The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery

The field of phenomics has been investigating network structure among large arrays of phenotypes, and genome-wide association studies (GWAS) have been used to investigate the relationship between genetic variation and single diseases/outcomes. A novel approach has emerged combining both the exploration of phenotypic structure and genotypic variation, known as the phenome-wide association study (PheWAS). The Population Architecture using Genomics and Epidemiology (PAGE) network is a National Human Genome Research Institute (NHGRI)-supported collaboration of four groups accessing eight extensively characterized epidemiologic studies. The primary focus of PAGE is deep characterization of well-replicated GWAS variants and their relationships to various phenotypes and traits in diverse epidemiologic studies that include European Americans, African Americans, Mexican Americans/Hispanics, Asians/Pacific Islanders, and Native Americans. The rich phenotypic resources of PAGE studies provide a unique opportunity for PheWAS as each genotyped variant can be tested for an association with the wide array of phenotypic measurements available within the studies of PAGE, including prevalent and incident status for multiple common clinical conditions and risk factors, as well as clinical parameters and intermediate biomarkers. The results of PheWAS can be used to discover novel relationships between SNPs, phenotypes, and networks of interrelated phenotypes; identify pleiotropy; provide novel mechanistic insights; and foster hypothesis generation. The PAGE network has developed infrastructure to support and perform PheWAS in a high-throughput manner. As implementing the PheWAS approach has presented several challenges, the infrastructure and methodology, as well as insights gained in this project, are presented herein to benefit the larger scientific community.

Dietary sources and sociodemographic and economic factors affecting vitamin D and calcium intakes in Flemish preschoolers

BACKGROUND/OBJECTIVES

Low calcium and vitamin D intakes have been associated with health risks in childhood and adulthood. This study aims to investigate dietary sources of calcium and vitamin D intake, and its associated sociodemographic, economic and lifestyle factors among preschoolers.

SUBJECTS/METHODS

Three-day estimated diet records from 696 Flemish preschoolers 2.5-6.5 years old (51% boys) were used (66% of 1052 collected diaries). Contribution of 58 food groups to calcium and vitamin D intake were computed. Multiple linear regression was used to examine associations of intakes with sociodemographic, economic and lifestyle factors.

RESULTS

Mean calcium intake (844 mg per day) was above, and mean vitamin D intake (2.0 μg per day) largely below the Belgian recommendations. Milk, sweetened milk drinks and cheese were the main sources of calcium intakes (26, 25 and 11%, respectively). Butter and margarine were the main vitamin D sources (26%), followed by growth milk (=fortified milk) (20%) and fish (15%). Calcium and vitamin D intake were negatively associated with participants' age, and calcium positively with parental education and family size. The child's gender, supplement use and physical activity level, and the employment status and smoking behaviour of the parents were not associated with calcium or vitamin D intake.

CONCLUSIONS

Flemish preschoolers had too low vitamin D intakes while most had adequate calcium intakes. Milk (including sweetened, fortified/growth milk) was the main food source of calcium intake and the second important source of vitamin D intake after butter and margarine. Calcium intake was positively associated with parental education, while vitamin D intake was not.

Effect of dietary fibre on reproductive performance of sows during the first two parities

The aim of this study was to investigate the effect of dietary fibre on reproductive performance during the first two parities. Gilts were randomly allocated to receive three fibrous diets from days 1-90 of gestation, including low fibre [low fiber (LF), 10.8% neutral detergent fiber (NDF), n=132], middle fibre [middle fiber (MF), 15.8% NDF, n=132] and high fibre diet (HF, 20.8% NDF, n=135), until completion of the second parity. Response criteria included backfat measurements, litter size and pig weight at parturition and day 22 of lactation, weaning-oestrus-interval, oestrus rate, sow farrowing and culling rate, uniformity of newborns and relative organ weights. The results showed sows fed LF diet in parity 1 gained more backfat (p<0.05) during gestation but lost more (p<0.05) during lactation than sows fed HF diet. Furthermore, sows fed LF diet farrowed more pigs (+0.7-1.1 pigs, p<0.05) and pigs born alive (+1.0 pigs, p<0.05) relative to sows fed HF diet. Likewise, sows fed LF and MF diets had greater litter weights at parturition (both p=0.06) and day 22 after lactation (both p<0.05). In parity 2, yet, it was MF diet to increase both total pigs born and pigs born alive (+0.9-1.1 pigs, p<0.05) and litter weight (p=0.05) relative to other diets. After 22 d of lactation, intriguingly, sows fed HF diet had most pigs alive (p<0.01-0.07) and heavier litter weight (p=0.07 or 0.2). Feeding HF diet also increased internal organs weight of newborns (p<0.05). Collectively, feeding LF and MF diets had beneficial effects on litter weight at parturition and day 22 of lactation in parity 1, and feeding MF diet until parity 2 was able to improve litter size and weight at parturition, but this positive effect disappeared after 22 days of lactation, instead feeding HF diet showed the optimal litter performance.

GLT-1 overexpression attenuates bladder nociception and local/cross-organ sensitization of bladder nociception

Glutamatergic pathways mediate transmission of pain. Strategies to reduce glutamatergic neurotransmission may have beneficial effects to mitigate nociception. Recent work revealed that overexpression of the astrocytic glutamate transporter (GLT-1) by transgenic or pharmacologic approaches produced a diminished visceral nociceptive response to colonic distension. The purpose of this study was to determine the effect of GLT-1 overexpression on the visceromotor response to bladder distension. Increased glutamate uptake activity produced by 1-wk ceftriaxone (CTX) treatment attenuated 60-64% the visceromotor response to graded bladder distension compared with vehicle-treated mice. One-hour pretreatment with selective GLT-1 antagonist dihydrokainate reversed the blunted visceromotor response to bladder distension produced by 1-wk CTX, suggesting that GLT-1 overexpression mediated the analgesic effect of CTX. Moreover, sensitization of the visceromotor response to bladder distension produced by local bladder irritation (acrolein) was also attenuated by 1-wk CTX treatment. A model of cross-organ sensitization of bladder visceromotor response to distension was next studied to determine whether increased expression of GLT-1 can mitigate colon to bladder sensitization. Intracolonic trinitrobenzene sulfonic acid (TNBS) administered 1 h before eliciting the visceromotor response to graded bladder distension produced a 75-138% increase in visceromotor response compared with animals receiving intracolonic vehicle. In marked contrast, animals treated with 1-wk CTX + intracolonic TNBS showed no enhanced visceromotor response compared with the 1-wk vehicle + intracolonic vehicle group. The study suggests that GLT-1 overexpression attenuates the visceromotor response to bladder distension and both local irritant-induced and cross-organ-sensitized visceromotor response to bladder distension.

Human papillomavirus 16 or 18 infection and prostate cancer risk: a meta-analysis

OBJECTIVE

Whether the oncogenic human papillomavirus (HPV) infection, especially infection with the most common subtypes 16 or 18, is related to prostate carcinogenesis remains conflicting. A meta-analysis with updated data was performed to obtain a more precise estimate of the association between them.

METHODS

Eligible studies were retrieved via both computer searches and review of references. The relation of HPV-16 or HPV-18 infection to prostate cancer (PC) was quantified separately. Stratified analyses based on HPV detection methods and geographic regions were also performed. Estimates of OR with 95% CI were summarized using the fixed-effect or random-effect models as appropriate.

RESULTS

Twenty-five eligible studies were retrieved. All the 25 studies were assigned for exploring the relation of HPV-16 infection to PC, while 13 studies provided additional information on HPV-18 simultaneously. In the overall estimates, the pooled OR indicated no significant increase of PC risk related with either HPV-16 (OR 1.09; 95% CI 0.97-1.23; P(heterogeneity) = 0.135) or HPV-18 (OR 1.05; 95% CI 0.89-1.24; P(heterogeneity) = 0.314) infection. Further quantitative assay of stratified data could also not yield any significant result, except the stratified analysis on HPV-16 DNA detection, which revealed higher HPV-16 DNA prevalence in PC cases (OR 1.54; 95% CI 1.07-2.20; P(heterogeneity) = 0.130).

CONCLUSIONS

Even though the overall estimates did not provide a supportive evidence for the causal role of HPV in prostate carcinogenesis, higher HPV-16 DNA prevalence in PC cases from the stratified analysis still indicated a potential association between HPV infection and PC risk in our meta-analysis.

Relationship between plasma pazopanib concentration and incidence of adverse events in renal cell carcinoma

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Background: Pazopanib (P), an oral angiogenesis inhibitor targeting VEGFR, PDGFR, and c-Kit, is approved by the US FDA for the treatment of advanced renal cell cancer (mRCC). Exploratory analyses of data from a Ph II mRCC study (Hutson T, J Clin Oncol. 27, 2009:1) indicated that 70% of patients (pt) receiving 800mg once daily had a week (wk) 4 plasma P trough (Cmin) >20.6μ g/mL that is associated with improved efficacy (Suttle B, J Clin Oncol. 28, 2010:S3048). In this further analysis of the dataset, we investigated the relation between plasma P concentrations at wk 4 and clinically important adverse events (AE) reported within the first 12 wks of treatment.

Methods: The % of patients with hypertension (defined as ≥ 15mmHg - baseline on 3 occasions)- a recognized PD marker for this class of agents- or other AEs (CTC grades), occurring during the first 12 wks of treatment were calculated by wk4 Cmin quartiles (Q1-Q4: median and range).

Results: P concentrations at 4 wks and AE data were available for 205 out of 225 pts. The incidence of hypertension was 58% in Q1, increasing with concentration to 78% at Q4. The incidence of diarrhea, hair color change, ALT increase, HFS (marked increase), and stomatitis were concentration-dependent, with ≥ 2 fold increase from Q1 to Q4. The incidence of nausea, fatigue, vomiting, dysgeusia, and rash were variable or displayed a flat relationship with Cmin.

Conclusions: The incidence of some AEs, such as diarrhea, ALT, HFS (marked relation), and stomatitis increased with plasma Cmin while others did not. We suggest that concentration-dependent AEs are more likely to respond to P dose reduction and as such, provides support for development of a dose optimization strategy.

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The impact of comorbidity on survival among men with localized prostate cancer

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Background: To provide patients and clinicians more accurate estimates of co-morbidity specific survival stratified by patient age, tumor stage and tumor grade.

Methods: We conducted a ten year competing risk analysis of 19,639 men age 66 years and older identified by the Surveillance, Epidemiology and End Results (SEER) program linked to Medicare program files. All men were diagnosed with localized prostate cancer and received no surgery or radiation within 180 days of diagnosis. The analysis was stratified by tumor grade and stage and by age and co-morbidity at diagnosis classified using the Charlson co-morbidity index. Underlying causes of death were obtained from SEER.

Results: During the first ten years following diagnosis men with moderately and poorly differentiated prostate cancer were more likely to die from causes other than their disease. For men age 66-74 years with stage T1c Gleason score 5-7 disease at diagnosis, ten year overall mortality rates and prostate cancer specific rates were 28.8%, 50.5%, 83.1% and 4.8%, 2.0%, 5.3% respectively for men with Charlson scores 0, 1 and > 2. For men age 66-74 years with T1c Gleason score 8-10 disease at diagnosis, the corresponding rates were 55.0%, 52.0%, 64.3% and 25.7%, 20.2%, 13.7% respectively for men with Charlson scores 0, 1, > 2. Death from competing medical hazards was roughly comparable for men with stage T2 disease and higher for all men over age 75.

Conclusions: Patients and clinicians should consider using co-morbidity specific data to estimate the threat posed by localized prostate cancer.

No significant financial relationships to disclose.

Gastrointestinal toxicities following radiation therapy for localized prostate cancer

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Background: Radiation therapy (RAD) is commonly employed to treat localized prostate cancer; however, representative data regarding treatment related toxicities compared to conservative management (CM) is sparse.

Methods: We performed a population-based cohort study, using Medicare claims data linked to the Surveillance, Epidemiology, and End Results data, to evaluate gastrointestinal (GI) toxicities in men aged 65-85 years treated with either primary RAD or CM for T1-T2 prostate cancer diagnosed in 1992-2005. In this study, only GI toxicities requiring interventional procedures occurring after 6 months of cancer diagnosis were included. Competing risk models were used with the following covariates: year of diagnosis, comorbidity, age, tumor stage, cancer grade, hormone use within 1 year of diagnosis, region, race, poverty and marital status.

Results: Among 41,859 patients in this study, 28,021 patients received radiation therapy, 19,287 with external beam radiation therapy (EBRT) alone, and 5,138 with brachytherapy alone. The most common GI toxicity was GI bleeding or ulceration. GI toxicity rates were 6.1% after 3D-conformal therapy (3D-CRT), 2.8% after intensity modulated radiation therapy (IMRT), 2.6% after brachytherapy, 8.2% after proton therapy and 1.1% for CM patients. In the multivariate models, RAD group was associated with a higher hazard of GI toxicities (hazard ratio [HR] 4.68; 95% CI, 3, 93-5.58) than CM. Comparing to 3D-CRT, brachytherapy (HR 0.62; 95% CI, 0.51-0.75) and IMRT (HR 0.67; 95% CI, 0.55-0.82) are associated with a lower hazard of GI toxicities, while proton therapy is associated with a higher hazard of GI toxicities (HR 2.15; 95% CI, 1.45-3.17).

Conclusions: Radiation therapy is associated with a higher risk of GI toxicities than CM. Among different modalities of radiation therapy, protons therapy is associated with the highest risk of GI toxicities, followed by 3D-CRT, IMRT, and brachytherapy. The increased GI toxicities for patients with proton therapy may reflect a learning curve in the early years.

No significant financial relationships to disclose.

Is radiation therapy superior to conservative management in men with localized prostate cancer?

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Background: Radiation therapy is commonly employed for localized prostate cancer; however, there is little data regarding the comparative effectiveness of radiation therapy (RAD) vs. conservative management (CM).

Methods: We performed a population-based cohort study, using Medicare claims data linked to the Surveillance, Epidemiology, and End Results data, to evaluate outcomes in 42,039 men aged 65-85 years treated with either primary RAD or CM for T1-T2 prostate cancer diagnosed in 1992-2005. To overcome potential biases associated with unmeasured confounding variables, we used instrumental variable analysis (IVA), a pseudo-randomization technique that captures the randomness associated with geographic variations in the use of RAD, to control for overt and hidden confounders.

Results: The majority of patients (57%) had low-risk disease (Gleason score ≤7, PSA <10, and T stage ≤T2a), and RAD was commonly used (60%) with considerable geographic variations. With median age 74 years and median follow-up 119 months, higher RAD use was not associated with improved survival in low-risk patients (10-year disease-specific survival differed by −0.9%, 94.9% vs. 95.8% in the highest and lowest tertile RAD use areas respectively; 95% C.I. −.1 to 0.6%). Among high-risk patients (Gleason score >7 or PSA >20), highest tertile RAD areas showed a borderline improved (2.7%) 10-year disease-survival (83.9% vs. 81.2% in the highest and lowest tertile radiation use areas; 95% C.I. −1.1% to 7.0%). The results in the moderate-risk group were between that of the low- and high-risk group. Primary RAD did not reduce future ADT use (odds ratios 0.95 for low-risk, 1.02 for moderate-risk, and 1.07 for high-risk with corresponding P values of 0.50, 0.86, and 0.51, respectively).

Conclusions: In patients aged over 65 years old with low-risk prostate cancer, primary RAD is unlikely to improve 10-year disease-specific survival or prevent future ADT use. Weighing the potential risks and benefits of radiation therapy is critical for decision making.

No significant financial relationships to disclose.

Plasma cytokine and angiogenic factors (CAFs) predictive of clinical benefit and prognosis in patients (Pts) with advanced or metastatic renal cell cancer (mRCC) treated in phase III trials of pazopanib (PAZO)

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Background: PAZO is a multikinase inhibitor approved for the treatment of mRCC. From phase II study of PAZO in mRCC (VEG102616), plasma CAF analysis from 3 different platforms (cross platform correlation r >0.70) revealed several candidate CAFs including HGF, IL-6, IL-8, TIMP-1, VEGF, E-Selectin and OPN were found to be significantly correlated with clinical benefit (Tran ASCO 2010, #4522). To validate these findings, plasma were analyzed for CAFs from mRCC pts enrolled in phase III randomized, placebo controlled trial with PAZO where progression-free survival (PFS) of 9.2 months of PAZO and 4.2 months of placebo (hazard ratio:0.46 p<.0001) and overall response rate 30% was observed (Sternberg, JCO, 2010).

Methods: Plasma samples (n=344) from phase III randomized, placebo-controlled trial (VEG105192) were analyzed for candidate CAFs by a CLIA-certified laboratory (Aushon Biosystems, MA). These markers of PAZO and placebo arms were correlated with PFS by Cox regression and plotted in Kaplan Meier by using median concentration of each marker as a cutoff.

Results: Higher levels of IL-8 (p<0.006), HGF (p<0.01), OPN (p<0.001) and TIMP-1 (p<0.006) were associated with shorter PFS in PAZO treated pts. Higher levels of all these markers except HGF were also associated with shorter PFS in the placebo arm (IL-8 (p<0.002), OPN (p<0.001), IL-6 (<0.001), TIMP-1 borderline at p= 0.052) and were therefore prognostic. Only IL-6 was predictive of PFS benefit; pts with high IL-6 had a greater relative benefit from PAZO compared to placebo with a HR of 0.32 in the high IL-6 group and 0.57 in the low IL-6 group (p value for interaction 0.009).

Conclusions: This study validated HGF, IL-8, OPN, and TIMP-1 as markers associated with clinical benefit with PAZO treatment. IL-8 and OPN were confirmed as prognostic markers in the placebo arm and IL-6 was both a prognostic marker and predictive marker for pazopanib therapy.

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In Situ, Real-Time Analysis of the Growth of Ferroelectric and Conductive Oxide Heterostructures by a New Time-of-Flight Pulsed Ion Beam Surface Analysis Technique

A new time-of-flight ion scattering and recoil spectroscopy (TOF-ISARS) technique has been developed and is now used to perform in situ, real-time analysis of ferroelectric and conductive oxide layers during growth. Initial results presented here show various major effects, namely: (a) RuO2 films on MgO substrates appear to be terminated in O atoms on the top layer located in between Ru atoms lying in the layer underneath (This effect may have major implications for the explanation of the elimination of polarization fatigue demonstrated for RuO2/PZT/RuO2 heterostructure capacitors); (b) deposition of a Ru monolayer on top of a Pb monolayer results in surface segregation of Pb until a complete Pb layer develops over the Ru monolayer; and (c) a Pb/Zr/Ti layered structure yields a top Pb layer with first evidence of the existence of Pb vacancies, which also may have major implications in relation to the electrical characteristics of PZT-based capacitors.

Environmental Effects on Subcritical Delamination of Dielectric and Metal Films from Organosilicate Glass (OSG) Thin Films

Subcritical delamination of dielectric and metal films from organosilicate glass (OSG) thin films was studied in controlled ambient with different levels of relative humidity and in aqueous environments of varying pH. The material systems studied include OSG/SiO2, OSG/TaN and OSG/SiNx. For both sets of experiments, subcritical crack growth in OSG is found to be described by a model originally developed for soda-lime silicate glass. The threshold energy release rate for water molecule-assisted cracking varies linearly with the natural logarithm of water partial pressure. In aqueous environments, the threshold value decreases linearly with increasing pH in accordance with a simple model. The slope of crack growth rate curve also decreases with increasing pH.

A multinational phase II study of liposome irinotecan (PEP02) for patients with gemcitabine-refractory metastatic pancreatic cancer

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Background: PEP02 is a novel nanoparticle liposome formulation of irinotecan (CPT-11) that has improved pharmacokinetics and tumor biodistribution of both CPT-11 and its active metabolite-SN38 compared to the free form drug. PEP02 has showed encouraging safety and efficacy in various tumor types, including significant antitumor activity in a human pancreatic cancer L3.6pl orthotopic nude mouse xenograft model. In previous phase I studies, PEP02 either alone or in combination with 5-FU/LV demonstrated prolonged disease control in 5 of 7 (71%) patients (pts) with gemcitabine (GEM)-refractory advanced pancreatic cancer (PC). This phase II study aims to evaluate PEP02 monotherapy as 2nd-line treatment in pts with metastatic, GEM-refractory PC.

Methods: Pts were eligible if they had metastatic pancreatic adenocarcinoma, KPS ≥ 70, and progressed following one line of GEM-based therapy. Treatment consisted of PEP02 120 mg/m2 administered as a 90-minute infusion every 3 weeks. A Simon's 2-stage design was used with 16 pts in the first stage and 39 pts in total; primary objective was 3-month survival rate (OS3-month).

Results: Between March 2009 and August 2010, 37 pts were enrolled at 3 centers in the U.S. and Taiwan. Characteristics for the first 31 evaluable pts: 13 M/18 F; age 39-82 yrs; 19 Asian/12 Caucasian, KPS 100/90/80/70: 5/14/4/8. Mean number of treatment cycles is 5 (range, 1-22). Disease control rate (minor response + stable disease >2 cycles) is 52%. 8 of 24 pts (33%) with elevated baseline CA19-9 have had >50% biomarker decline. To date, 23/31 pts (74%) have survived > 3 months, with 4 pts still alive after 1 year. Reasons for study discontinuation: 74% progressive disease, 9% drug-related toxicity, 17% other. Preliminary safety data is available for the first stage. Most common G3/4 adverse events included: fatigue (31%), neutropenia (25%), nausea/vomiting (19%), and diarrhea (13%).

Conclusions: This study has already met its primary endpoint (predicted OS3-month >65%). PEP02 appears to have both activity and tolerable side effects for pts with metastatic, GEM-refractory PC, and represents a promising option for this pt population with few standard options.

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