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1.  Role of a Genetic Variant on the 15q25.1 Lung Cancer Susceptibility Locus in Smoking-Associated Nasopharyngeal Carcinoma 
PLoS ONE  2014;9(10):e109036.
The 15q25.1 lung cancer susceptibility locus, containing CHRNA5, could modify lung cancer susceptibility and multiple smoking related phenotypes. However, no studies have investigated the association between CHRNA5 rs3841324, which has been proven to have the highest association with CHRNA5 mRNA expression, and the risk of other smoking-associated cancers, except lung cancer. In the current study we examined the association between rs3841324 and susceptibility to smoking-associated nasopharyngeal carcinoma (NPC).
In this case-control study we genotyped the CHRNA5 rs3841324 polymorphism with 400 NPC cases and 491 healthy controls who were Han Chinese and frequency-matched by age (±5 years), gender, and alcohol consumption. Univariate and multivariate logistic regression analyses were used to calculate the odds ratio (OR) and 95% confidence intervals (95% CI).
We found that individuals with CHRNA5 rs3841324 combined variant genotypes (ins/del+del/del) had a >1.5-fold elevated risk for NPC than those with the ins/ins genotype (adjusted OR = 1.52; 95% CI, 1.16–2.00), especially among ever smokers (adjusted OR = 2.07; 95% CI, 1.23–3.48). The combined variant genotypes acted jointly with cigarette smoking to contribute to a 4.35-fold increased NPC risk (adjusted OR = 4.35; 95% CI, 2.57–7.38). There was a dose-response relationship between deletion alleles and NPC susceptibility (trend test, P = 0.011).
Our results suggest that genetic variants on the 15q25.1 lung cancer susceptibility locus may influence susceptibility to NPC, particularly for smoking-associated NPC. Such work may be helpful to facilitate an understanding of the etiology of smoking-associated cancers and improve prevention efforts.
PMCID: PMC4203692  PMID: 25329654
2.  Cutaneous alpha, beta and gamma human papillomaviruses in relation to squamous cell carcinoma of the skin: a population-based study 
Human papillomavirus (HPV) infection is common worldwide and, in immunodeficient populations, may contribute to the pathogenesis of keratinocyte cancers, particularly squamous cell carcinomas (SCC). However, their role in SCC in the general population is less clear. We conducted a comprehensive analysis to investigate the independent effects of seropositivity for cutaneous alpha, beta and gamma HPV types on risk of SCC, and a meta-analysis of the available literature. In a population-based case-control study from New Hampshire, USA (n=1408), histologically-confirmed SCC cases and controls were tested for L1 antibodies to alpha, beta and gamma cutaneous HPV types 2–5, 7–10, 15, 17, 20, 23, 24, 27b, 36, 38, 48–50, 57, 65, 75–77, 88, 92, 95, 96, 101, 103, and 107 using multiplex serology. An increasing risk of SCC with number of beta HPVs to which an individual tested positive was observed even among those seronegative for gamma types (P for trend = 0.016) with an odds ratio of 1.95 (95% confidence interval (CI) = 1.07–3.56) for four or more beta types positive. In a meta-analysis of six case-control studies, increased SCC risks in relation to beta HPV seropositivity were found across studies, (meta odds ratio = 1.45, CI = 1.27–1.66). While the prevalence of gamma HPVs assayed was somewhat higher among SCC cases than controls, the association was only weakly evident among those seronegative for beta HPVs. Overall, the association between cutaneous HPVs and skin cancers appears to be specific to SCC and to genus beta HPVs in a general US population.
PMCID: PMC3713187  PMID: 23536363
human papillomavirus; squamous cell carcinoma; population-based; case-control; meta-analysis
3.  Diverse convergent evidence in the genetic analysis of complex disease: coordinating omic, informatic, and experimental evidence to better identify and validate risk factors 
BioData Mining  2014;7:10.
In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true associations. Unfortunately this standard validation approach cannot completely eliminate false positive conclusions, and it can also mask many true associations that might otherwise advance our understanding of pathology. These issues beg the question: How can we increase the amount of knowledge gained from high throughput genetic data? To address this challenge, we present an approach that complements standard statistical validation methods by drawing attention to both potential false negative and false positive conclusions, as well as providing broad information for directing future research. The Diverse Convergent Evidence approach (DiCE) we propose integrates information from multiple sources (omics, informatics, and laboratory experiments) to estimate the strength of the available corroborating evidence supporting a given association. This process is designed to yield an evidence metric that has utility when etiologic heterogeneity, variable risk factor frequencies, and a variety of observational data imperfections might lead to false conclusions. We provide proof of principle examples in which DiCE identified strong evidence for associations that have established biological importance, when standard validation methods alone did not provide support. If used as an adjunct to standard validation methods this approach can leverage multiple distinct data types to improve genetic risk factor discovery/validation, promote effective science communication, and guide future research directions.
PMCID: PMC4112852  PMID: 25071867
Replication; Validation; Complex disease; Heterogeneity; GWAS; Omics; Type 2 error; Type 1 error; False negatives; False positives
4.  Non Melanoma Skin Cancer and Subsequent Cancer Risk 
PLoS ONE  2014;9(6):e99674.
Several studies have shown an increased risk of cancer after non melanoma skin cancers (NMSC) but the individual risk factors underlying this risk have not been elucidated, especially in relation to sun exposure and skin sensitivity to sunlight.
The aim of this study was to examine the individual risk factors associated with the development of subsequent cancers after non melanoma skin cancer.
Participants in the population-based New Hampshire Skin Cancer Study provided detailed risk factor data, and subsequent cancers were identified via linkage with the state cancer registry. Deaths were identified via state and national death records. A Cox proportional hazard model was used to estimate risk of subsequent malignancies in NMSC patients versus controls and to assess the potential confounding effects of multiple risk factors on this risk.
Among 3584 participants, risk of a subsequent cancer (other than NMSC) was higher after basal cell carcinoma (BCC) (adjusted HR 1.40 [95% CI 1.15, 1.71]) than squamous cell carcinoma (SCC) (adjusted HR 1.18 [95% CI 0.95, 1.46]) compared to controls (adjusted for age, sex and current cigarette smoking). After SCC, risk was higher among those diagnosed before age 60 (HR 1.96 [95% CI 1.24, 3.12]). An over 3-fold risk of melanoma after SCC (HR 3.62; 95% CI 1.85, 7.11) and BCC (HR 3.28; 95% CI 1.66, 6.51) was observed, even after further adjustment for sun exposure-related factors and family history of skin cancer. In men, prostate cancer incidence was higher after BCC compared to controls (HR 1.64; 95% CI 1.10, 2.46).
Our population-based study indicates an increased cancer risk after NMSC that cannot be fully explained by known cancer risk factors.
PMCID: PMC4061037  PMID: 24937304
This dose escalation study was performed to determine the recommended phase II dose of oral capecitabine to be delivered concurrently with thoracic radiation therapy and weekly docetaxel in patients with locally advanced esophageal carcinoma.
Patients with operable stage II or III esophageal carcinoma were staged by endoscopic ultrasonography (EUS) and CT. Two cycles of docetaxel (80 mg/m2) and carboplatin (target area under the concentration curve 6 mg*min/mL) were delivered over 6 weeks. This was followed by concurrent weekly docetaxel (15 mg/m2), thoracic radiotherapy (50.4 Gy in 28 fractions), and increasing doses of capecitabine (500 mg to 3500 mg) given prior to each fraction of radiotherapy. Following re-staging, responding patients continued to esophagectomy within 4–8 weeks of completing chemoradiotherapy.
Forty-four patients (pts) were enrolled and 40 were evaluable for the dose-ranging component of concurrent chemoradiotherapy. EUS stages at enrollment were T3N1 (29 pts), T3N0 (4 pts), T2N1 (6 pts), and T4N0 (1 pts). The maximum tolerated dose of capecitabine was 3500 mg. Thirty-six patients had surgery; 83% had R0 resection and 17% had complete pathological response. Median overall survival was 23.5 months, with 34% and 27% alive at three and five years.
The recommended phase II dose of capecitabine is 3500 mg when given concurrently with 50.4 Gy of thoracic radiotherapy in 28 fractions and weekly docetaxel. This trimodality therapy for operable locally advanced esophageal carcinoma was very well-tolerated and remarkably active. This regimen holds promise for treatment of esophageal carcinoma and warrants further investigation.
PMCID: PMC3600150  PMID: 23370365
6.  Assessment of the Changes in 9L and C6 Glioma pO2 by EPR Oximetry as a Prognostic Indicator of Differential Response to Radiotherapy 
Radiation research  2013;179(3):343-351.
Tumor hypoxia impedes the outcome of radiotherapy. As the extent of hypoxia in solid tumors varies during the course of radiotherapy, methods that can provide repeated assessment of tumor pO2 such as EPR oximetry may enhance the efficacy of radiotherapy by scheduling irradiations when the tumors are oxygenated. The repeated measurements of tumor pO2 may also identify responders, and thereby facilitate the design of better treatment plans for nonresponding tumors. We have investigated the temporal changes in the ectopic 9L and C6 glioma pO2 irradiated with single radiation doses less than 10 Gy by EPR oximetry. The 9L and C6 tumors were hypoxic with pO2 of approximately 5–9 mmHg. The pO2 of C6 tumors increased significantly with irradiation of 4.8–9.3 Gy. However, no change in the 9L tumor pO2 was observed. The irradiation of the oxygenated C6 tumors with a second dose of 4.8 Gy resulted in a significant delay in growth compared to hypoxic and 2 Gy × 5 treatment groups. The C6 tumors with an increase in pO2 of greater than 50% from the baseline of irradiation with 4.8 Gy (responders) had a significant tumor growth delay compared to nonresponders. These results indicate that the ectopic 9L and C6 tumors responded differently to radiotherapy. We propose that the repeated measurement of the oxygen levels in the tumors during radiotherapy can be used to identify responders and to design tumor oxygen guided treatment plans to improve the outcome.
PMCID: PMC3633145  PMID: 23391148
7.  RESPECT-PTSD: Re-Engineering Systems for the Primary Care Treatment of PTSD, A Randomized Controlled Trial 
Although collaborative care is effective for treating depression and other mental disorders in primary care, there have been no randomized trials of collaborative care specifically for patients with Posttraumatic stress disorder (PTSD).
To compare a collaborative approach, the Three Component Model (3CM), with usual care for treating PTSD in primary care.
The study was a two-arm, parallel randomized clinical trial. PTSD patients were recruited from five primary care clinics at four Veterans Affairs healthcare facilities and randomized to receive usual care or usual care plus 3CM. Blinded assessors collected data at baseline and 3-month and 6-month follow-up.
Participants were 195 Veterans. Their average age was 45 years, 91% were male, 58% were white, 40% served in Iraq or Afghanistan, and 42% served in Vietnam.
All participants received usual care. Participants assigned to 3CM also received telephone care management. Care managers received supervision from a psychiatrist.
PTSD symptom severity was the primary outcome. Depression, functioning, perceived quality of care, utilization, and costs were secondary outcomes.
There were no differences between 3CM and usual care in symptoms or functioning. Participants assigned to 3CM were more likely to have a mental health visit, fill an antidepressant prescription, and have adequate antidepressant refills. 3CM participants also had more mental health visits and higher outpatient pharmacy costs.
Results suggest the need for careful examination of the way that collaborative care models are implemented for treating PTSD, and for additional supports to encourage primary care providers to manage PTSD.
PMCID: PMC3539037  PMID: 22865017
posttraumatic stress disorder; integrated primary care; veterans; randomized clinical trials; treatment
8.  Bone Marrow Transplant for Multiple Myeloma: Impact of Distance From the Transplant Center 
This study investigated the impact of prognostic variables, including the distance a patient lives from a transplant center, on the outcome of autologous hematopoietic stem cell transplantation (ASCT) for multiple myeloma.
This retrospective analysis included 77 myeloma patients who received an ASCT at Dartmouth Hitchcock Medical Center between 1996 and 2009, 70 of whom were treated between 2002 and 2009. Using linear regression and univariate analysis, we examined the impact of distance from the transplant center on survival. Kaplan-Meier curves identified overall and event-free survival. An association between distance from the transplant center and survival was examined using Cox regression analysis, while adjusting for patient-, disease-, and treatment-related variables.
Increasing distance from the transplant center correlated with improved overall survival (P=.004), but had no impact on disease-free survival (P=.26).
These results suggest that the distance from a transplant center should not be a barrier to ASCT for eligible patients with multiple myeloma.
PMCID: PMC3855803  PMID: 22398804
Thrombotic; thrombocytopenia; purpura; ADAMTS13; microangiopathic; hemolytic
9.  Prevalence of Venous Thromboembolism in Patients With Secondary Polycythemia 
To investigate an association between secondary polycythemia and venous thromboembolism (VTE) risk, we performed a case–control study to compare the prevalence of VTE in participants with secondary polycythemia due to chronic obstructive pulmonary disease (COPD; N = 86) to that in age- and sex-matched controls with COPD without secondary polycythemia (N = 86). Although there was a significant difference in mean hematocrit between cases and controls (53.5% vs 43.6%, respectively; P < .005), we identified no difference in the number of total or idiopathic VTE events in the 2 groups. Patients with VTE, however, had a significantly higher body mass index than patients without VTE. Our findings suggest that secondary polycythemia alone may not be a significant risk factor for VTE but that VTE risk in this population may be related to known risk factors such as obesity. The role of phlebotomy for VTE risk reduction secondary polycythemia is therefore questionable.
PMCID: PMC3831025  PMID: 23007895
polycythemia; venous thromboembolism; phlebotomy; obesity
10.  Use of MRI in Preoperative Planning for Women with Newly Diagnosed DCIS: Risk or Benefit? 
Annals of surgical oncology  2012;19(10):10.1245/s10434-012-2548-3.
The role of magnetic resonance imaging (MRI) in preoperative planning for women diagnosed with breast cancer remains controversial. The risks and benefits in women with newly diagnosed ductal carcinoma in situ (DCIS) are largely unknown.
Patients and Methods
Retrospective chart review comparing women treated for DCIS who did and did not undergo MRI for preoperative planning. End points included number of additional biopsies prompted by MRI, surgical reexcision rates, weight of excisions, mastectomy rates, and conversion to mastectomy after attempted breast conservation.
218 patients met study criteria. Sixty-four patients did not undergo preoperative MRI, and 154 patients did. There was no statistically significant difference (P = not significant, NS) in reexcision rates between the 34.1 % (42/ 123) of women who did and 20/51 (39.2 %) women who did not undergo MRI. Despite use of preoperative MRI, 11/123 women (8.9 %) were converted to mastectomy due to positive margins compared with 4/51 (7.8 %) in the women who did not undergo MRI (P = NS). In women undergoing MRI, average weight of excision at definitive surgery was 49.5 g, while in women who did not undergo MRI, average weight of excision at definitive surgery was 48.7 g.
Our data show that MRI does not significantly decrease reexcision rates or conversion to mastectomy after attempted breast-conservation surgery. Based on our findings, we do not believe preoperative MRI adds benefit to the care of this patient population. Prospective trials are necessary to further investigate the risks and benefits of preoperative MRI in women with DCIS.
PMCID: PMC3809001  PMID: 22911365
11.  Diagnostic cellular abnormalities in neoplastic and non-neoplastic lesions of the epidermis: a morphological and statistical study 
Journal of cutaneous pathology  2013;40(4):10.1111/cup.12090.
Distinguishing cellular abnormalities in reactive and malignant lesions is challenging. We compared the incidence and severity of cytological abnormalities in malignant/premalignant and benign epidermal lesions.
One hundred fifty-two biopsies representing 69 malignant/premalignant squamous lesions and 83 benign conditions were studied. Cytological features, including nuclear hyperchromasia, nuclear overlap (crowding), irregular nuclei, high nuclear/cytoplasmic (N/C) ratio, conspicuous nucleoli, delicate inconspicuous nucleoli, clumped chromatin, pleomorphic parakeratosis, normal and abnormal mitotic figures and necrotic keratinocytes, were evaluated and graded. Statistical analysis was performed.
Irregular nuclei, increased N/C ratio, conspicuous single prominent nucleoli, nuclear overlap (crowding), pleomorphic parakeratosis, nuclear hyperchromasia, necrotic keratinocytes, normal and abnormal mitotic figures and coarse chromatin were seen more frequently in malignant neoplasms (p < 0.05). Abnormal mitotic figures, although uncommon (20.3%), were only noted in the malignant/premalignant group. Certain cytological features were common among both malignant and benign lesions, suggesting that they are of little value.
In the setting of an atypical cutaneous squamous proliferation, nuclear irregularity, increased N/C ratio, conspicuous nucleoli, crowding and hyperchromasia are the most useful indicators of malignancy. In contrast, mitotic figures, necrotic cells and coarse chromatin are less useful. The presence of abnormal mitotic figures is very helpful when present; however, their overall rarity limits their utility.
PMCID: PMC3809146  PMID: 23398548
atypical features; cutaneous squamous cell carcinoma; non-melanoma skin cancer; squamous cell carcinomas
12.  Increased Rates of Long-Term Complications after MammoSite Brachytherapy Compared with Whole Breast Radiation Therapy 
Journal of the American College of Surgeons  2013;217(3):10.1016/j.jamcollsurg.2013.03.028.
Due to its short duration of therapy and low rates of local recurrence, women undergoing breast conservation are increasingly opting for partial breast irradiation with the MammoSite (Cytyc/Hologic) catheter. In early follow-up studies, few complications were reported. Few data, however, exist regarding longer-term complications. We compared the long-term local toxicities of MammoSite partial breast irradiation with those resulting from whole breast radiation.
This was a retrospective study performed in a single academic medical center. All patients who underwent breast-conserving surgery between 2003 and 2008, who met institutional criteria for brachytherapy, were included. We compared women treated with MammoSite with patients treated with whole breast radiation therapy (WBRT). Endpoints included incidence of palpable masses at the lumpectomy site, telangiectasias, and local recurrence.
Seventy-one MammoSite patients and 245 WBRT patients were well matched with regard to clinical characteristics. Median follow-up was 4 years. A palpable mass developed at the site of lumpectomy in 27% of the MammoSite patients compared with 7% of the WBRT patients (p < 0.0001). Telangiectasias developed more frequently in the MammoSite group than in the WBRT group (24% vs 4%, p < 0.001). Forty-two percent of patients treated with MammoSite developed a palpable mass, telangectasia, or both.
Palpable masses and telangiectasias are frequent long-term complications after MammoSite brachytherapy and occur at a significantly higher rate after MammoSite brachytherapy than after WBRT. This increased rate of long-term local toxicity should be considered when counseling women on options for adjuvant radiation therapy after breast-conserving surgery.
PMCID: PMC3808115  PMID: 23830216
13.  Effect of calcium supplementation on fracture risk: a double-blind randomized controlled trial1, 2, 3 
The effect of supplementation with calcium alone on risk fractures in a healthy population is not clear.
The objective was to determine whether 4 y of calcium supplementation would reduce the fracture risk during treatment and subsequent follow-up in a randomized placebo-controlled trial.
The participants were aged <80 y at study entry (mean age: 61 y), were generally healthy, and had a recent diagnosis of colorectal adenoma. A total of 930 participants (72% men; mean age: 61 y) were randomly assigned to receive 4 y of treatment with 3 g CaCO3 (1200 mg elemental Ca) daily or placebo and were followed for a mean of 10.8 y. The primary outcomes of this analysis were all fractures and minimal trauma fractures (caused by a fall from standing height or lower while sitting, standing, or walking).
There were 46 fractures (15 from minimal trauma) in 464 participants in the calcium group and 54 (29 from minimal trauma) in 466 participants in the placebo group. The overall risk of fracture differed significantly between groups during the treatment phase [hazard ratio (HR): 0.28; 95% CI: 0.09, 0.85], but not during the subsequent posttreatment follow-up (HR: 1.10; 95% CI: 0.71, 1.69). Minimal trauma fractures were also less frequent in the calcium group during treatment (HR: 0; 95% CI: 0, 0.50).
Calcium supplementation reduced the risk of all fractures and of minimal trauma fractures among healthy individuals. The benefit appeared to dissipate after treatment was stopped.
PMCID: PMC3773875  PMID: 18541589
14.  Immune Response in Patients With Newly Diagnosed Glioblastoma Multiforme Treated With Intranodal Autologous Tumor Lysate-dendritic Cell Vaccination After Radiation Chemotherapy 
Patients with glioblastoma multiforme (GBM) are profoundly immunosuppressed and may benefit from restoration of an antitumor immune response in combination with conventional radiation therapy and temozolomide (TMZ). The optimal strategies to evaluate clinically relevant immune responses to treatment have yet to be determined. The primary objective of our study was to determine immunologic response to cervical intranodal vaccination with autologous tumor lysate-loaded dendritic cells (DCs) in patients with GBM after radiation therapy and TMZ. We used a novel hierarchical clustering analysis of immune parameters measured before and after vaccination. Secondary objectives were to assess treatment feasibility and to correlate immune response with progression-free survival (PFS) and overall survival. Ten eligible patients received vaccination. Tumor-specific cytotoxic T-cell response measured after vaccination was enhanced for the precursor frequency of CD4+ T and CD4+ interferon γ-producing cells. Hierarchical clustering analysis of multiple functional outcomes discerned 2 groups of patients according to their immune response, and additionally showed that patients in the top quintile for at least one immune function parameter had improved survival. There were no serious adverse events related to DC vaccination. All patients were alive at 6 months after diagnosis and the 6-month PFS was 90%. The median PFS was 9.5 months and overall survival was 28 months. In patients with GBM, immune therapy with DC vaccination after radiation and TMZ resulted in tumor-specific immune responses that were associated with prolonged survival. Our data suggest that DC vaccination in combination with radiation and chemotherapy in patients with GBM is feasible, safe, and may induce tumor-specific immune responses.
PMCID: PMC3766324  PMID: 21499132
dendritic cells; glioblastoma; vaccine; immune response
Health physics  2012;103(3):255-267.
With possibilities for radiation terrorism and intensified concerns about nuclear accidents since the recent Fukushima Daiichi event, the potential exposure of large numbers of individuals to radiation that could lead to acute clinical effects has become a major concern. For the medical community to cope with such an event and avoid overwhelming the medical care system, it is essential to identify not only individuals who have received clinically significant exposures and need medical intervention but also those who do not need treatment. The ability of electron paramagnetic resonance to measure radiation-induced paramagnetic species, which persist in certain tissues (e.g., teeth, fingernails, toenails, bone, and hair), has led this technique to become a prominent method for screening significantly exposed individuals. Although the technical requirements needed to develop this method for effective application in a radiation event are daunting, remarkable progress has been made. In collaboration with General Electric, and through funding committed by the Biomedical Advanced Research and Development Authority, electron paramagnetic resonance tooth dosimetry of the upper incisors is being developed to become a Food and Drug Administration-approved and manufacturable device designed to carry out triage for a threshold dose of 2 Gy. Significant progress has also been made in the development of electron paramagnetic resonance nail dosimetry based on measurements of nails in situ under point-of-care conditions, and in the near future this may become a second field-ready technique. Based on recent progress in measurements of nail clippings, we anticipate that this technique may be implementable at remotely located laboratories to provide additional information when the measurements of dose on site need to be supplemented. We conclude that electron paramagnetic resonance dosimetry is likely to be a useful part of triage for a large-scale radiation incident.
PMCID: PMC3649772  PMID: 22850230
electron paramagnetic resonance dosimetry; in vivo tooth dosimetry; in vivo nail dosimetry; ex vivo nail dosimetry
16.  Mapping Disease at an Approximated Individual Level Using Aggregate Data: A Case Study of Mapping New Hampshire Birth Defects 
Background: Limited by data availability, most disease maps in the literature are for relatively large and subjectively-defined areal units, which are subject to problems associated with polygon maps. High resolution maps based on objective spatial units are needed to more precisely detect associations between disease and environmental factors. Method: We propose to use a Restricted and Controlled Monte Carlo (RCMC) process to disaggregate polygon-level location data to achieve mapping aggregate data at an approximated individual level. RCMC assigns a random point location to a polygon-level location, in which the randomization is restricted by the polygon and controlled by the background (e.g., population at risk). RCMC allows analytical processes designed for individual data to be applied, and generates high-resolution raster maps. Results: We applied RCMC to the town-level birth defect data for New Hampshire and generated raster maps at the resolution of 100 m. Besides the map of significance of birth defect risk represented by p-value, the output also includes a map of spatial uncertainty and a map of hot spots. Conclusions: RCMC is an effective method to disaggregate aggregate data. An RCMC-based disease mapping maximizes the use of available spatial information, and explicitly estimates the spatial uncertainty resulting from aggregation.
PMCID: PMC3799515  PMID: 24018838
birth defects; aggregate data; disaggregation; Monte Carlo; disease mapping; New Hampshire
17.  A Simple and Computationally Efficient Approach to Multifactor Dimensionality Reduction Analysis of Gene-Gene Interactions for Quantitative Traits 
PLoS ONE  2013;8(6):e66545.
We present an extension of the two-class multifactor dimensionality reduction (MDR) algorithm that enables detection and characterization of epistatic SNP-SNP interactions in the context of a quantitative trait. The proposed Quantitative MDR (QMDR) method handles continuous data by modifying MDR’s constructive induction algorithm to use a T-test. QMDR replaces the balanced accuracy metric with a T-test statistic as the score to determine the best interaction model. We used a simulation to identify the empirical distribution of QMDR’s testing score. We then applied QMDR to genetic data from the ongoing prospective Prevention of Renal and Vascular End-Stage Disease (PREVEND) study.
PMCID: PMC3689797  PMID: 23805232
18.  The association of lifestyle and dietary factors with the risk of serrated polyps of the colorectum 
Some serrated polyps of the colorectum are likely pre-invasive lesions, evolving through a newly recognized serrated pathway to colorectal cancer. To assess possible risk and protective factors for serrated polyps – and particularly to explore differences in risk factors between polyps in the right and left colorectum – we pooled data from three large multi-center chemoprevention trials. A serrated polyp (SP) was defined broadly as any serrated lesion (hyperplastic, sessile serrated adenoma, traditional serrated adenoma, mixed adenoma) diagnosed during each trial’s main treatment period, of about three to four years. Using generalized linear regression, we computed risk ratios and 95% confidence intervals (CI’s) as measures of the association between risk of serrated polyps and demographic, lifestyle, and dietary variables. Of the 2830 subjects that completed at least one follow-up exam after randomization, 675 (23.9 %) had at least one left sided serrated polyp and 261 (9.2 %) had at least one right sided lesion. In the left colorectum, obesity, cigarette smoking, dietary fat, total energy intake, and red meat intake were associated with an increased risk of serrated polyps. In the right colon, aspirin treatment was associated with a reduced risk and family history of polyps and folate treatment were associated with an increased risk of serrated polyps. Our results suggest that several common lifestyle and dietary variables are associated with risk of serrated polyps, and some of these may differ for the right and left colorectum.
PMCID: PMC3669681  PMID: 19661090
serrated polyps; proximal colon; distal colon; lifestyle factors; diet
19.  Quantitative Multifactor Dimensionality Reduction Method for Detecting Gene-Gene Interaction 
Background and Objective: The problem of identifying SNP-SNP interactions in case-control studies has been studied extensively and a number of new techniques have been developed. Little progress has been made, however in the analysis of SNP-SNP interactions in relation to continuous data. Methods: We present an extension of the two class multifactor dimensionality reduction (MDR) algorithm that enables detection and characterization of epistatic SNP-SNP interactions in the context of Quantitative trait. The proposed Quantitative MDR (Quant-MDR) method handles continuous data by modifying MDR's constructive induction algorithm to use T Test. Results: We then applied Quant-MDR to genetic data from the ongoing prospective Prevention of Renal and Vascular End-Stage Disease (PREVEND) study. We identified that BR2_58CT&ATR1AC is the top SNP-SNP interaction that assciated with Tissue plasminogen activator (tPA) level for male and ACEID&BRB2EX1 is the top interaction for female tPA expression. Discussion and Conclusions: Quant-MDR is capable of detecting interaction models with weak main effects. These epistatic models tend to be dropped by traditional linear regression approaches. With improved efficiency to handle genome wide datasets, Quant-MDR will play an important role in a research strategy that embraces the complexity of the genotype-phenotype mapping relationship.
PMCID: PMC3635314
20.  Inherent and Benzo[a]pyrene-Induced Differential Aryl Hydrocarbon Receptor Signaling Greatly Affects Life Span, Atherosclerosis, Cardiac Gene Expression, and Body and Heart Growth in Mice 
Toxicological Sciences  2012;126(2):391-404.
Little is known of the environmental factors that initiate and promote disease. The aryl hydrocarbon receptor (AHR) is a key regulator of xenobiotic metabolism and plays a major role in gene/environment interactions. The AHR has also been demonstrated to carry out critical functions in development and disease. A qualitative investigation into the contribution by the AHR when stimulated to different levels of activity was undertaken to determine whether AHR-regulated gene/environment interactions are an underlying cause of cardiovascular disease. We used two congenic mouse models differing at the Ahr gene, which encodes AHRs with a 10-fold difference in signaling potencies. Benzo[a]pyrene (BaP), a pervasive environmental toxicant, atherogen, and potent agonist for the AHR, was used as the environmental agent for AHR activation. We tested the hypothesis that activation of the AHR of different signaling potencies by BaP would have differential effects on the physiology and pathology of the mouse cardiovascular system. We found that differential AHR signaling from an exposure to BaP caused lethality in mice with the low-affinity AHR, altered the growth rates of the body and several organs, induced atherosclerosis to a greater extent in mice with the high-affinity AHR, and had a huge impact on gene expression of the aorta. Our studies also demonstrated an endogenous role for AHR signaling in regulating heart size. We report a gene/environment interaction linking differential AHR signaling in the mouse to altered aorta gene expression profiles, changes in body and organ growth rates, and atherosclerosis.
PMCID: PMC3307607  PMID: 22228805
aryl hydrocarbon receptor; gene/environment interactions; Western diet; benzo[a]pyrene; atherosclerosis; body and organ growth
21.  HSD3B and Gene-Gene Interactions in a Pathway-Based Analysis of Genetic Susceptibility to Bladder Cancer 
PLoS ONE  2012;7(12):e51301.
Bladder cancer is the 4th most common cancer among men in the U.S. We analyzed variant genotypes hypothesized to modify major biological processes involved in bladder carcinogenesis, including hormone regulation, apoptosis, DNA repair, immune surveillance, metabolism, proliferation, and telomere maintenance. Logistic regression was used to assess the relationship between genetic variation affecting these processes and susceptibility in 563 genotyped urothelial cell carcinoma cases and 863 controls enrolled in a case–control study of incident bladder cancer conducted in New Hampshire, U.S. We evaluated gene–gene interactions using Multifactor Dimensionality Reduction (MDR) and Statistical Epistasis Network analysis. The 3′UTR flanking variant form of the hormone regulation gene HSD3B2 was associated with increased bladder cancer risk in the New Hampshire population (adjusted OR 1.85 95%CI 1.31–2.62). This finding was successfully replicated in the Texas Bladder Cancer Study with 957 controls, 497 cases (adjusted OR 3.66 95%CI 1.06–12.63). The effect of this prevalent SNP was stronger among males (OR 2.13 95%CI 1.40–3.25) than females (OR 1.56 95%CI 0.83–2.95), (SNP-gender interaction P = 0.048). We also identified a SNP-SNP interaction between T-cell activation related genes GATA3 and CD81 (interaction P = 0.0003). The fact that bladder cancer incidence is 3–4 times higher in males suggests the involvement of hormone levels. This biologic process-based analysis suggests candidate susceptibility markers and supports the theory that disrupted hormone regulation plays a role in bladder carcinogenesis.
PMCID: PMC3526593  PMID: 23284679
22.  Gene Expression Profile of Peripheral Blood Lymphocytes from Renal Cell Carcinoma Patients Treated with IL-2, Interferon-α and Dendritic Cell Vaccine 
PLoS ONE  2012;7(12):e50221.
Lymphocytes are a key component of the immune system and their differentiation and function are directly influenced by cancer. We examined peripheral blood lymphocyte (PBL) gene expression as a biomarker of illness and treatment effect using the Affymetrix Human Gene ST1 platform in patients with metastatic renal cell carcinoma (mRCC) who received combined treatment with IL-2, interferon-?-2a and dendritic cell vaccine. We examined gene expression, cytokine levels in patient serum and lymphocyte subsets as determined by flow cytometry (FCM). Pre-treatment PBLs from patients with mRCC exhibit a gene expression profile and serum cytokine profile consistent with inflammation and proliferation not found in healthy donors (HD). PBL gene expression from patients with mRCC showed increased mRNA of genes involved with T-cell and TREG-cell activation pathways, which was also reflected in lymphocyte subset distribution. Overall, PBL gene expression post-treatment (POST) was not significantly different than pre-treatment (PRE). Nevertheless, treatment related changes in gene expression (post-treatment minus pre-treatment) revealed an increased expression of T-cell and B-cell receptor signaling pathways in responding (R) patients compared to non-responding (NR) patients. In addition, we observed down-regulation of TREG-cell pathways post-treatment in R vs. NR patients. While exploratory in nature, this study supports the hypothesis that enhanced inflammatory cytotoxic pathways coupled with blunting of the regulatory pathways is necessary for effective anti-cancer activity associated with immune therapy. This type of analysis can potentially identify additional immune therapeutic targets in patients with mRCC.
PMCID: PMC3513309  PMID: 23226513
23.  Regulatory T-Cells and Associated Pathways in Metastatic Renal Cell Carcinoma (mRCC) Patients Undergoing DC-Vaccination and Cytokine-Therapy 
PLoS ONE  2012;7(10):e46600.
To evaluate CD4+CD25+FOXP3+ T regulatory cells (TREG) and associated immune-regulatory pathways in peripheral blood lymphocytes (PBL) of metastatic renal cell carcinoma (mRCC) patients and healthy volunteers. We subsequently investigated the effects of immunotherapy on circulating TREG combining an extensive phenotype examination, DNA methylation analysis and global transcriptome analysis.
Eighteen patients with mRCC and twelve volunteers (controls) were available for analysis. TREG phenotype was examined using flow cytometry (FCM). TREG were also quantified by analyzing the epigenetic status of the FOXP3 locus using methylation specific PCR. As a third approach, RNA of the PBL was hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays and the gene signatures were explored using pathway analysis.
We observed higher numbers of TREG in pre-treatment PBL of mRCC patients compared to controls. A significant increase in TREG was detected in all mRCC patients after the two cycles of immunotherapy. The expansion of TREG was significantly higher in non-responders than in responding patients. Methylation specific PCR confirmed the FCM data and circumvented the variability and subjectivity of the FCM method. Gene Set Enrichment Analysis (GSEA) of the microarray data showed significant enrichment of FOXP3 target genes, CTLA-4 and TGF-ß associated pathways in the patient cohort.
Immune monitoring of the peripheral blood and tumor tissue is important for a wide range of diseases and treatment strategies. Adoption of methodology for quantifying TREG with the least variability and subjectivity will enhance the ability to compare and interpret findings across studies.
PMCID: PMC3485261  PMID: 23118856
The environmental agent 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD or dioxin) causes a multitude of human illnesses. In order to more fully understand the underlying biology of TCDD toxicity, we tested the hypothesis that new candidate genes could be identified using polysome RNA from TCDD-treated mouse Hepa-1c1c7 cells. We found that (i) differentially expressed whole cell and cytoplasm RNA levels are both poor predictors of polysome RNA levels; (ii) for a majority of RNAs, differential RNA levels are regulated independently in the nucleus, cytoplasm, and polysomes; (iii) for the remaining polysome RNAs, levels are regulated via several different mechanisms, including a “tagging” of mRNAs in the nucleus for immediate polysome entry; and (iv) most importantly, a gene list derived from differentially expressed polysome RNA generated new genes and cell pathways potentially related to TCDD biology.
PMCID: PMC3162130  PMID: 21570461
Polysomes; gene expression; gene regulation; TCDD; microarrays; Hepa-1c1c7
25.  Advances towards using finger/toenail dosimetry to triage a large population after potential exposure to ionizing radiation 
Radiation measurements  2011;46(9):882-887.
Rapid and accurate retrospective dosimetry is of critical importance and strategic value for the emergency medical response to a large-scale radiological/nuclear event. One technique that has the potential for rapid and accurate dosimetry measurements is electron paramagnetic resonance (EPR) spectroscopy of relatively stable radiation-induced signals (RIS) in fingernails and toenails. Two approaches are being developed for EPR nail dosimetry. In the approach using ex vivo measurements on nail clippings, accurate estimation of the dose-dependent amplitude of the RIS is complicated by the presence of mechanically-induced signals (MIS) that are generated during the nail clipping. Recent developments in ex vivo nail dosimetry, including a thorough characterization of the MIS and an appreciation of the role of hydration and the development of effective analytic techniques, have led to improvements in the accuracy and precision of this approach. An in vivo nail dosimetry approach is also very promising, as it eliminates the problems of MIS from the clipping and it has the potential to be an effective and efficient approach for field deployment. Two types of EPR resonators are being developed for in vivo measurements of fingernails and toenails.
PMCID: PMC3223932  PMID: 22125410
EPR dosimetry; nail clippings; in vivo nail dosimetry; ex vivo nail dosimetry

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