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Consonni D, Pierobon M, Gail MH, Rubagotti M, Rotunno M, Goldstein A, Goldin L, Lubin J, Wacholder S, Caporaso NE, Bertazzi PA, Tucker MA, Pesatori AC, Landi MT. Lung cancer prognosis before and after recurrence in a population-based setting. J Natl Cancer Inst 2015; 107:djv059. [PMID: 25802059 DOI: 10.1093/jnci/djv059] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Population-based estimates of absolute risk of lung cancer recurrence, and of mortality rates after recurrence, can inform clinical management. METHODS We evaluated prognostic factors for recurrences and survival in 2098 lung cancer case patients from the general population of Lombardy, Italy, from 2002 to 2005. We conducted survival analyses and estimated absolute risks separately for stage IA to IIIA surgically treated and stage IIIB to IV non-surgically treated patients. RESULTS Absolute risk of metastases exceeded that of local recurrence in every stage and cell type, highlighting the systemic threat of lung cancer. In stage I, the probability of dying within the first year after diagnosis was 2.7%, but it was 48.3% within first year after recurrence; in stage IV, the probabilities were 57.3% and 80.6%, respectively. Over half the patients died within one year of first metastasis. Although in stages IA to IB about one-third of patients had a recurrence, stage IIA patients had a recurrence risk (61.2%) similar to stage IIB (57.9%) and IIIA (62.8%) patients. Risk of brain metastases in stage IA to IIIA surgically treated non-small cell lung cancer patients increased with increasing tumor grade. Absolute risk of recurrence was virtually identical in adenocarcinoma and squamous cell carcinoma patients. CONCLUSIONS This population-based study provides clinically useful estimates of risks of lung cancer recurrence and mortality that are applicable to the general population. These data highlight the need for more effective adjuvant treatments overall and within specific subgroups. The estimated risks of various endpoints are useful for designing clinical trials, whose power depends on absolute numbers of events.
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Fuhrman BJ, Feigelson HS, Flores R, Gail MH, Xu X, Ravel J, Goedert JJ. Associations of the fecal microbiome with urinary estrogens and estrogen metabolites in postmenopausal women. J Clin Endocrinol Metab 2014; 99:4632-40. [PMID: 25211668 PMCID: PMC4255131 DOI: 10.1210/jc.2014-2222] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/07/2014] [Indexed: 01/16/2023]
Abstract
CONTEXT The gut microbiota may influence the risk of breast cancer through effects on endogenous estrogens. OBJECTIVE The objective of the study was to investigate whether urinary estrogens and estrogen metabolites are associated with the diversity and composition of the fecal microbiome. DESIGN AND SETTING This was a cross-sectional study among women enrolled in Kaiser Permanente of Colorado. PARTICIPANTS A total of 60 women drawn from a random sample of healthy postmenopausal women (aged 55-69 y), without current or recent use of antibiotics or hormone therapy and no history of cancer or gastrointestinal disease participated in the study. OUTCOME MEASURES AND METHODS: Creatinine-standardized urinary estrogens (estrone and estradiol) and 13 hydroxylated estrogen metabolites were measured in spot urines by liquid chromatography-tandem mass spectrometry. The fecal microbiome was assessed using pyrosequencing of 16S rRNA amplicons. General linear models were used to test for associations of diversity and composition of the fecal microbiome with parent estrogen (estrone + estradiol), total estrogens, and estrogen metabolites and the ratio of estrogen metabolites to parent estrogen, which has been predictive of postmenopausal breast cancer risk in previous studies. RESULTS The ratio of metabolites to parents was directly associated with whole-tree phylogenetic diversity (R = 0.35, P = .01). Relative abundances of the order Clostridiales (R = 0.32, P = .02) and the genus Bacteroides (R = -0.30, P = .03) were also correlated with the ratio of metabolites to parents. Associations were independent of age, body mass index, and study design factors. CONCLUSIONS Our data suggest that women with a more diverse gut microbiome exhibit an elevated urinary ratio of hydroxylated estrogen metabolites to parent estrogen. Further research is warranted to confirm and relate these findings to clinical disease.
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Gail MH, You WC, Li WQ. RE: Effects of Helicobacter pylori treatment on gastric cancer incidence and mortality in subgroups. Response. J Natl Cancer Inst 2014; 106:dju348. [PMID: 25381391 DOI: 10.1093/jnci/dju348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Yu G, Dye BA, Gail MH, Shi J, Klepac-Ceraj V, Paster BJ, Wang GQ, Wei WQ, Fan JH, Qiao YL, Dawsey SM, Freedman ND, Abnet CC. The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China. BMC Public Health 2014; 14:1110. [PMID: 25348940 PMCID: PMC4223728 DOI: 10.1186/1471-2458-14-1110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/22/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Bacteria affect oral health, but few studies have systematically examined the role of bacterial communities in oral diseases. We examined this relationship in a large population-based Chinese cancer screening cohort. METHODS Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in upper digestive tract (UDT) samples collected from 659 participants. Oral health was assessed using US NHANES (National Health and Nutrition Examination Survey) protocols. We assessed both dental health (total teeth missing; tooth decay; and the decayed, missing, and filled teeth (DMFT) score) and periodontal health (bleeding on probing (BoP) extent score, loss of attachment extent score, and a periodontitis summary estimate). RESULTS Microbial richness, estimated by number of genera per sample, was positively correlated with BoP score (P = 0.015), but negatively correlated with tooth decay and DMFT score (P = 0.008 and 0.022 respectively). Regarding β-diversity, as estimated by the UniFrac distance matrix for pairwise differences among samples, at least one of the first three principal components of the UniFrac distance matrix was correlated with the number of missing teeth, tooth decay, DMFT, BoP, or periodontitis. Of the examined genera, Parvimonas was positively associated with BoP and periodontitis. Veillonellacease [G-1] was associated with a high DMFT score, and Filifactor and Peptostreptococcus were associated with a low DMFT score. CONCLUSIONS Our results suggest distinct relationships between UDT microbiota and dental and periodontal health. Poor dental health was associated with a less microbial diversity, whereas poor periodontal health was associated with more diversity and the presence of potentially pathogenic species.
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Lai GY, Weinstein SJ, Taylor PR, McGlynn KA, Virtamo J, Gail MH, Albanes D, Freedman ND. Effects of α-tocopherol and β-carotene supplementation on liver cancer incidence and chronic liver disease mortality in the ATBC study. Br J Cancer 2014; 111:2220-3. [PMID: 25314069 PMCID: PMC4264440 DOI: 10.1038/bjc.2014.514] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 07/14/2014] [Accepted: 09/01/2014] [Indexed: 12/31/2022] Open
Abstract
Background: Recent data suggest the possible benefits of α-tocopherol and β-carotene supplementation on liver cancer and chronic liver disease (CLD), but the long-term trial data are limited. Methods: We evaluated the efficacy of supplemental 50 mg day−1α-tocopherol and 20 mg day−1β-carotene on incident liver cancer and CLD mortality in a randomised trial of 29 105 Finnish male smokers, who received supplementation for 5–8 years and were followed for 16 additional years for outcomes. Results: Supplemental α-tocopherol, β-carotene, or both, relative to placebo, did not reduce the risk of liver cancer or CLD, either overall, during the intervention or during the post-intervention period. Conclusions: Long-term supplemental α-tocopherol or β-carotene had no effect on liver cancer or CLD mortality over 24 years of follow-up.
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Gierach GL, Li H, Loud JT, Greene MH, Chow CK, Lan L, Prindiville SA, Eng-Wong J, Soballe PW, Giambartolomei C, Mai PL, Galbo CE, Nichols K, Calzone KA, Olopade OI, Gail MH, Giger ML. Relationships between computer-extracted mammographic texture pattern features and BRCA1/2 mutation status: a cross-sectional study. Breast Cancer Res 2014. [PMID: 25159706 DOI: 10.1186/preaccept-1744229618121391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Mammographic density is similar among women at risk of either sporadic or BRCA1/2-related breast cancer. It has been suggested that digitized mammographic images contain computer-extractable information within the parenchymal pattern, which may contribute to distinguishing between BRCA1/2 mutation carriers and non-carriers. METHODS We compared mammographic texture pattern features in digitized mammograms from women with deleterious BRCA1/2 mutations (n = 137) versus non-carriers (n = 100). Subjects were stratified into training (107 carriers, 70 non-carriers) and testing (30 carriers, 30 non-carriers) datasets. Masked to mutation status, texture features were extracted from a retro-areolar region-of-interest in each subject's digitized mammogram. Stepwise linear regression analysis of the training dataset identified variables to be included in a radiographic texture analysis (RTA) classifier model aimed at distinguishing BRCA1/2 carriers from non-carriers. The selected features were combined using a Bayesian Artificial Neural Network (BANN) algorithm, which produced a probability score rating the likelihood of each subject's belonging to the mutation-positive group. These probability scores were evaluated in the independent testing dataset to determine whether their distribution differed between BRCA1/2 mutation carriers and non-carriers. A receiver operating characteristic analysis was performed to estimate the model's discriminatory capacity. RESULTS In the testing dataset, a one standard deviation (SD) increase in the probability score from the BANN-trained classifier was associated with a two-fold increase in the odds of predicting BRCA1/2 mutation status: unadjusted odds ratio (OR) = 2.00, 95% confidence interval (CI): 1.59, 2.51, P = 0.02; age-adjusted OR = 1.93, 95% CI: 1.53, 2.42, P = 0.03. Additional adjustment for percent mammographic density did little to change the OR. The area under the curve for the BANN-trained classifier to distinguish between BRCA1/2 mutation carriers and non-carriers was 0.68 for features alone and 0.72 for the features plus percent mammographic density. CONCLUSIONS Our findings suggest that, unlike percent mammographic density, computer-extracted mammographic texture pattern features are associated with carrying BRCA1/2 mutations. Although still at an early stage, our novel RTA classifier has potential for improving mammographic image interpretation by permitting real-time risk stratification among women undergoing screening mammography.
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Gierach GL, Li H, Loud JT, Greene MH, Chow CK, Lan L, Prindiville SA, Eng-Wong J, Soballe PW, Giambartolomei C, Mai PL, Galbo CE, Nichols K, Calzone KA, Olopade OI, Gail MH, Giger ML. Relationships between computer-extracted mammographic texture pattern features and BRCA1/2 mutation status: a cross-sectional study. Breast Cancer Res 2014; 16:424. [PMID: 25159706 PMCID: PMC4268674 DOI: 10.1186/s13058-014-0424-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 07/31/2014] [Indexed: 12/24/2022] Open
Abstract
Introduction Mammographic density is similar among women at risk of either sporadic or BRCA1/2-related breast cancer. It has been suggested that digitized mammographic images contain computer-extractable information within the parenchymal pattern, which may contribute to distinguishing between BRCA1/2 mutation carriers and non-carriers. Methods We compared mammographic texture pattern features in digitized mammograms from women with deleterious BRCA1/2 mutations (n = 137) versus non-carriers (n = 100). Subjects were stratified into training (107 carriers, 70 non-carriers) and testing (30 carriers, 30 non-carriers) datasets. Masked to mutation status, texture features were extracted from a retro-areolar region-of-interest in each subject’s digitized mammogram. Stepwise linear regression analysis of the training dataset identified variables to be included in a radiographic texture analysis (RTA) classifier model aimed at distinguishing BRCA1/2 carriers from non-carriers. The selected features were combined using a Bayesian Artificial Neural Network (BANN) algorithm, which produced a probability score rating the likelihood of each subject’s belonging to the mutation-positive group. These probability scores were evaluated in the independent testing dataset to determine whether their distribution differed between BRCA1/2 mutation carriers and non-carriers. A receiver operating characteristic analysis was performed to estimate the model’s discriminatory capacity. Results In the testing dataset, a one standard deviation (SD) increase in the probability score from the BANN-trained classifier was associated with a two-fold increase in the odds of predicting BRCA1/2 mutation status: unadjusted odds ratio (OR) = 2.00, 95% confidence interval (CI): 1.59, 2.51, P = 0.02; age-adjusted OR = 1.93, 95% CI: 1.53, 2.42, P = 0.03. Additional adjustment for percent mammographic density did little to change the OR. The area under the curve for the BANN-trained classifier to distinguish between BRCA1/2 mutation carriers and non-carriers was 0.68 for features alone and 0.72 for the features plus percent mammographic density. Conclusions Our findings suggest that, unlike percent mammographic density, computer-extracted mammographic texture pattern features are associated with carrying BRCA1/2 mutations. Although still at an early stage, our novel RTA classifier has potential for improving mammographic image interpretation by permitting real-time risk stratification among women undergoing screening mammography. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0424-8) contains supplementary material, which is available to authorized users.
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Li H, Gail MH, Braithwaite RS, Gold HT, Walter D, Liu M, Gross CP, Makarov DV. Are hospitals "keeping up with the Joneses"?: Assessing the spatial and temporal diffusion of the surgical robot. HEALTHCARE (AMSTERDAM, NETHERLANDS) 2014; 2:152-157. [PMID: 25821720 PMCID: PMC4376012 DOI: 10.1016/j.hjdsi.2013.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND The surgical robot has been widely adopted in the United States in spite of its high cost and controversy surrounding its benefit. Some have suggested that a "medical arms race" influences technology adoption. We wanted to determine whether a hospital would acquire a surgical robot if its nearest neighboring hospital already owned one. METHODS We identified 554 hospitals performing radical prostatectomy from the Healthcare Cost and Utilization Project Statewide Inpatient Databases for seven states. We used publicly available data from the website of the surgical robot's sole manufacturer (Intuitive Surgical, Sunnyvale, CA) combined with data collected from the hospitals to ascertain the timing of robot acquisition during year 2001 to 2008. One hundred thirty four hospitals (24%) had acquired a surgical robot by the end of 2008. We geocoded the address of each hospital and determined a hospital's likelihood to acquire a surgical robot based on whether its nearest neighbor owned a surgical robot. We developed a Markov chain method to model the acquisition process spatially and temporally and quantified the "neighborhood effect" on the acquisition of the surgical robot while adjusting simultaneously for known confounders. RESULTS After adjusting for hospital teaching status, surgical volume, urban status and number of hospital beds, the Markov chain analysis demonstrated that a hospital whose nearest neighbor had acquired a surgical robot had a higher likelihood itself acquiring a surgical robot. (OR=1.71, 95% CI: 1.07-2.72, p=0.02). CONCLUSION There is a significant spatial and temporal association for hospitals acquiring surgical robots during the study period. Hospitals were more likely to acquire a surgical robot during the robot's early adoption phase if their nearest neighbor had already done so.
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Li WQ, Ma JL, Zhang L, Brown LM, Li JY, Shen L, Pan KF, Liu WD, Hu Y, Han ZX, Crystal-Mansour S, Pee D, Blot WJ, Fraumeni JF, You WC, Gail MH. Effects of Helicobacter pylori treatment on gastric cancer incidence and mortality in subgroups. J Natl Cancer Inst 2014; 106:dju116. [PMID: 24925350 DOI: 10.1093/jnci/dju116] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Among 2258 Helicobacter pylori-seropositive subjects randomly assigned to receive one-time H. pylori treatment with amoxicillin-omeprazole or its placebo, we evaluated the 15-year effect of treatment on gastric cancer incidence and mortality in subgroups defined by age, baseline gastric histopathology, and post-treatment infection status. We used conditional logistic and Cox regressions for covariable adjustments in incidence and mortality analyses, respectively. Treatment was associated with a statistically significant decrease in gastric cancer incidence (odds ratio = 0.36; 95% confidence interval [CI] = 0.17 to 0.79) and mortality (hazard ratio = 0.26; 95% CI = 0.09 to 0.79) at ages 55 years and older and a statistically significant decrease in incidence among those with intestinal metaplasia or dysplasia at baseline (odds ratio = 0.56; 95% CI = 0.34 to 0.91). Treatment benefits for incidence and mortality among those with and without post-treatment infection were similar. Thus H. pylori treatment can benefit older members and those with advanced baseline histopathology, and benefits are present even with post-treatment infection, suggesting treatment can benefit an entire population, not just the young or those with mild histopathology.
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Yu G, Gail MH, Shi J, Klepac-Ceraj V, Paster BJ, Dye BA, Wang GQ, Wei WQ, Fan JH, Qiao YL, Dawsey SM, Freedman ND, Abnet CC. Association between upper digestive tract microbiota and cancer-predisposing states in the esophagus and stomach. Cancer Epidemiol Biomarkers Prev 2014; 23:735-41. [PMID: 24700175 DOI: 10.1158/1055-9965.epi-13-0855] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The human upper digestive tract microbial community (microbiota) is not well characterized and few studies have explored how it relates to human health. We examined the relationship between upper digestive tract microbiota and two cancer-predisposing states, serum pepsinogen I/pepsinogen II ratio (PGI/II; predictor of gastric cancer risk) and esophageal squamous dysplasia (ESD; the precursor lesion of esophageal squamous cell carcinoma; ESCC) in a cross-sectional design. METHODS The Human Oral Microbe Identification Microarray was used to test for the presence of 272 bacterial species in 333 upper digestive tract samples from a Chinese cancer screening cohort. Serum PGI and PGII were determined by ELISA. ESD was determined by chromoendoscopy with biopsy. RESULTS Lower microbial richness (number of bacterial genera per sample) was significantly associated with lower PGI/II ratio (P = 0.034) and the presence of ESD (P = 0.018). We conducted principal component (PC) analysis on a β-diversity matrix (pairwise difference in microbiota), and observed significant correlations between PC1, PC3, and PGI/II (P = 0.004 and 0.009, respectively), and between PC1 and ESD (P = 0.003). CONCLUSIONS Lower microbial richness in upper digestive tract was independently associated with both cancer-predisposing states in the esophagus and stomach (presence of ESD and lower PGI/II). IMPACT These novel findings suggest that the upper digestive tract microbiota may play a role in the etiology of chronic atrophic gastritis and ESD, and therefore in the development of gastric and esophageal cancers.
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Feigelson HS, Bischoff K, Ardini MAE, Ravel J, Gail MH, Flores R, Goedert JJ. Feasibility of self-collection of fecal specimens by randomly sampled women for health-related studies of the gut microbiome. BMC Res Notes 2014; 7:204. [PMID: 24690120 PMCID: PMC3974920 DOI: 10.1186/1756-0500-7-204] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/21/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The field of microbiome research is growing rapidly. We developed a method for self-collection of fecal specimens that can be used in population-based studies of the gut microbiome. We conducted a pilot study to test the feasibility of our methods among a random sample of healthy, postmenopausal women who are members of Kaiser Permanente Colorado (KPCO). We aimed to collect questionnaire data, fecal and urine specimens from 60 women, aged 55-69, who recently had a normal screening mammogram. We designed the study such that all questionnaire data and specimens could be collected at home. RESULTS We mailed an invitation packet, consent form and opt-out postcard to 300 women, then recruited by telephone women who did not opt-out. Verbally consented women were mailed an enrollment package including a risk factor questionnaire, link to an online diet questionnaire, specimen collection kit, and instructions for collecting stool and urine. Specimens were shipped overnight to the biorepository. Of the 300 women mailed an invitation packet, 58 (19%) returned the opt-out postcard. Up to 3 attempts were made to telephone the remaining women, of whom 130 (43%) could not be contacted, 23 (8%) refused, and 12 (4%) were ineligible. Enrollment packages were mailed to 77 women, of whom 59 returned the risk factor questionnaire and specimens. We found no statistically significant differences between enrolled women and those who refused participation or could not be contacted. CONCLUSIONS We demonstrated that a representative sample of women can be successfully recruited for a gut microbiome study; however, significant personal contact and carefully timed follow-up from the study personnel are required. The methods employed by our study could successfully be applied to analytic studies of a wide range of clinical conditions that have been postulated to be influenced by the gut microbial population.
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Loud JT, Gierach GL, Veenstra TD, Falk RT, Nichols K, Guttmann A, Xu X, Greene MH, Gail MH. Circulating estrogens and estrogens within the breast among postmenopausal BRCA1/2 mutation carriers. Breast Cancer Res Treat 2014; 143:517-29. [PMID: 24442642 PMCID: PMC3955055 DOI: 10.1007/s10549-013-2821-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 12/20/2013] [Indexed: 12/19/2022]
Abstract
Accurately quantifying parent estrogens (PE) estrone (E1) and estradiol (E2) and their metabolites (EM) within breast tissue and serum may permit detailed investigations of their contributions to breast carcinogenesis among BRCA1/2 mutation carriers. We conducted a study of PE/EM in serum, nipple aspirate fluid (NAF), and ductal lavage supernatant (DLS) among postmenopausal BRCA1/2 mutation carriers. PE/EM (conjugated and unconjugated) were measured in paired serum/NAF (n = 22 women) and paired serum/DLS samples (n = 24 women) using quantitative liquid chromatography-tandem mass spectrometry (LC/MS/MS). The relationships between serum and tissue-specific PE/EM were measured using Pearson's correlation coefficients. Conjugated forms of PE/EM constituted the majority of estrogen in serum (88 %), NAF (59 %) and DLS (69 %). PE/EM in NAF and serum were highly correlated [E1 (r = 0.97, p < 0.0001), E2 (r = 0.90, p < 0.0001) and estriol (E3) (r = 0.74, p < 0.0001)] as they were in DLS and serum [E1 (r = 0.92, p < 0.0001; E2 (r = 0.70, p = 0.0001; E3 (r = 0.67, p = 0.0004)]. Analyses of paired total estrogen values for NAF and serum, and DLS and serum yielded ratios of 0.22 (95 % CI 0.19-0.25) and 0.28 (95 % CI 0.24-0.32), respectively. This report is the first to employ LC/MS/MS to quantify PE/EM in novel breast tissue-derived biospecimens (i.e., NAF and DLS). We demonstrate that circulating PE and EM are strongly and positively correlated with tissue-specific PE and EM measured in NAF and DLS among postmenopausal BRCA1/2 mutation carriers. If confirmed, future etiologic studies could utilize the more readily obtainable serum hormone levels as a reliable surrogate measure of exposure at the tissue level.
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Wu J, Pfeiffer RM, Gail MH. Strategies for developing prediction models from genome-wide association studies. Genet Epidemiol 2013; 37:768-77. [PMID: 24166696 DOI: 10.1002/gepi.21762] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/31/2013] [Accepted: 09/10/2013] [Indexed: 12/30/2022]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of single nucleotide polymorphisms (SNPs) associated with complex human diseases. However, risk prediction models based on them have limited discriminatory accuracy. It has been suggested that including many such SNPs can improve predictive performance. Here, we studied various aspects of model building to improve discriminatory accuracy, as measured by the area under the receiver operating characteristic curve (AUC), including: (1) How well does a one-phase procedure that selects SNPs and estimates odds ratios on the same data perform? (2) How should training data be allocated between SNP selection (Phase 1) and estimation (Phase 2) in a two-phase procedure? (3) Should SNP selection be based on P-value thresholding or ranking P-values? (4) How many SNPs should be selected? and (5) Is multivariate estimation preferred to univariate estimation in the presence of linkage disequilibrium (LD)? We used realistic estimates of the distributions of genetic effect sizes, allele frequencies, and LD patterns based on GWAS data for Crohn's disease and prostate cancer. Theory and simulations were used to estimate AUC. Empirical risk models based on 10,000 cases and controls had considerably lower AUC than theoretically achievable. The most critical aspect of prediction model building was initial SNP selection. The single-phase procedure achieved higher AUC than the two-phase procedure. Multivariate estimation did not perform as well as univariate (marginal) estimation. For complex diseases and samples of 10,000 or fewer cases and controls, one should limit the number of SNPs to tens or hundreds.
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Gail MH, Sheehy T, Cosentino M, Pee D, Diaz-Mayoral NA, Garcia-Closas M, Caporaso NE, Pitt K, Ziegler RG. Maximizing DNA yield for epidemiologic studies: no more buffy coats? Am J Epidemiol 2013; 178:1170-6. [PMID: 23857774 PMCID: PMC3783090 DOI: 10.1093/aje/kwt079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/29/2013] [Indexed: 11/13/2022] Open
Abstract
Some molecular analyses require microgram quantities of DNA, yet many epidemiologic studies preserve only the buffy coat. In Frederick, Maryland, in 2010, we estimated DNA yields from 5 mL of whole blood and from equivalent amounts of all-cell-pellet (ACP) fraction, buffy coat, and residual blood cells from fresh blood (n = 10 volunteers) and from both fresh and frozen blood (n = 10). We extracted DNA with the QIAamp DNA Blood Midi Kit (Qiagen Sciences, Germantown, Maryland) for silica spin column capture and measured double-stranded DNA. Yields from frozen blood fractions were not statistically significantly different from those obtained from fresh fractions. ACP fractions yielded 80.6% (95% confidence interval: 66, 97) of the yield of frozen whole blood and 99.3% (95% confidence interval: 86, 100) of the yield of fresh blood. Frozen buffy coat and residual blood cells each yielded only half as much DNA as frozen ACP, and the yields were more variable. Assuming that DNA yield and quality from frozen ACP are stable, we recommend freezing plasma and ACP. Not only does ACP yield twice as much DNA as buffy coat but it is easier to process, and its yield is less variable from person to person. Long-term stability studies are needed. If one wishes to separate buffy coat before freezing, one should also save the residual blood cell fraction, which contains just as much DNA.
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Sun Z, Chen T, Thorgeirsson SS, Zhan Q, Chen J, Park JH, Lu P, Hsia CC, Wang N, Xu L, Lu L, Huang F, Zhu Y, Lu J, Ni Z, Zhang Q, Wu Y, Liu G, Wu Z, Qu C, Gail MH. Dramatic reduction of liver cancer incidence in young adults: 28 year follow-up of etiological interventions in an endemic area of China. Carcinogenesis 2013; 34:1800-5. [PMID: 23322152 PMCID: PMC3731800 DOI: 10.1093/carcin/bgt007] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 12/16/2022] Open
Abstract
Qidong City, China, has had high liver cancer incidence from endemic hepatitis B virus (HBV) infection and dietary exposure to aflatoxin. Based on etiologic studies, we began interventions in 1980 to reduce dietary aflatoxin and initiate neonatal HBV vaccination. We studied trends in liver cancer incidence rates in the 1.1 million inhabitants of Qidong and examined trends in aflatoxin exposure, staple food consumption, HBV infection markers and annual income. Aflatoxin exposure declined greatly in association with economic reform, increased earnings and educational programs to shift staple food consumption in the total population from moldy corn to fresh rice. A controlled neonatal HBV vaccination trial began in 1983 and ended in November, 1990, when vaccination was expanded to all newborns. Liver cancer incidence fell dramatically in young adults. Compared with 1980-83, the age-specific liver cancer incidence rates in 2005-08 significantly decreased 14-fold at ages 20-24, 9-fold at ages 25-29, 4-fold at ages 30-34, 1.5-fold at ages 35-39, 1.2-fold at ages 40-44 and 1.4-fold at ages 45-49, but increased at older ages. The 14-fold reduction at ages 20-24 might reflect the combined effects of reduced aflatoxin exposure and partial neonatal HBV vaccination. Decrease incidence in age groups >25 years could mainly be attributable to rapid aflatoxin reduction. Compared with 1980-83, liver cancer incidence in 1990-93 significantly decreased 3.4-fold at ages 20-24, and 1.9-fold at ages 25-29 when the first vaccinees were <11 years old.
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García-Closas M, Gail MH, Kelsey KT, Ziegler RG. Searching for blood DNA methylation markers of breast cancer risk and early detection. J Natl Cancer Inst 2013; 105:678-80. [PMID: 23578855 DOI: 10.1093/jnci/djt090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Gail MH, Pfeiffer RM, Cai T. Six articles related to risk assessment and prediction based on work presented at the October 12–14, 2011 Conference on Risk Assessment and Evaluation of Predictions in Silver Spring, Maryland. LIFETIME DATA ANALYSIS 2013; 19:139-141. [PMID: 23563996 DOI: 10.1007/s10985-013-9253-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Cozen W, Yu G, Gail MH, Ridaura VK, Nathwani BN, Hwang AE, Hamilton AS, Mack TM, Gordon JI, Goedert JJ. Fecal microbiota diversity in survivors of adolescent/young adult Hodgkin lymphoma: a study of twins. Br J Cancer 2013; 108:1163-7. [PMID: 23443674 PMCID: PMC3619077 DOI: 10.1038/bjc.2013.60] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/09/2013] [Accepted: 01/20/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Adolescent/young adult Hodgkin lymphoma (AYAHL) survivors report fewer exposures to infections during childhood compared with controls, and they have functional lymphocyte aberrations. The gut microbiota plays a central role in immunity. METHODS We investigated whether fecal microbial diversity differed between 13 AYAHL survivors and their unaffected co-twin controls. Pyrosequencing of fecal bacterial 16S rRNA amplicons yielded 252 943 edited reads that were assigned to species-level operational taxonomic units (OTUs) and standardised for sequencing depth by random sampling. Microbial diversity was compared within vs between twin pairs and by case-control status. RESULTS The number of unique OTUs was more similar within twin pairs compared with randomly paired participants (P=0.0004). The AYAHL cases had fewer unique OTUs compared with their co-twin controls (338 vs 369, P=0.015); this difference was not significant (169 vs 183, P=0.10) when restricted to abundant OTUs. CONCLUSION In this small study, AYAHL survivors appear to have a deficit of rare gut microbes. Further work is needed to determine if reduced microbial diversity is a consequence of the disease, its treatment, or a particularly hygienic environment.
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Flores R, Shi J, Fuhrman B, Xu X, Veenstra TD, Gail MH, Gajer P, Ravel J, Goedert JJ. Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study. J Transl Med 2012; 10:253. [PMID: 23259758 PMCID: PMC3552825 DOI: 10.1186/1479-5876-10-253] [Citation(s) in RCA: 345] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/17/2012] [Indexed: 12/14/2022] Open
Abstract
Background High systemic estrogen levels contribute to breast cancer risk for postmenopausal women, whereas low levels contribute to osteoporosis risk. Except for obesity, determinants of non-ovarian systemic estrogen levels are undefined. We sought to identify members and functions of the intestinal microbial community associated with estrogen levels via enterohepatic recirculation. Methods Fifty-one epidemiologists at the National Institutes of Health, including 25 men, 7 postmenopausal women, and 19 premenopausal women, provided urine and aliquots of feces, using methods proven to yield accurate and reproducible results. Estradiol, estrone, 13 estrogen metabolites (EM), and their sum (total estrogens) were quantified in urine and feces by liquid chromatography/tandem mass spectrometry. In feces, β-glucuronidase and β-glucosidase activities were determined by realtime kinetics, and microbiome diversity and taxonomy were estimated by pyrosequencing 16S rRNA amplicons. Pearson correlations were computed for each loge estrogen level, loge enzymatic activity level, and microbiome alpha diversity estimate. For the 55 taxa with mean relative abundance of at least 0.1%, ordinal levels were created [zero, low (below median of detected sequences), high] and compared to loge estrogens, β-glucuronidase and β-glucosidase enzymatic activity levels by linear regression. Significance was based on two-sided tests with α=0.05. Results In men and postmenopausal women, levels of total urinary estrogens (as well as most individual EM) were very strongly and directly associated with all measures of fecal microbiome richness and alpha diversity (R≥0.50, P≤0.003). These non-ovarian systemic estrogens also were strongly and significantly associated with fecal Clostridia taxa, including non-Clostridiales and three genera in the Ruminococcaceae family (R=0.57−0.70, P=0.03−0.002). Estrone, but not other EM, in urine correlated significantly with functional activity of fecal β-glucuronidase (R=0.36, P=0.04). In contrast, fecal β-glucuronidase correlated inversely with fecal total estrogens, both conjugated and deconjugated (R≤-0.47, P≤0.01). Premenopausal female estrogen levels, which were collected across menstrual cycles and thus highly variable, were completely unrelated to fecal microbiome and enzyme parameters (P≥0.6). Conclusions Intestinal microbial richness and functions, including but not limited to β-glucuronidase, influence levels of non-ovarian estrogens via enterohepatic circulation. Thus, the gut microbial community likely affects the risk for estrogen-related conditions in older adults. Understanding how Clostridia taxa relate to systemic estrogens may identify targets for interventions. Trial registration Not applicable.
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Gail MH. Comment on ‘Principles of research’ by Jerome Cornfield. Stat Med 2012; 31:2771-2. [DOI: 10.1002/sim.5390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wu LC, Grabaud BI, Gail MH. Tipping the balance of benefits and harms to favor screening mammography starting at age 40 years. Ann Intern Med 2012; 157:597; author reply 597-8. [PMID: 23070497 DOI: 10.7326/0003-4819-157-8-201210160-00019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Flores R, Shi J, Gail MH, Ravel J, Goedert JJ. Assessment of the human faecal microbiota: I. Measurement and reproducibility of selected enzymatic activities. Eur J Clin Invest 2012; 42:848-54. [PMID: 22409163 PMCID: PMC3399928 DOI: 10.1111/j.1365-2362.2012.02660.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The intestinal microbial community has major effects on human health, but optimal research methods are unsettled. To facilitate epidemiologic and clinical research, we sought to optimize conditions and to assess reproducibility of selected core functions of the distal gut microbiota, β-glucuronidase and β-glucosidase bioactivities. METHODS AND RESULTS A colorimetric kinetic method was optimized and used to quantify activities of β-glucuronidase and β-glucosidase in human faeces. Enzyme detection was optimal with neutral pH, snap freezing in liquid nitrogen and rapid thawing to 37 °C before protein extraction. Enzymatic stability was assessed by delayed freezing for 2-48 h to mimic field settings. Activities decayed approximately 20% within 2 h and 40% within 4 h at room temperature. To formally assess reproducibility, 51 volunteers (25 men; mean age 39) used two devices to self-collect and rapidly chill four replicates of a stool. Devices were compared for mean enzymatic activities and intraclass correlation coefficients (ICC) in paired replicates of the self-collected specimens. Reproducibility was excellent with both devices for β-glucuronidase (ICC 0·92). The larger collection device had significantly higher reproducibility for β-glucosidase (ICC 0·92 vs. 0·76, P < 0·0001) and higher mean activities for both enzymes (P < 0·0001). CONCLUSIONS Optimal measurement of these core activities of the microbiota required a sufficient quantity of rapidly chilled or frozen specimens collected in phosphate buffered saline at pH7·0. Application of these methods to clinical and epidemiologic research could provide insights on how the intestinal microbiota affects human health.
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Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ. Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. Eur J Clin Invest 2012; 42:855-63. [PMID: 22385292 PMCID: PMC3369017 DOI: 10.1111/j.1365-2362.2012.02659.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND We conducted a pilot study of reproducibility and associations of microbial diversity and composition in faecal microbial DNA. METHODS AND RESULTS Participants (25 men and 26 women, aged 17-65 years) provided questionnaire data and multiple samples of one stool collected with two Polymedco and two Sarstedt devices preloaded with RNAlater. 16S rRNA genes in each faecal DNA aliquot were amplified, sequenced (Roche/454 Life Sciences) and assigned to taxa. Devices were compared for ease of use and reproducibility [intraclass correlation coefficient (ICC)] between duplicate aliquots on diversity and taxonomic assignment. Associations were tested by linear regression. Both collection devices were easy to use. Both alpha diversity (Shannon index) and beta diversity (UniFrac) were higher between than within duplicates (P ≤ 10(-8) ) and did not differ significantly by device (P ≥ 0·62). Reproducibility was good (ICC≥0·77) for alpha diversity and taxonomic assignment to the most abundant phyla, Firmicutes and Bacteroidetes (71·5% and 25·0% of sequences, respectively), but reproducibility was low (ICC≤0·48) for less abundant taxa. Alpha diversity was lower with nonantibiotic prescription medication (P = 0·02), with younger age (P = 0·03) and marginally with higher body mass index (P = 0·08). CONCLUSIONS With sampling from various parts of a stool, both devices provided good reproducibility on overall microbial diversity and classification for the major phyla, but not for minor phyla. Implementation of these methods should provide insights into how broad microbial parameters, but not necessarily rare microbes, affect risk of various conditions.
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Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ. Association of fecal microbial diversity and taxonomy with selected enzymatic functions. PLoS One 2012; 7:e39745. [PMID: 22761886 PMCID: PMC3386201 DOI: 10.1371/journal.pone.0039745] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/25/2012] [Indexed: 12/26/2022] Open
Abstract
Few microbial functions have been compared to a comprehensive survey of the human fecal microbiome. We evaluated determinants of fecal microbial β-glucuronidase and β-glucosidase activities, focusing especially on associations with microbial alpha and beta diversity and taxonomy. We enrolled 51 healthy volunteers (26 female, mean age 39) who provided questionnaire data and multiple aliquots of a stool, from which proteins were extracted to quantify β-glucuronidase and β-glucosidase activities, and DNA was extracted to amplify and pyrosequence 16S rRNA gene sequences to classify and quantify microbiome diversity and taxonomy. Fecal β-glucuronidase was elevated with weight loss of at least 5 lb. (P = 0.03), whereas β-glucosidase was marginally reduced in the four vegetarians (P = 0.06). Both enzymes were correlated directly with microbiome richness and alpha diversity measures, directly with the abundance of four Firmicutes Clostridia genera, and inversely with the abundance of two other genera (Firmicutes Lactobacillales Streptococcus and Bacteroidetes Rikenellaceae Alistipes) (all P = 0.05–0.0001). Beta diversity reflected the taxonomic associations. These observations suggest that these enzymatic functions are performed by particular taxa and that diversity indices may serve as surrogates of bacterial functions. Independent validation and deeper understanding of these associations are needed, particularly to characterize functions and pathways that may be amenable to manipulation.
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