CBCRisk-Black: a personalized contralateral breast cancer risk prediction model for black women.

PURPOSE: Black breast cancer (BC) survivors have a higher risk of developing contralateral breast cancer (CBC) than Whites. Existing CBC risk prediction tools are developed based on mostly White women. To address this racial disparity, it is crucial to develop tools tailored for Black women to help them inform about their actual risk of CBC. METHODS: We propose an absolute risk prediction model, CBCRisk-Black, specifically for Black BC patients. It uses data on Black women from two sources: Breast Cancer Surveillance Consortium (BCSC) and Surveillance, Epidemiology, and End Results (SEER). First, a matched lasso logistic regression model for estimating relative risks (RR) is developed. Then, it is combined with relevant hazard rates and attributable risks to obtain absolute risks. Six-fold cross-validation is used to internally validate CBCRisk-Black. We also compare CBCRisk-Black with CBCRisk, an existing CBC risk prediction model. RESULTS: The RR model uses data from BCSC on 744 Black women (186 cases). CBCRisk-Black has four risk factors (RR compared to baseline): breast density (2.13 for heterogeneous/extremely dense), family history of BC (2.28 for yes), first BC tumor size (2.14 for T3/T4, 1.56 for TIS), and age at first diagnosis of BC (1.41 for < 40). The area under the receiver operating characteristic curve (AUC) for 3- and 5-year predictions are 0.72 and 0.65 for CBCRisk-Black while those are 0.65 and 0.60 for CBCRisk. CONCLUSION: CBCRisk-Black may serve as a useful tool to clinicians in counseling Black BC patients by providing a more accurate and personalized CBC risk estimate.

Joint risk prediction for hazardous use of alcohol, cannabis, and tobacco among adolescents: A preliminary study using statistical and machine learning.

For some, substance use during adolescence may be a stepping stone on the way to substance use disorders in adulthood. Risk prediction models may help identify adolescent users at elevated risk for hazardous substance use. This preliminary analysis used cross-sectional data (n = 270, ages 13-18) from the baseline dataset of a randomized controlled trial intervening with adolescent alcohol and/or cannabis use. Models were developed for jointly predicting quantitative scores on three measures of hazardous substance use (Rutgers Alcohol Problems Index, Adolescent Cannabis Problem Questionnaire, and Hooked on Nicotine Checklist) based on personal risk factors using two statistical and machine learning methods: multivariate covariance generalized linear models (MCGLM) and penalized multivariate regression with a lasso penalty. The predictive accuracy of a model was evaluated using root mean squared error computed via leave-one-out cross-validation. The final proposed model was an MCGLM model. It has eleven risk factors: age, early life stress, age of first tobacco use, age of first cannabis use, lifetime use of other substances, age of first use of other substances, maternal education, parental attachment, family cigarette use, family history of hazardous alcohol use, and family history of hazardous cannabis use. Different subsets of these risk factors feature in the three outcome-specific components of this joint model. The quantitative risk estimate provided by the proposed model may help identify adolescent substance users of cannabis, alcohol, and tobacco who may be at an elevated risk of developing hazardous substance use.

A preliminary risk prediction model for cannabis use disorder.

The ongoing trend toward legalization of cannabis for medicinal/recreational purposes is expected to increase the prevalence of cannabis use disorder (CUD). Thus, it is imperative to be able to predict the quantitative risk of developing CUD for a cannabis user based on their personal risk factors. Yet no such model currently exists. In this study, we perform preliminary analysis toward building such a model. The data come from n = 94 regular cannabis users recruited from Albuquerque, New Mexico during 2007-2010. As the data are cross-sectional, we only consider risk factors that remain relatively stable over time. We apply statistical and machine learning classification techniques that allow n to be small relative to the number of predictors. We use predictive accuracy estimated using leave-one-out-cross-validation to evaluate model performance. The final model is a LASSO logistic regression model consisting of the following seven risk factors: age; level of enjoyment from initial cigarette smoking; total score on Impulsive Sensation-Seeking Scale questionnaire; score on cognitive instability factor of Barratt Impulsivity Scale questionnaire; and scores on neuroticism, openness, and conscientiousness personality traits of Neuroticism, Extraversion, and Openness inventory. This model has an overall accuracy of 0.66 and the area under its receiver operating characteristic curve is 0.65. In summary, a preliminary relative risk model for predicting the quantitative risk of CUD is developed. It can be employed to identify users at high risk of CUD who may be provided with early intervention.

A Bayesian Hierarchical Framework for Pathway Analysis in Genome-Wide Association Studies.

BACKGROUND: Pathway analysis allows joint consideration of multiple SNPs belonging to multiple genes, which in turn belong to a biologically defined pathway. This type of analysis is usually more powerful than single-SNP analyses for detecting joint effects of variants in a pathway. METHODS: We develop a Bayesian hierarchical model by fully modeling the 3-level hierarchy, namely, SNP-gene-pathway that is naturally inherent in the structure of the pathways, unlike the currently used ad hoc ways of combining such information. We model the effects at each level conditional on the effects of the levels preceding them within the generalized linear model framework. To deal with the high dimensionality, we regularize the regression coefficients through an appropriate choice of priors. The model is fit using a combination of iteratively weighted least squares and expectation-maximization algorithms to estimate the posterior modes and their standard errors. A normal approximation is used for inference. RESULTS: We conduct simulations to study the proposed method and find that our method has higher power than some standard approaches in several settings for identifying pathways with multiple modest-sized variants. We illustrate the method by analyzing data from two genome-wide association studies on breast and renal cancers. CONCLUSION: Our method can be helpful in detecting pathway association.

Dose-dependent effect of mammographic breast density on the risk of contralateral breast cancer.

PURPOSE: Increased mammographic breast density is a significant risk factor for breast cancer. It is not clear if it is also a risk factor for the development of contralateral breast cancer. METHODS: The data were obtained from Breast Cancer Surveillance Consortium and included women diagnosed with invasive breast cancer or ductal carcinoma in situ between ages 18 and 88 and years 1995 and 2009. Each case of contralateral breast cancer was matched with three controls based on year of first breast cancer diagnosis, race, and length of follow-up. A total of 847 cases and 2541 controls were included. The risk factors included in the study were mammographic breast density, age of first breast cancer diagnosis, family history of breast cancer, anti-estrogen treatment, hormone replacement therapy, menopausal status, and estrogen receptor status, all from the time of first breast cancer diagnosis. Both univariate analysis and multivariate conditional logistic regression analysis were performed. RESULTS: In the final multivariate model, breast density, family history of breast cancer, and anti-estrogen treatment remained significant with p values less than 0.01. Increasing breast density had a dose-dependent effect on the risk of contralateral breast cancer. Relative to 'almost entirely fat' category of breast density, the adjusted odds ratios (and p values) in the multivariate analysis for 'scattered density,' 'heterogeneously dense,' and 'extremely dense' categories were 1.65 (0.036), 2.10 (0.002), and 2.32 (0.001), respectively. CONCLUSION: Breast density is an independent and significant risk factor for development of contralateral breast cancer. This risk factor should contribute to clinical decision making.

A model for individualized risk prediction of contralateral breast cancer.

PURPOSE: Patients diagnosed with invasive breast cancer (BC) or ductal carcinoma in situ are increasingly choosing to undergo contralateral prophylactic mastectomy (CPM) to reduce their risk of contralateral BC (CBC). This is a particularly disturbing trend as a large proportion of these CPMs are believed to be medically unnecessary. Many BC patients tend to substantially overestimate their CBC risk. Thus, there is a pressing need to educate patients effectively on their CBC risk. We develop a CBC risk prediction model to aid physicians in this task. METHODS: We used data from two sources: Breast Cancer Surveillance Consortium and Surveillance, Epidemiology, and End Results to build the model. The model building steps are similar to those used in developing the BC risk assessment tool (popularly known as Gail model) for counseling women on their BC risk. Our model, named CBCRisk, is exclusively designed for counseling women diagnosed with unilateral BC on the risk of developing CBC. RESULTS: We identified eight factors to be significantly associated with CBC-age at first BC diagnosis, anti-estrogen therapy, family history of BC, high-risk pre-neoplasia status, estrogen receptor status, breast density, type of first BC, and age at first birth. Combining the relative risk estimates with the relevant hazard rates, CBCRisk projects absolute risk of developing CBC over a given period. CONCLUSIONS: By providing individualized CBC risk estimates, CBCRisk may help in counseling of BC patients. In turn, this may potentially help alleviate the rate of medically unnecessary CPMs.

Characterization of Cement Particles Found in Peri-implantitis-Affected Human Biopsy Specimens.

PURPOSE: Peri-implantitis is a disease characterized by soft tissue inflammation and continued loss of supporting bone, which can result in implant failure. Peri-implantitis is a multifactorial disease, and one of its triggering factors may be the presence of excess cement in the soft tissues surrounding an implant. This descriptive study evaluated the composition of foreign particles from 36 human biopsy specimens with 19 specimens selected for analysis. The biopsy specimens were obtained from soft tissues affected by peri-implantitis around cement-retained implant crowns and compared with the elemental composition of commercial luting cement. MATERIALS AND METHODS: Nineteen biopsy specimens were chosen for the comparison, and five test cements (TempBond, Telio, Premier Implant Cement, Intermediate Restorative Material, and Relyx) were analyzed using scanning electron microscopy equipped with energy dispersive x-ray spectroscopy. This enabled the identification of the chemical composition of foreign particles embedded in the tissue specimens and the composition of the five cements. Statistical analysis was conducted using classification trees to pair the particles present in each specimen with the known cements. RESULTS: The particles in each biopsy specimen could be associated with one of the commercial cements with a level of probability ranging between .79 and 1. TempBond particles were found in one biopsy specimen, Telio particles in seven, Premier Implant Cement particles in four, Relyx particles in four, and Intermediate Restorative Material particles in three. CONCLUSION: Particles found in human soft tissue biopsy specimens around implants affected by peri-implant disease were associated with five commercially available dental cements.

Krüppel-like Factor 4 activates HBG gene expression in primary erythroid cells.

The SP1/Krüppel-like Factor (SP1/KLF) family of transcription factors plays a role in diverse cellular processes, including proliferation, differentiation and control of gene transcription. The discovery of KLF1 (EKLF), a key regulator of HBB (ß-globin) gene expression, expanded our understanding of the role of KLFs in erythropoiesis. In this study, we investigated a mechanism of HBG (γ-globin) regulation by KLF4. siRNA-mediated gene silencing and enforced expression of KLF4 in K562 cells substantiated the ability of KLF4 to positively regulate endogenous HBG gene transcription. The physiological significance of this finding was confirmed in primary erythroid cells, where KLF4 knockdown at day 11 significantly attenuated HBG mRNA levels and enforced expression at day 28 stimulated the silenced HBG genes. In vitro binding characterization using the γ-CACCC and ß-CACCC probes demonstrated KLF4 preferentially binds the endogenous γ-CACCC, while CREB binding protein (CREBBP) binding was not selective. Co-immunoprecipitation studies confirmed protein-protein interaction between KLF4 and CREBBP. Furthermore, sequential chromatin immunoprecipitation assays showed co-localization of both factors in the γ-CACCC region. Subsequent luciferase reporter studies demonstrated that KLF4 trans-activated HBG promoter activity and that CREBBP enforced expression resulted in gene repression. Our data supports a model of antagonistic interaction of KLF4/CREBBP trans-factors in HBG regulation.

Critical analysis of prostate-specific antigen doubling time calculation methodology.

BACKGROUND: Prostate-specific antigen (PSA) doubling time (PSADT) has emerged as an important surrogate marker of disease progression and survival in men with prostate carcinoma. The literature is replete with different methods for calculating PSADT. The objective of the current study was to identify the method that best described PSA growth over time and predicted disease-specific survival in men with androgen-independent prostate carcinoma. METHODS: PSADT was calculated for 122 patients with androgen-independent prostate carcinoma using 2 commonly used methods: best-line fit (BLF) and first and last observations (FLO). Then, PSADT was calculated by using both a random coefficient linear (RCL) model and a random coefficient quadratic (RCQ) model. Statistical analysis was used to compare the ability of the methods to fit the patients' PSA profiles and to predict disease-specific survival. RESULTS: The RCQ model provided the best fit of the patients' PSA profiles, as determined according to the significance of the added parameters for the RCQ equation (P < or = 0.002). The PSADT estimates from the FLO method, the RCL model, and the RCQ model were highly significant predictors (P < 0.001) of disease-specific survival, whereas estimates from the BLF method were not found to be significant predictors (P = 0.66). PSADT estimates from the RCQ and RCL models provided an improved correlation of disease-specific survival (both R(2) = 0.55) compared to the FLO (R(2) = 0.11) and BFL (R(2) = 0.003) methods. CONCLUSIONS: Random coefficient methods provided a more reliable fit of PSA profiles than other models and were superior to other available models for predicting disease-specific survival in patients with androgen-independent prostate carcinoma. The authors concluded that consideration should be given to applying the RCL or RCQ models in future assessments of PSADT as a predictive parameter.