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2. Development and Validation of a Novel Integrated Clinical-Genomic Risk Group Classification for Localized Prostate Cancer

Author

Spratt, Daniel E, Zhang, Jingbin, Santiago-Jiménez, María, Dess, Robert T, Davis, John W, Den, Robert B, Dicker, Adam P, Kane, Christopher J, Pollack, Alan, Stoyanova, Radka, Abdollah, Firas, Ross, Ashley E, Cole, Adam, Uchio, Edward, Randall, Josh M, Nguyen, Hao, Zhao, Shuang G, Mehra, Rohit, Glass, Andrew G, Lam, Lucia LC, Chelliserry, Jijumon, du Plessis, Marguerite, Choeurng, Voleak, Aranes, Maria, Kolisnik, Tyler, Margrave, Jennifer, Alter, Jason, Jordan, Jennifer, Buerki, Christine, Yousefi, Kasra, Haddad, Zaid, Davicioni, Elai, Trabulsi, Edouard J, Loeb, Stacy, Tewari, Ashutosh, Carroll, Peter R, Weinmann, Sheila, Schaeffer, Edward M, Klein, Eric A, Karnes, R Jeffrey, Feng, Felix Y, and Nguyen, Paul L

Subjects
Urologic Diseases, Prevention, Clinical Research, Cancer, Prostate Cancer, Genetics, Human Genome, Aging, 4.2 Evaluation of markers and technologies, Detection, screening and diagnosis, Aged, Genomics, Humans, Male, Middle Aged, Prognosis, Prostatic Neoplasms, Risk, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

Purpose It is clinically challenging to integrate genomic-classifier results that report a numeric risk of recurrence into treatment recommendations for localized prostate cancer, which are founded in the framework of risk groups. We aimed to develop a novel clinical-genomic risk grouping system that can readily be incorporated into treatment guidelines for localized prostate cancer. Materials and Methods Two multicenter cohorts (n = 991) were used for training and validation of the clinical-genomic risk groups, and two additional cohorts (n = 5,937) were used for reclassification analyses. Competing risks analysis was used to estimate the risk of distant metastasis. Time-dependent c-indices were constructed to compare clinicopathologic risk models with the clinical-genomic risk groups. Results With a median follow-up of 8 years for patients in the training cohort, 10-year distant metastasis rates for National Comprehensive Cancer Network (NCCN) low, favorable-intermediate, unfavorable-intermediate, and high-risk were 7.3%, 9.2%, 38.0%, and 39.5%, respectively. In contrast, the three-tier clinical-genomic risk groups had 10-year distant metastasis rates of 3.5%, 29.4%, and 54.6%, for low-, intermediate-, and high-risk, respectively, which were consistent in the validation cohort (0%, 25.9%, and 55.2%, respectively). C-indices for the clinical-genomic risk grouping system (0.84; 95% CI, 0.61 to 0.93) were improved over NCCN (0.73; 95% CI, 0.60 to 0.86) and Cancer of the Prostate Risk Assessment (0.74; 95% CI, 0.65 to 0.84), and 30% of patients using NCCN low/intermediate/high would be reclassified by the new three-tier system and 67% of patients would be reclassified from NCCN six-tier (very-low- to very-high-risk) by the new six-tier system. Conclusion A commercially available genomic classifier in combination with standard clinicopathologic variables can generate a simple-to-use clinical-genomic risk grouping that more accurately identifies patients at low, intermediate, and high risk for metastasis and can be easily incorporated into current guidelines to better risk-stratify patients.

Published
2018

3. Individual Patient-Level Meta-Analysis of the Performance of the Decipher Genomic Classifier in High-Risk Men After Prostatectomy to Predict Development of Metastatic Disease

Author

Spratt, Daniel E, Yousefi, Kasra, Deheshi, Samineh, Ross, Ashley E, Den, Robert B, Schaeffer, Edward M, Trock, Bruce J, Zhang, Jingbin, Glass, Andrew G, Dicker, Adam P, Abdollah, Firas, Zhao, Shuang G, Lam, Lucia LC, du Plessis, Marguerite, Choeurng, Voleak, Haddad, Zaid, Buerki, Christine, Davicioni, Elai, Weinmann, Sheila, Freedland, Stephen J, Klein, Eric A, Karnes, R Jeffrey, and Feng, Felix Y

Subjects
Aging, Cancer, Prevention, Aged, Biomarkers, Tumor, Follow-Up Studies, Humans, Male, Middle Aged, Multivariate Analysis, Neoplasm Grading, Neoplasm Metastasis, Nomograms, Prognosis, Prostatectomy, Prostatic Neoplasms, Risk Assessment, Risk Factors, Clinical Sciences, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

Purpose To perform the first meta-analysis of the performance of the genomic classifier test, Decipher, in men with prostate cancer postprostatectomy. Methods MEDLINE, EMBASE, and the Decipher genomic resource information database were searched for published reports between 2011 and 2016 of men treated by prostatectomy that assessed the benefit of the Decipher test. Multivariable Cox proportional hazards models fit to individual patient data were performed; meta-analyses were conducted by pooling the study-specific hazard ratios (HRs) using random-effects modeling. Extent of heterogeneity between studies was determined with the I2 test. Results Five studies (975 total patients, and 855 patients with individual patient-level data) were eligible for analysis, with a median follow-up of 8 years. Of the total cohort, 60.9%, 22.6%, and 16.5% of patients were classified by Decipher as low, intermediate, and high risk, respectively. The 10-year cumulative incidence metastases rates were 5.5%, 15.0%, and 26.7% ( P < .001), respectively, for the three risk classifications. Pooling the study-specific Decipher HRs across the five studies resulted in an HR of 1.52 (95% CI, 1.39 to 1.67; I2 = 0%) per 0.1 unit. In multivariable analysis of individual patient data, adjusting for clinicopathologic variables, Decipher remained a statistically significant predictor of metastasis (HR, 1.30; 95% CI, 1.14 to 1.47; P < .001) per 0.1 unit. The C-index for 10-year distant metastasis of the clinical model alone was 0.76; this increased to 0.81 with inclusion of Decipher. Conclusion The genomic classifier test, Decipher, can independently improve prognostication of patients postprostatectomy, as well as within nearly all clinicopathologic, demographic, and treatment subgroups. Future study of how to best incorporate genomic testing in clinical decision-making and subsequent treatment recommendations is warranted.

Published
2017

6. Data from A Long-term Prospective Study of Type-Specific Human Papillomavirus Infection and Risk of Cervical Neoplasia Among 20,000 Women in the Portland Kaiser Cohort Study

Author

Schiffman, Mark, primary, Glass, Andrew G., primary, Wentzensen, Nicolas, primary, Rush, Brenda B., primary, Castle, Philip E., primary, Scott, David R., primary, Buckland, Julie, primary, Sherman, Mark E., primary, Rydzak, Greg, primary, Kirk, Peter, primary, Lorincz, Attila T., primary, Wacholder, Sholom, primary, and Burk, Robert D., primary

Published
2023
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7. Supplementary Tables 1-2 from A Long-term Prospective Study of Type-Specific Human Papillomavirus Infection and Risk of Cervical Neoplasia Among 20,000 Women in the Portland Kaiser Cohort Study

Author

Schiffman, Mark, primary, Glass, Andrew G., primary, Wentzensen, Nicolas, primary, Rush, Brenda B., primary, Castle, Philip E., primary, Scott, David R., primary, Buckland, Julie, primary, Sherman, Mark E., primary, Rydzak, Greg, primary, Kirk, Peter, primary, Lorincz, Attila T., primary, Wacholder, Sholom, primary, and Burk, Robert D., primary

Published
2023
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8. Supplementary Tables 3-4 from A Long-term Prospective Study of Type-Specific Human Papillomavirus Infection and Risk of Cervical Neoplasia Among 20,000 Women in the Portland Kaiser Cohort Study

Author

Schiffman, Mark, primary, Glass, Andrew G., primary, Wentzensen, Nicolas, primary, Rush, Brenda B., primary, Castle, Philip E., primary, Scott, David R., primary, Buckland, Julie, primary, Sherman, Mark E., primary, Rydzak, Greg, primary, Kirk, Peter, primary, Lorincz, Attila T., primary, Wacholder, Sholom, primary, and Burk, Robert D., primary

Published
2023
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13. Mammographic Density Decline, Tamoxifen Response, and Prognosis by Molecular Characteristics of Estrogen Receptor–Positive Breast Cancer

Author

Abubakar, Mustapha, primary, Mullooly, Maeve, additional, Nyante, Sarah, additional, Pfeiffer, Ruth M, additional, Aiello Bowles, Erin J, additional, Cora, Renata, additional, Bodelon, Clara, additional, Butler, Eboneé, additional, Butcher, Donna, additional, Sternberg, Lawrence, additional, Troester, Melissa A, additional, Weinmann, Sheila, additional, Sherman, Mark, additional, Glass, Andrew G, additional, Berrington de Gonzalez, Amy, additional, and Gierach, Gretchen L, additional

Published
2022
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26. Additional file 1 of Risk factors for breast cancer development by tumor characteristics among women with benign breast disease

Author

Figueroa, Jonine D., Gierach, Gretchen L., Duggan, Máire A., Shaoqi Fan, Pfeiffer, Ruth M., Yihong Wang, Falk, Roni T., Loudig, Olivier, Abubakar, Mustapha, Ginsberg, Mindy, Kimes, Teresa M., Richert-Boe, Kathryn, Glass, Andrew G., and Rohan, Thomas E.

Subjects
skin and connective tissue diseases
Abstract

Additional file 1: Supplemental methods. Supplementary Figure 1. Steps of multiple imputation (for more details see Appendix A). Supplementary Table 1. Characteristics of BBD histology and breast cancers among cases by calendar year of BBD and breast cancer diagnoses (N = 514). Supplemental Table 2. Comparison of associations between select patient characteristics and histologic features with breast cancer risk in conditional and unconditional logistic regression models using multiple imputation dataset (N = 1028). Supplemental Table 3. Associations between select patient characteristics and histologic features with breast cancer risk by tumor grade (N = 922). Supplemental Table 4. Associations between select patient characteristics and histologic features with breast cancer risk by tumor size (N = 1013). Supplementary Table 5. Associations between demographic and histologic features with breast cancer risk by BBD calendar year before vs. after 1993 (N = 1028). Appendix A. Distribution of numeric variables before (top) and after (bottom) multiple imputations.

Published
2021
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27. Abnormal outcomes following cervical cancer screening: event duration and health utility loss

Author

Insinga, Ralph P., Glass, Andrew G., Myers, Evan R., and Rush, Brenda B.

Subjects
Women -- Care and treatment -- Methods, Cancer -- Diagnosis, Cervical cancer -- Diagnosis -- Care and treatment, Pap test -- Methods, Health, Diagnosis, Care and treatment, Methods
Abstract

Background. For decision analytic models, little empirical data are available from which to model the amount of time women spend with various cervical cytologic and histologic diagnoses following an abnormal [...]

Published
2007

28. Relation of Quantitative Histologic and Radiologic Breast Tissue Composition Metrics With Invasive Breast Cancer Risk

Author

Abubakar, Mustapha, primary, Fan, Shaoqi, additional, Bowles, Erin Aiello, additional, Widemann, Lea, additional, Duggan, Máire A, additional, Pfeiffer, Ruth M, additional, Falk, Roni T, additional, Lawrence, Scott, additional, Richert-Boe, Kathryn, additional, Glass, Andrew G, additional, Kimes, Teresa M, additional, Figueroa, Jonine D, additional, Rohan, Thomas E, additional, and Gierach, Gretchen L, additional

Published
2021
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30. High NRBP1 expression in prostate cancer is linked with poor clinical outcomes and increased cancer cell growth

Author

Ruiz, Christian, Oeggerli, Martin, Germann, Markus, Gluderer, Silvia, Stocker, Hugo, Andreozzi, Mariacarla, Thalmann, George N., Cecchini, Marco G., Zellweger, Tobias, Stürm, Susanna, Koivisto, Pasi A., Helin, Heikki J., Gelmann, Edward P., Glass, Andrew G., Gasser, Thomas C., Terracciano, Luigi M., Bachmann, Alexander, Wyler, Stephen, Bubendorf, Lukas, and Rentsch, Cyrill A.

Published
2012
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32. Relation of Quantitative Histologic and Radiologic Breast Tissue Composition Metrics with Invasive Breast Cancer Risk

Author

Abubakar, Mustapha, primary, Fan, Shaoqi, additional, Bowles, Erin Aiello, additional, Widemann, Lea, additional, Duggan, Máire A., additional, Pfeiffer, Ruth M., additional, Falk, Roni T., additional, Lawrence, Scott, additional, Richert-Boe, Kathryn, additional, Glass, Andrew G., additional, Kimes, Teresa M., additional, Figueroa, Jonine D., additional, Rohan, Thomas E., additional, and Gierach, Gretchen L., additional

Published
2020
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43. Absolute risk of a subsequent abnormal Pap among oncogenic human papillomavirus DNA-positive, cytologically negative women

Author

Castle, Philip E., Wacholder, Sholom, Sherman, Mark E., Lorincz, Attila T., Glass, Andrew G., Scott, David R., Rush, Brenda B., Demuth, Franklin, and Schiffman, Mark

Subjects
Papillomavirus infections -- Diagnosis, Papillomavirus infections -- Physiological aspects, Pap test -- Methods, Pap test -- Analysis, Cervical cancer -- Diagnosis, Cervical cancer -- Physiological aspects, Health
Published
2002

44. Diagnostic X-ray procedures and risk of leukemia, lymphoma, and multiple myeloma

Author

Boice, John D., Jr., Morin, Michele M., Glass, Andrew G., Friedman, Gary D., Stovall, Marilyn, Hoover, Robert N., and Fraumeni, Joseph F., Jr.

Subjects
Radiography, Medical -- Health aspects, Leukemia -- Risk factors, Lymphomas -- Risk factors, Multiple myeloma -- Risk factors, X-rays -- Health aspects
Abstract

A recent report from a committee of the National Academy of Sciences indicated that the lifetime cancer risk from low doses of radiation may be higher than is usually believed, raising questions about the potential dangers of diagnostic X-ray procedures. Research concerning this issue has suffered from methodologic limitations and from limitations inherent in the problem itself (for example, the possibility that X-rays are often performed because of symptoms of already-present disease). To learn more about the potential dangers of diagnostic X-rays, a case-control study of a large number of patients enrolled in two prepaid health plans was carried out. This approach identifies people with the diseases of interest, called cases (leukemia, non-Hodgkin's lymphoma, and multiple myeloma, representing malignancies of blood cells in which low-dose radiation has been implicated), and compares them with disease-free patients of similar age, sex, and health plan membership duration, called controls. Cases and controls were compared for their histories of diagnostic X-rays to arrive at a cumulative bone marrow dose for each subject. Results showed that slightly more than half of the 25,421 procedures performed for these patients were chest X-rays, with an average of 11.6 X-ray procedures per patient. The 207 cases with chronic lymphocytic leukemia (CLL, a slowly-progressing disorder) had been exposed to diagnostic radiation less frequently than the 238 CLL controls. For all other leukemias combined (358 cases), a nonsignificant elevation of risk (relative risk, 1.17) was seen for cases but there was no dose-response relationship after X-rays given just prior to disease diagnosis were excluded; this was also the case for non-Hodgkin's lymphoma. Thus there was little support for an association between diagnostic X-rays and the causation of either leukemia or non-Hodgkin's lymphoma. Large numbers of X-ray procedures did seem to increase the risk of multiple myeloma: those with the highest number of exposures were at a four-fold greater risk for this disease. The findings suggest that diagnostic X-rays are not a significant health hazard, but that unnecessary procedures should be avoided. (Consumer Summary produced by Reliance Medical Information, Inc.)

Published
1991

48. Determinants of genital human papillomavirus infection in low-risk women in Portland, Oregon

Author

Bauer, Heidi M., Hildesheim, Allan, Schiffman, Mark H., Glass, Andrew G., Rush, Brenda B., Scott, David R., Cadell, Diane M., Kurman, Robert J., and Manos, M. Michele

Subjects
Papillomavirus infections -- Risk factors, Women -- Diseases, Health
Abstract

Objectives: To confirm the risk factors for genital human papillomavirus (HPV) infection. Goal of this study. To investigate risk factors for HPV detection independent of the correlated risk factors for cervical neoplasia in a low-risk population. Study Design: HPV DNA was assessed among 483 cytologically normal women with no known history of cervical neoplasia. A cervicovaginal lavage was collected for HPV detection and typing using a PCR-based DNA amplification system. Information on risk factors of subjects was obtained through a questionnaire. Results. HPV DNA was found in 17.7% of study women. On univariate analysis, factors associated with increasing HPV prevalence included younger age, fewer years of education, lower income, higher lifetime number of sex partners, lower age at first intercourse, nulliparity, oral contraceptive use, and current smoking. After statistical adjustment, we found younger age and higher number of sex partners were strongly and independently associated with higher HPV prevalence. We also observed increased HPV prevalence among women with lower levels of education and lower incomes. Conclusion: These findings and corroborative data from the companion reports in this issue of the journal support the sexual route of transmission of the virus., Women who become sexually active at a young age and have multiple sex partners may be at greater risk for genital human papillomavirus infection. Genital human papillomavirus (HPV) is responsible for genital warts and is suspected of causing cervical cancer. A study to determine the prevalence of HPV infection among low-risk women included 453 women between the ages 16 and 81 in Portland, OR. Their average age was 34 years. Vaginal surface cells and blood samples were taken from each subject. HPV was detected in 17.7% of the specimens. Women from 16 to 24 years old had the highest rate of infection among all age groups at 32.1%. In addition, women who had first intercourse before age 16 had an infection rate of 31.9%. Those who were 21 years of age or older at first intercourse had an HPV infection rate of only 8.6%. Subjects with a lifetime number of six to nine sex partners had an infection rate of 28.8%.

Published
1993

49. Epidemiologic evidence showing that human papillomavirus infection causes most cervical intraepithelial neoplasia

Author

Schiffman, Mark H., Bauer, Heidi M., Hoover, Robert N., Glass, Andrew G., Cadell, Diane M., Rush, Brenda B., Scott, David R., Sherman, Mark E., Kurman, Robert J., Wacholder, Sholom, Stanton, Cynthia K., and Manos, M. Michele

Subjects
Papillomavirus infections -- Complications, Cervix dysplasia -- Causes of, Precancerous conditions -- Causes of, Health
Abstract

Background: Experimental studies have provided strong evidence that human papillomavirus (HPV) is the long-sought venereal cause of cervical neoplasia, but the epidemiologic evidence has been inconsistent. Purpose: Given improvements in HPV testing that have revealed a strong link between sexual activity history and cervical HPV infection, we conducted a large case-control study of HPV and cervical intraepithelial neoplasia (CIN) to evaluate whether sexual behavior and the other established risk factors for CIN influence risk primarily via HPV infection. Methods: We studied 500 women with CIN and 500 control subjects receiving cytologic screening at Kaiser Permanente, a large prepaid health plan, in Portland, Ore. The established epidemiologic risk factors for CIN were assessed by telephone interview. We performed HPV testing of cervicovaginal lavage specimens by gene amplification using polymerase chain reaction with a consensus primer to target the L1 gene region of HPV. Unconditional logistic regression analysis was used to estimate relative risk of CIN and to adjust the epidemiologic associations for HPV test results to demonstrate whether the associations were mediated by HPV. Results: The case subjects demonstrated the typical epidemiologic profile of CIN: They had more sex partners, more cigarette smoking, earlier ages at first sexual intercourse, and lower socioeconomic status. Statistical adjustment for HPV infection substantially reduced the size of each of these case-control differences. Seventy-six percent of cases could be attributed to HPV infection; the results of cytologic review suggested that the true percentage was even higher. Once HPV infection was taken into account, an association of parity with risk of CIN was observed in both HPV-negative and HPV-positive women. Conclusion: The data show that the great majority of all grades of CIN can be attributed to HPV infection, particularly with the cancer-associated types of HPV. Implications: In light of this conclusion, the investigation of the natural history of HPV has preventive as well as etiologic importance. [J Natl Cancer Inst 85:958-964, 1993]

Published
1993

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