer and show that pathway-based approaches to analysis of GWAS data can yield important insights into the collective role of genetic risk variants in cancer.

Rotating night shift work is associated with increased risk of breast cancer, likely via circadian disruption. We hypothesized that circadian pathway genes influence breast cancer risk, particularly in rotating night shift workers. We selected 178 common variants across 15 genes pertinent to the circadian system. Using a mixed candidate- and tag-single nucleotide polymorphism approach, we tested for associations between these variants and breast cancer risk in 1,825 women within the Nurses' Health Study II cohort and investigated potential interactions between genotype and rotating shift-work in a subset of 1,318 women. Multiple-testing-adjusted p-values were obtained by permutation (n=10,000). None of the selected variants was significantly associated with breast cancer risk. However, when accounting for potential effect modification, rs23051560 (Ala394Thr) in the largest circadian gene, Neuronal PAS domain protein 2 (NPAS2) was most strongly associated with breast cancer risk (nominal test for interaction p-value=0.0005; 10,000-permutation-based main-effects p-value among women with <24 months of shift-work=0.003). The observed multiplicative association with breast cancer risk per minor allele (A) was 0.65 (95%CI=0.51-0.82) among women with <24 months of shift-work, and 1.19 (95%CI=0.93-1.54) with ≥24 months of shift-work. Women homozygous for the minor allele (AA) with ≥24 months of shift-work had a 2.83-times higher breast cancer risk compared to homozygous AA women with <24 months of shift-work (95%CI=1.47-5.56). In smmary, common variation in circadian genes plays at most a small role in breast cancer risk among women of European ancestry. The impact of NPAS2 Ala394Thr in the presence of rotating shift-work requires further investigation. © 2012 Wiley-Liss, Inc.

BACKGROUND: Mammographic density adjusted for age and body mass index (BMI) is a heritable marker of breast cancer susceptibility. Little is known about the biological mechanisms underlying the association between mammographic density and breast cancer risk. We examined whether common low-penetrance breast cancer susceptibility variants contribute to inter-individual differences in mammographic density measures. METHODS: We established an international consortium (DENSNP) of 19 studies from 10 countries, comprising 16,895 Caucasian women, to conduct a pooled cross-sectional analysis of common breast cancer susceptibility variants in 14 independent loci and mammographic density measures. Dense and non-dense areas, and percent density, were measured using interactive-thresholding techniques. Mixed linear models were used to assess the association between genetic variants and the square roots of mammographic density measures adjusted for study, age, case status, body mass index (BMI) and menopausal status. RESULTS: Consistent with their breast cancer associations, the C-allele of rs3817198 in LSP1 was positively associated with both adjusted dense area (p=0.00005) and adjusted percent density (p=0.001) whereas the A-allele of rs10483813 in RAD51L1 was inversely associated with adjusted percent density (p=0.003), but not with adjusted dense area (p=0.07). CONCLUSION: We identified two common breast cancer susceptibility variants associated with mammographic measures of radio-dense tissue in the breast gland.Impact: We examined the association of 14 established breast cancer susceptibility loci with mammographic density phenotypes within a large genetic consortium and identified two breast cancer susceptibility variants, LSP1-rs3817198 and RAD51L1-rs10483813, associated with mammographic measures and in the same direction as the breast cancer association.

BACKGROUND: Little is known about relationships among reproductive factors, estrogens and estrogen metabolites (jointly referred to as EM), and estrogen metabolism patterns.METHODS: In a cross-sectional analysis, we examined the associations of age at menarche, menstrual cycle length and regularity, parity, age at first and last birth, breastfeeding, and duration of and time since use of oral contraceptives (OC) with mid-luteal phase urinary EM in a sample of 603 premenopausal women, ages 33-51, within the Nurses' Health Study II (NHSII). Fifteen individual urinary EM were measured using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and analyzed both individually and in metabolic pathways.RESULTS: Compared to women with extremely regular cycles, those with irregular cycles had lower levels of total EM (percent difference=24%; ptrend=0.01), estradiol (23%; ptrend=0.02), and 16-hydroxylation pathway EM (32%; ptrend<0.01). Longer menstrual cycles were associated with higher levels of estrone (percent difference ≥32 vs.<26 days: 25%; ptrend=0.03), estradiol (24%; ptrend=0.01), and 16-hydroxylation pathway EM (22%; ptrend=0.02). Among parous women, older age at first birth was associated with lower 16-hydroxylation pathway EM (percent difference age at first birth ≥35 vs. ≤25 years: 20%; ptrend=0.02). The other reproductive factors were not statistically significantly associated with individual urinary EM or EM pathways. Conclusions and Impact: These data, based on a LC-MS/MS assay with high specificity and precision, provide an initial, comprehensive evaluation of the associations between reproductive factors and estrogen metabolism patterns.

ABSTRACT: INTRODUCTION: A younger age at menarche and an older age at menopause are well established risk factors for breast cancer. Recent genome-wide association studies have identified several novel genetic loci associated with these two traits. However, the association between these loci and breast cancer risk is unknown. METHODS: In this study, we investigated 19 and 17 newly identified single nucleotide polymorphisms (SNPs) from the ReproGen Consortium that have been associated with age at menarche and age at natural menopause, respectively, and assessed their associations with breast cancer risk in 6 population-based studies among up to 3,683 breast cancer cases and 34,174 controls in white women of European ancestry. In addition, we used these SNPs to calculate genetic risk scores (GRSs) based on their associations with each trait. RESULTS: After adjusting for age and potential population stratification, two age at menarche associated SNPs (rs1079866 and rs7821178) and one age at natural menopause associated SNP (rs2517388) were associated with breast cancer risk (p values, 0.003, 0.009 and 0.023, respectively). The odds ratios for breast cancer corresponding to per-risk-allele were 1.14 (95% CI, 1.05 to 1.24), 1.08 (95% CI, 1.02 to 1.15) and 1.10 (95% CI, 1.01 to 1.20), respectively, and were in the direction predicted by their associations with age at menarche or age at natural menopause. These associations did not appear to be attenuated by further controlling for self-reported age at menarche, age at natural menopause, or known breast cancer susceptibility loci. Although we did not observe a statistically significant association between any GRS for reproductive aging and breast cancer risk, the 4th and 5th highest quintiles of the younger age at menarche GRS had odds ratios of 1.14 (95% CI, 1.01 to 1.28) and 1.13 (95% CI, 1.00 to 1.27), respectively, compared to the lowest quintile. CONCLUSION: Our study suggests that three genetic variants, independent of their associations with age at menarche or age at natural menopause, were associated with breast cancer risk and may contribute modestly to breast cancer risk prediction; however, the combination of the 19 age at menarche or the 17 age at natural menopause associated SNPs did not appear to be useful for identifying a high risk subgroup for breast cancer.

ABSTRACT: INTRODUCTION: Previous research in the Nurses' Health Study (NHS) and NHSII observed that, among women diagnosed with benign breast disease (BBD), those with predominant type 1/no type 3 lobules (a marker of complete involution) versus other lobule types were at lower risk of subsequent breast cancer. Studies in animal models suggest that insulin-like growth factor-1 (IGF-1) may inhibit involution of lobules in the breast; however, this has not been studied in humans. METHODS: We conducted a cross-sectional study among 472 women in the NHSII who were diagnosed with biopsy-confirmed proliferative BBD between 1991 and 2002 and provided blood samples between 1996 and 1999. A pathologist, blinded to exposure status, classified lobule type in normal adjacent tissue on available biopsy slides according to the number of acini per lobule. For each participant, the pathologist determined the predominant lobule type (i.e., type 1, 2, or 3) and whether any type 1 or any type 3 lobules were present. Lobule type then was classified as: 1) predominant type 1/no type 3 lobules, which is suggestive of complete involution or 2) other lobule types. Multivariate logistic models were used to assess the associations between plasma IGF-1, IGF binding protein-3 (IGFBP-3), and the ratio of IGF-1-to-IGFBP-3 levels with lobule type. RESULTS: In univariate analyses, greater age, higher body mass index, postmenopausal status, nulliparity, and lower IGF-1 levels were associated with predominant type1/no type 3 lobules (P<0.05). In multivariate models adjusting for age and assay batch, higher IGF-1 levels were associated with decreased odds of predominant type 1/no type 3 lobules (OR quartile 4 vs. quartile 1=0.37, 95%CI: 0.15 to 0.89). Greater ratios of IGF-1-to-IGFBP-3 levels also were associated with decreased odds of predominant type1/no type 3 lobules (OR quartile 4 vs. quartile 1=0.26, 95%CI: 0.11 to 0.64). These results were slightly attenuated after adjustment for other potential predictors of lobule type. CONCLUSIONS: Higher IGF-1 levels and a greater IGF-1-to-IGFBP-3 ratio were associated with decreased odds of having predominant type 1 lobules/no type 3 lobules among women with proliferative BBD in the NHSII. This study provides further evidence for the role of insulin-like growth factors in the structure of breast lobules and lobular involution.

Family history of cancer remains underused in general clinical practice. We assess age at diagnosis and the role of family history in risk of breast cancer. Prospective follow-up of nurses' health study participants from 1980 to 2006. Updated assessment of family history in mother and sister including age at diagnosis. We used youngest age at diagnosis for family member when classifying risk. We confirmed 4327 incident invasive breast cancers confirmed. Breast cancer incidence models fitted to women with and without family history to assess variation in the risk for established risk factors. Compared to women with no family history those whose mother was diagnosed before age 50 had an adjusted relative risk of 1.69 (95% CI 1.39-2.05) and those with mother diagnosed at 50 or older had a relative risk of 1.37 (1.22-1.53). Sister history was associated with increased relative risk; 1.66 (1.38-1.99) for those with sister history before age 50 and 1.52 (1.29-1.77) for those with sister diagnosed at age 50 or older. Women with either mother or sister diagnosed before age 50 had a relative risk of 1.70 (1.48-1.95) significantly higher than those with diagnosis at age 50 or older (RR = 1.30;(1.27-1.54), P = 0.016). The magnitude of risk associated with established reproductive and lifestyle risk factors did not differ significantly between women with and those without family history with the exception of risk after bilateral oophorectomy in which setting women with family history had greater reduction in risk of subsequent breast cancer. Women with a family member diagnosed with breast cancer before age 50 had increased risk of breast cancer compared to women with family members diagnosed at older ages. Consistent findings for risk factors regardless of family history adds to robust evidence for risk identification and risk stratification in clinical settings where prevention strategies will apply equally to women with and without family history.

Leukocyte telomere length (LTL) is a potential indicator of cellular aging; however, its relation to physical activity and sedentary behavior is unclear. The authors examined cross-sectionally associations among activity, sedentary behavior, and LTL among 7,813 women aged 43-70 years in the Nurses' Health Study. Participants self-reported activity by questionnaire in 1988 and 1992 and sedentary behavior in 1992. Telomere length in peripheral blood leukocytes, collected in 1989-1990, was measured by quantitative polymerase chain reaction. The least-squares mean telomere length (z-score) was calculated after adjustment for age and other potential confounders. For total activity, moderately or highly active women had a 0.07-standard deviation (SD) increase in LTL (2-sided P(trend)= 0.02) compared with those least active. Greater moderate- or vigorous-intensity activity was also associated with increased LTL (SD = 0.11 for 2-4 vs.<1 hour/week and 0.04 for ≥7 vs.<1 hour/week; 2-sided P(trend)= 0.02). Specifically, calisthenics or aerobics was associated with increased LTL (SD = 0.10 for ≥2.5 vs. 0 hours/week; 2-sided P(trend)= 0.04). Associations remained after adjustment for body mass index. Other specific activities and sitting were unassociated with LTL. Although associations were modest, these findings suggest that even moderate amounts of activity may be associated with longer telomeres, warranting further investigation in large prospective studies.