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ABSTRACT: As genotyping for Lynch syndrome has become widespread, more and more people are being counseled about whether to be genotyped
for mutations in mismatch repair genes. Recently a number of quantitative models have been developed to identify potential
Lynch syndrome patients and serve as decision aids for patients at genetic counseling clinics. In contrast to existing clinical
guidelines that give dichotomous classifications, these models provide a probability that a family or individual has Lynch
syndrome. These models have been shown to be useful tools in identifying likely carriers of Lynch syndrome mutations. Correctly
used, they have the potential to greatly improve the current diagnosis and management of Lynch syndrome families. To help
clinicians and genetic counseling professionals understand the differences among these models and use the models wisely, we
review the key features of each model and offer some guidelines on their use.
Current Colorectal Cancer Reports 04/2012; 3(4):206-211.
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ABSTRACT: Major efforts to sequence cancer genomes are now occurring throughout the world. Though the emerging data from these studies are illuminating, their reconciliation with epidemiologic and clinical observations poses a major challenge. In the current study, we provide a mathematical model that begins to address this challenge. We model tumors as a discrete time branching process that starts with a single driver mutation and proceeds as each new driver mutation leads to a slightly increased rate of clonal expansion. Using the model, we observe tremendous variation in the rate of tumor development-providing an understanding of the heterogeneity in tumor sizes and development times that have been observed by epidemiologists and clinicians. Furthermore, the model provides a simple formula for the number of driver mutations as a function of the total number of mutations in the tumor. Finally, when applied to recent experimental data, the model allows us to calculate the actual selective advantage provided by typical somatic mutations in human tumors in situ. This selective advantage is surprisingly small--0.004 ± 0.0004--and has major implications for experimental cancer research.
Proceedings of the National Academy of Sciences 09/2010; 107(43):18545-50. · 9.68 Impact Factor
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ABSTRACT: Large-scale sequencing of cancer genomes has uncovered thousands of DNA alterations, but the functional relevance of the majority of these mutations to tumorigenesis is unknown. We have developed a computational method, called Cancer-specific High-throughput Annotation of Somatic Mutations (CHASM), to identify and prioritize those missense mutations most likely to generate functional changes that enhance tumor cell proliferation. The method has high sensitivity and specificity when discriminating between known driver missense mutations and randomly generated missense mutations (area under receiver operating characteristic curve, >0.91; area under Precision-Recall curve, >0.79). CHASM substantially outperformed previously described missense mutation function prediction methods at discriminating known oncogenic mutations in P53 and the tyrosine kinase epidermal growth factor receptor. We applied the method to 607 missense mutations found in a recent glioblastoma multiforme sequencing study. Based on a model that assumed the glioblastoma multiforme mutations are a mixture of drivers and passengers, we estimate that 8% of these mutations are drivers, causally contributing to tumorigenesis.
Cancer Research 08/2009; 69(16):6660-7. · 7.86 Impact Factor
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Journal of Clinical Oncology 01/2009; 27(4):642-3; author reply 643-4. · 18.37 Impact Factor
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ABSTRACT: Voxel-based morphometry (VBM) is widely used as a high-resolution approach to understanding the relationship between anatomical structures and variables of interest. Controlling for the false discovery rate (FDR) is an attractive choice for thresholding the resulting statistical maps and has been commonly used in fMRI studies. However, we caution against the use of nonadaptive FDR control procedures, such as the most commonly used Benjamini-Hochberg procedure (B-H), in VBM analyses. This is because, in VBM analyses, specific risk factors may be associated with volume change in a global, rather than local, manner, which means the proportion of truly associated voxels among all voxels is large. In such a case, the achieved FDR obtained by nonadaptive procedures can be substantially lower than the nominal, or controlled, level. Such conservatism deprives researchers of power for detecting true associations. In this article, we advocate for the use of adaptive FDR control in VBM-type analyses. Specifically, we examine two representative adaptive procedures: the two-stage step-up procedure by Benjamini, Krieger and Yekutieli (2006: Biometrika 93:491-507) and the procedure of Storey and Tibshirani ([2003]: Proc Natl Acad Sci USA 100:9440-9445). We demonstrate mathematically, with simulations, and with a data example that these procedures provide improved performance over the B-H procedure.
Human Brain Mapping 12/2008; 30(7):2304-11. · 5.88 Impact Factor
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ABSTRACT: Oxidative stress-mediated destruction of normal parenchymal cells during hepatic inflammatory responses contributes to the pathogenesis of immune-mediated hepatitis and is implicated in the progression of acute inflammatory liver injury to chronic inflammatory liver disease. The transcription factor NF-E2-related factor 2 (Nrf2) regulates the expression of a battery of antioxidative enzymes and Nrf2 signaling can be activated by small-molecule drugs that disrupt Keap1-mediated repression of Nrf2 signaling. Therefore, genetic and pharmacologic approaches were used to activate Nrf2 signaling to assess protection against inflammatory liver injury. Profound increases in indicators of cell death were observed in both Nrf2 wild-type (Nrf2-WT) mice and Nrf2-disrupted (Nrf2-KO) mice 24 h following intravenous injection of concanavalin A (12.5 mg/kg, ConA), a model for T cell-mediated acute inflammatory liver injury. However, hepatocyte-specific conditional Keap1 null (Alb-Cre:Keap1(flox/-), cKeap1-KO) mice with constitutively enhanced expression of Nrf2-regulated antioxidative genes as well as Nrf2-WT mice but not Nrf2-KO mice pretreated with three daily doses of a triterpenoid that potently activates Nrf2 (30 mumol/kg, cyano-3,12-dioxooleana-1,9(11)-dien-28-oyl-imidazolide [CDDO-Im]) were highly resistant to ConA-mediated inflammatory liver injury. CDDO-Im pretreatment of both Nrf2-WT and Nrf2-KO mice resulted in equivalent suppression of serum proinflammatory soluble proteins suggesting that the hepatoprotection afforded by CDDO-Im pretreatment of Nrf2-WT mice but not Nrf2-KO mice was not due to suppression of systemic proinflammatory signaling, but instead was due to activation of Nrf2 signaling in the liver. Enhanced hepatic expression of Nrf2-regulated antioxidative genes inhibited inflammation-mediated oxidative stress, thereby preventing hepatocyte necrosis. Attenuation of hepatocyte death in cKeap1-KO mice and CDDO-Im pretreated Nrf2-WT mice resulted in decreased late-phase proinflammatory gene expression in the liver thereby diminishing the sustained influx of inflammatory cells initially stimulated by the ConA challenge. Taken together, these results clearly illustrate that targeted cytoprotection of hepatocytes through Nrf2 signaling during inflammation prevents the amplification of inflammatory responses in the liver.
Toxicological Sciences 08/2008; 104(1):218-27. · 4.65 Impact Factor
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ABSTRACT: Previous work showed that individual airway size, before any spasmogen, varied widely in the same animals on different days. The effect of this variable baseline size on the airway response to a subsequent challenge is unknown. The present study examined how the variability in individual airway baseline size in dogs was related to that after methacholine challenge on 4 different days using high-resolution computed tomography scans. Dogs were anesthetized and ventilated, and on 4 separate days randomly varying between 1 and 8 wk apart, baseline scans were acquired, followed by a continuous intravenous infusion of methacholine at three rates in increasing order (17, 67, and 200 microg/min). As the measure of variability, we used the coefficient of variation (CV) of the four airway luminal measurements of each airway at baseline and at each dose of methacholine. For most airways, there was wide variability both between and within dogs in the response to a given dose of methacholine (CV = 33-38%). Airways with any level of methacholine stimulation had greater variability than those at baseline. The airway variability was greatest at the lowest dose of methacholine administered but was elevated at all the doses. In conclusion, there was substantial day-to-day variability in baseline airway size. Most importantly, the same dose of methacholine to the same individual airway showed even greater variability than that at baseline. If we consider that increased heterogeneity may potentiate clinical symptoms, then airway response variability may play an important role in the manifestation of airway disease.
Journal of Applied Physiology 06/2008; 104(5):1381-6. · 3.75 Impact Factor
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ABSTRACT: Mendelian models can predict who carries an inherited deleterious mutation of known disease genes based on family history. For example, the BRCAPRO model is commonly used to identify families who carry mutations of BRCA1 and BRCA2, based on familial breast and ovarian cancers. These models incorporate the age of diagnosis of diseases in relatives and current age or age of death. We develop a rigorous foundation for handling multiple diseases with censoring. We prove that any disease unrelated to mutations can be excluded from the model, unless it is sufficiently common and dependent on a mutation-related disease time. Furthermore, if a family member has a disease with higher probability density among mutation carriers, but the model does not account for it, then the carrier probability is deflated. However, even if a family only has diseases the model accounts for, if the model excludes a mutation-related disease, then the carrier probability will be inflated. In light of these results, we extend BRCAPRO to account for surviving all non-breast/ovary cancers as a single outcome. The extension also enables BRCAPRO to extract more useful information from male relatives. Using 1500 families from the Cancer Genetics Network, accounting for surviving other cancers improves BRCAPRO's concordance index from 0.758 to 0.762 (p=0.046), improves its positive predictive value from 35 to 39 per cent (p<10(-6)) without impacting its negative predictive value, and improves its overall calibration, although calibration slightly worsens for those with carrier probability<10 per cent.
Statistics in Medicine 05/2008; 27(22):4532-48. · 1.88 Impact Factor
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ABSTRACT: The authors used cross-sectional data (2001-2003) to consider the pathway through which past occupational lead exposure impacts cognitive function. They were motivated by studies linking cumulative lead dose with brain volumes, volumes with cognitive function, and lead dose with cognitive function. It was hypothesized that the brain regions associated with lead mediate a portion of the relation between lead dose and cognitive function. Data were derived from an ongoing US study of 513 former organolead manufacturing workers. Magnetic resonance imaging was used to perform a novel analysis to investigate mediation. Volumes associated with cognitive function and lead dose were derived by using registered images and were used in a subsequent mediation analysis. Cumulative lead dose was associated with adverse function in the visuo-construction, executive function, and eye-hand coordination domains. Regarding these domains, there was strong evidence of volumetric mediation of lead's effect on cognition in the visuo-construction domain and a moderate amount for executive function and eye-hand coordination. A second path-analysis-based approach was also used. To address the possibility that chance associations explained these findings, a permuted analysis was conducted, the results of which supported the mediation inferences. The approach to evaluating volumetric mediation may have general applicability in epidemiologic neuroimaging settings.
American journal of epidemiology 03/2008; 167(4):429-37. · 5.59 Impact Factor
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ABSTRACT: To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach.
Statistical Applications in Genetics and Molecular Biology 02/2008; 7(1):Article11. · 1.52 Impact Factor
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Breast cancer research: BCR 02/2008; 10(2):401. · 5.24 Impact Factor
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ABSTRACT: To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach.
Statistical Applications in Genetics and Molecular Biology 02/2008; 7(1):11-11. · 1.52 Impact Factor
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ABSTRACT: Men who carry germline mutations in the BRCA2 gene have a higher risk of developing breast carcinoma than men in the general population. Men who carry germline mutations in the BRCA1 gene may also be at a higher risk for breast carcinoma, but this association is not as well established. We evaluated the risks of developing breast carcinoma for male BRCA1 and BRCA2 mutation carriers in the US population based on data from 1939 families with 97 male subjects with breast carcinoma that were collected from eight centers across the National Cancer Institute's Cancer Genetics Network. At all ages, the cumulative risks of male breast cancer were higher in both BRCA1 and BRCA2 mutation carriers than in noncarriers. The relative risks of developing breast cancer were highest for men in their 30s and 40s and decreased with increasing age. Both the relative and cumulative risks were higher for BRCA2 mutation carriers than for BRCA1 mutation carriers. The estimated cumulative risk of breast carcinoma for male BRCA1 mutation carriers at age 70 years was 1.2% (95% confidence interval [CI] = 0.22% to 2.8%) and for BRCA2 mutation carriers, 6.8% (95% CI = 3.2% to 12%).
CancerSpectrum Knowledge Environment 01/2008; 99(23):1811-4. · 14.07 Impact Factor
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ABSTRACT: To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach.
Statistical Applications in Genetics and Molecular Biology 01/2008; 7(1):11-11. · 1.52 Impact Factor
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Journal of the American Statistical Association 01/2008; 103(483):897-909.. · 1.99 Impact Factor
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JAMA The Journal of the American Medical Association 12/2007; 298(17):2007; author reply 2007-8. · 30.03 Impact Factor
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Giovanni Parmigiani, Sining Chen,
Edwin S Iversen,
Tara M Friebel,
Dianne M Finkelstein,
Hoda Anton-Culver,
Argyrios Ziogas,
Barbara L Weber,
Andrea Eisen,
Kathleen E Malone, [......],
Gail Tomlinson,
Christopher I Amos,
Louise C Strong,
Donald A Berry,
Jeffrey N Weitzel,
Sharon Sand,
Debra Dutson,
Rich Kerber,
Beth N Peshkin,
David M Euhus
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ABSTRACT: Deleterious mutations of the BRCA1 and BRCA2 genes confer susceptibility to breast and ovarian cancer. At least 7 models for estimating the probabilities of having a mutation are used widely in clinical and scientific activities; however, the merits and limitations of these models are not fully understood.
To systematically quantify the accuracy of the following publicly available models to predict mutation carrier status: BRCAPRO, family history assessment tool, Finnish, Myriad, National Cancer Institute, University of Pennsylvania, and Yale University.
Cross-sectional validation study, using model predictions and BRCA1 or BRCA2 mutation status of patients different from those used to develop the models.
Multicenter study across Cancer Genetics Network participating centers.
3 population-based samples of participants in research studies and 8 samples from genetic counseling clinics.
Discrimination between individuals testing positive for a mutation in BRCA1 or BRCA2 from those testing negative, as measured by the c-statistic, and sensitivity and specificity of model predictions.
The 7 models differ in their predictions. The better-performing models have a c-statistic around 80%. BRCAPRO has the largest c-statistic overall and in all but 2 patient subgroups, although the margin over other models is narrow in many strata. Outside of high-risk populations, all models have high false-negative and false-positive rates across a range of probability thresholds used to refer for mutation testing.
Three recently published models were not included.
All models identify women who probably carry a deleterious mutation of BRCA1 or BRCA2 with adequate discrimination to support individualized genetic counseling, although discrimination varies across models and populations.
Annals of internal medicine 11/2007; 147(7):441-50. · 16.73 Impact Factor
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ABSTRACT: We examined relations between brain volumes assessed by MRI and cognitive function in subjects in whom we have previously reported associations of cumulative lead dose with: (1) longitudinal declines in cognitive function; (2) smaller volumes of several regions of interest (ROIs) in the brain; and (3) increased prevalence and severity of white matter lesions. We used two complementary methods (ROI- [evaluating 20 ROIs] and voxel-wise) to examine associations between brain volumes and cognitive function using multiple linear regression. MRIs and cognitive testing were obtained from 532 former organolead workers with a mean (SD) age of 56.1 (7.7) years and a mean of 18.0 (11.0) years since the last occupational exposure to lead at the time of MRI acquisition. Cognitive testing was grouped into six domains of function (visuo-construction, verbal memory and learning, visual memory, executive functioning, eye-hand coordination, processing speed). Results indicated that larger ROI volumes were associated with better cognitive function in five of six cognitive domains, with significant associations observed for visuo-construction (15 of 20, p<or=0.05), processing speed (12, p<or=0.05), visual memory (11, p<or=0.05), executive functioning (11, p<or=0.05), and eye-hand coordination (11, p<or=0.05). Significant structure-function relations were also identified in the voxel-wise analysis with low false discovery rates (all less than 2.2%). Thus, larger volumes were associated with better cognitive function using both ROI- and voxel-based methods. In this cohort, an interesting group in which to examine structure-function relations, this finding provides a necessary condition to support the hypothesis that lead may influence cognitive function by its effect on brain volumes.
NeuroImage 09/2007; 37(2):633-41. · 5.89 Impact Factor
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ABSTRACT: The rapid fatality of pancreatic cancer is, in large part, the result of an advanced stage of diagnosis for the majority of patients. Identification of individuals at high risk of developing pancreatic cancer is a first step towards the early detection of this disease. Individuals who may harbor a major pancreatic cancer susceptibility gene are one such high-risk group. The goal of this study was to develop and validate PancPRO, a Mendelian model for pancreatic cancer risk prediction in individuals with familial pancreatic cancer, to identify high-risk individuals.
PancPRO was built by extending the Bayesian modeling framework developed for BRCAPRO, trained using published data, and validated using independent prospective data on 961 families enrolled onto the National Familial Pancreas Tumor Registry, including 26 individuals who developed incident pancreatic cancer during follow-up.
We developed a risk prediction model, PancPRO, and free software for the estimation of pancreatic cancer susceptibility gene carrier probabilities and absolute pancreatic cancer risk. Model validation demonstrated an observed to predicted pancreatic cancer ratio of 0.83 (95% CI, 0.52 to 1.20) and high discriminatory ability, with an area under the receiver operating characteristic curve of 0.75 (95% CI, 0.68 to 0.81) for PancPRO.
PancPRO is the first risk prediction model for pancreatic cancer. When we validated our model using the largest registry of familial pancreatic cancer, our model provided accurate risk assessment. Our findings highlight the importance of detailed family history for clinical cancer risk assessment and demonstrate that accurate genetic risk assessment is possible even when the causative genes are not known.
Journal of Clinical Oncology 05/2007; 25(11):1417-22. · 18.37 Impact Factor
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ABSTRACT: Genetic counseling is now routinely offered to individuals at high risk of carrying a BRCA1 or BRCA2 mutation. Risk prediction provided by the counselor requires reliable estimates of the mutation penetrance. Such penetrance has been investigated by studies worldwide. The reported estimates vary. To facilitate clinical management and counseling of the at-risk population, we address this issue through a meta-analysis.
We conducted a literature search on PubMed and selected studies that had nonoverlapping patient data, contained genotyping information, used statistical methods that account for the ascertainment, and reported risks in a useable format. We subsequently combined the published estimates using the DerSimonian and Laird random effects modeling approach.
Ten studies were eligible under the selection criteria. Between-study heterogeneity was observed. Study population, mutation type, design, and estimation methods did not seem to be systematic sources of heterogeneity. Meta-analytic mean cumulative cancer risks for mutation carriers at age 70 years were as follows: breast cancer risk of 57% (95% CI, 47% to 66%) for BRCA1 and 49% (95% CI, 40% to 57%) for BRCA2 mutation carriers; and ovarian cancer risk of 40% (95% CI, 35% to 46%) for BRCA1 and 18% (95% CI, 13% to 23%) for BRCA2 mutation carriers. We also report the prospective risks of developing cancer for currently asymptomatic carriers.
This article provides a set of risk estimates for BRCA1 and BRCA2 mutation carriers that can be used by counselors and clinicians who are interested in advising patients based on a comprehensive set of studies rather than one specific study.
Journal of Clinical Oncology 05/2007; 25(11):1329-33. · 18.37 Impact Factor
