SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns

Motivation

Testing SNP-SNP interactions is considered as a key for overcoming bottlenecks of genetic association studies. However, related statistical methods for testing SNP-SNP interactions are underdeveloped.

Results

We propose the SNP Interaction Pattern Identifier (SIPI), which tests 45 biologically meaningful interaction patterns for a binary outcome. SIPI takes non-hierarchical models, inheritance modes and mode coding direction into consideration. The simulation results show that SIPI has higher power than MDR (Multifactor Dimensionality Reduction), AA_Full, Geno_Full (full interaction model with additive or genotypic mode) and SNPassoc in detecting interactions. Applying SIPI to the prostate cancer PRACTICAL consortium data with approximately 21 000 patients, the four SNP pairs in EGFR-EGFR , EGFR-MMP16 and EGFR-CSF1 were found to be associated with prostate cancer aggressiveness with the exact or similar pattern in the discovery and validation sets. A similar match for external validation of SNP-SNP interaction studies is suggested. We demonstrated that SIPI not only searches for more meaningful interaction patterns but can also overcome the unstable nature of interaction patterns.

Availability and Implementation

The SIPI software is freely available at http://publichealth.lsuhsc.edu/LinSoftware/ .

Contact

hlin1@lsuhsc.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

Chemoprevention in African American Men With Prostate Cancer

BACKGROUND

Recommendations for cancer screening are uncertain for the early detection or prevention of prostate cancer in African American men. Thus, chemoprevention strategies are needed to specifically target African American men.

METHODS

The evidence was examined on the biological etiology of disparities in African Americans related to prostate cancer. Possible chemopreventive agents and biomarkers critical to prostate cancer in African American men were also studied.

RESULTS

High-grade prostatic intraepithelial neoplasia may be more prevalent in African American men, even after controlling for age, prostate-specific antigen (PSA) level, abnormal results on digital rectal examination, and prostate volume. Prostate cancer in African American men can lead to the overexpression of signaling receptors that may mediate increased proliferation, angiogenesis, and decreased apoptosis. Use of chemopreventive agents may be useful for select populations of men.

CONCLUSIONS

Green tea catechins are able to target multiple pathways to address the underlying biology of prostate carcinogenesis in African American men, so they may be ideal as a chemoprevention agent in these men diagnosed with high-grade prostatic intraepithelial neoplasia.

Sociodemographic and Provider Based Disparities in the Management of Stage I Testicular Cancer

INTRODUCTION

The treatment paradigm for stage I testicular cancer has changed in the setting of accurate staging, reliable followup and a greater understanding of treatment related side effects. We assessed the influences on management decisions in patients with stage I testicular cancer.

METHODS

We retrospectively identified 121 patients with stage I testicular cancer who were evaluated at our institution from 1999 to 2013. Sociodemographic characteristics, pathological features and provider specific factors were compared in patients who underwent surveillance vs treatment. Differences in medians and proportions were determined using the Kruskal-Wallis and chi-square tests. Multivariate logistic regression analysis was performed to identify independent predictors of treatment.

RESULTS

A total of 87 patients had stage I nonseminomatous germ cell tumor and 34 had pure seminoma. Patients with nonseminomatous germ cell tumor who were evaluated before 2011 and those seen by urological oncologists were more likely to undergo primary retroperitoneal lymph node dissection (p <0.01). Patients with nonseminomatous germ cell tumor who were evaluated by medical oncologists more often received chemotherapy (p <0.01). For nonseminomatous germ cell tumors treatment was independently associated with advanced tumor stage and lymph node invasion (OR 15.3, 95% CI 3.26-71.95, p = 0.001). In patients with pure seminoma the use of radiation therapy decreased from 40% to 5% after 2010 while surveillance increased from 47% to 74% (p = 0.056) and no recorded variable was predictive of treatment.

CONCLUSIONS

Advanced stage and lymph node invasion in patients with stage I nonseminomatous germ cell tumor are drivers of treatment. Management also depends on the specialty of the treating provider, suggesting the possibility of bias during patient counseling. In turn, this suggests the need for patient assessment through a multidisciplinary approach.

Perioperative Transfusion of Leukocyte-depleted Blood Products in Contemporary Radical Cystectomy Cohort Does Not Adversely Impact Short-term Survival

OBJECTIVE

To evaluate the effect of leukoreduced-only perioperative blood transfusion (PBT) and corresponding survival outcomes in a radical cystectomy cohort of patients.

MATERIALS AND METHODS

We analyzed data from 1026 patients who underwent radical cystectomy at our institution. PBT was defined as transfusion in the intraoperative or within the postoperative hospitalization period. Multivariable analyses using Cox proportional hazards were performed to measure the association between PBT, patient variables, and 3 primary end points: recurrence-free survival, disease-specific survival, and overall survival. Kaplan-Meier curves estimated survival times and were compared with log-rank test.

RESULTS

Overall, of a total of 1026 patients, 341 (33.2%) received leukoreduced PBT. The median follow-up was 27.5 months. Transfused patients were more likely to be female, had higher estimated blood loss, lower preoperative hemoglobin, were more likely to have received neoadjuvant chemotherapy, or had undergone a continent urinary diversion. Higher pathologic tumor and nodal stage were observed more frequently in patients who received PBT. On multivariable analysis, PBT was not associated with worse recurrence-free survival, disease-specific survival, and overall survival (all P > .05). Kaplan-Meier curves did not show any significant differences (all P > .05) between the transfused and nontransfused groups. In addition, no differences were found in regard to timing of transfusion, that is, intraoperative vs postoperative, in distinct analysis.

CONCLUSION

No significant association was found between leukoreduced PBT and worse survival outcomes at short-term follow-up in a contemporary cohort of cystectomy patients. Prospective long-term follow-up is warranted.

Prostate Cancer, Version 1.2016

The NCCN Guidelines for Prostate Cancer address staging and risk assessment after an initial diagnosis of prostate cancer and management options for localized, regional, and metastatic disease. Recommendations for disease monitoring, treatment of recurrent disease, and systemic therapy for metastatic castration-recurrent prostate cancer also are included. This article summarizes the NCCN Prostate Cancer Panel's most significant discussions for the 2016 update of the guidelines, which include refinement of risk stratification methods and new options for the treatment of men with high-risk and very-high-risk disease and progressive castration-naïve disease.

Geographical Factors Associated with Health Disparities in Prostate Cancer

Background

Treatment variation in prostate cancer is common, and it is driven by clinical and clinician factors, patient preferences, availability of resources, and access to physicians and treating facilities. Most research on treatment disparities in men with prostate cancer has focused on race and socioeconomic factors. However, the geography of disparities — capturing racial and socioeconomic differences based on where patients live — can provide insight into barriers to care and help identify outlier areas in which access to care, health resources, or both are more pronounced.

Methods

Research regarding treatment patterns and disparities in prostate cancer using the Geographical Information System (GIS) was searched. Studies were limited to English-language articles and research focused on US populations. A total of 43 articles were found; of those, 30 provided information about or used spatial or geographical analyses to assess and describe differences or disparities in prostate cancer and its treatment. Two additional GIS resources were included.

Results

The research on geographical and spatial determinants of prostate cancer disparities was reviewed. We also examined geographical analyses at the state level, focusing on Florida. Overall, we described a geographical framework to disparities that affect men with prostate cancer and reviewed existing published evidence supporting the interplay of geographical factors and disparities in prostate cancer.

Conclusions

Disparities in prostate cancer are common and persistent, and notable differences in treatment are observable across racial and socioeconomic strata. Geographical analysis provides additional information about where disparate groups live and also helps to map access to care. This information can be used by public health officials, health-systems administrators, clinicians, and policymakers to better understand and respond to geographical barriers that contribute to disparities in care.

Salvage robotic prostatectomy for radio recurrent prostate cancer: technical challenges and outcome analysis

INTRODUCTION

The published data on salvage robot assisted radical prostatectomy (sRARP) is limited. Our aim was to perform a systematic review of the literature on sRARP after radiation failure in patients with prostate cancer and systematically analyse the available evidence for operative and oncological outcomes.

EVIDENCE ACQUISITION

A systematic review of the literature using Pubmed, Scopus, Cochrane library and ScienceDirect databases was performed in June 2016 using medical subject headings and free-text protocol. The search was conducted by applying the following search terms: salvage therapy, salvage, prostatectomy and robotics.

EVIDENCE SYNTHESIS

We report on ten case series including 197 men undergoing sRARP after varying modalities of radiotherapy. Over two thirds are recurrence free at the time of follow-up but with continence rates of only 60% and potency rates of only 26%. Complications requiring intervention are few at 16% though higher than primary RARP.

CONCLUSIONS

sRARP is increasingly acceptable as a treatment modality to be offered to men who fail initial radiation treatment but should be accompanied by appropriate counselling regarding the potential functional outcomes and complications. Series with longer follow up will be helpful to assess the durability of oncological outcomes while improvements in patient selection and adaption of meticulous surgical technique around the apex could improve continence rates. The concept of concomitant extended PLND remains an issue for debate and the experience with this approach at the time of sRARP and its benefit need further scrutiny.

Effect of utilization of veno-venous bypass vs. cardiopulmonary bypass on complications for high level inferior vena cava tumor thrombectomy and concomitant radical nephrectomy

Purpose:

To determine if patients with renal cell carcinoma (RCC) with levels III and IV tumor thrombi are receive any reduction in complication rate utilizing veno-venous bypass (VVB) over cardiopulmonary bypass (CPB) for high level (III/IV) inferior vena cava (IVC) tumor thrombectomy and concomitant radical nephrectomy.

Materials and Methods:

From May 1990 to August 2011, we reviewed 21 patients that had been treated for RCC with radical nephrectomy and concomitant IVC thrombectomy employing either CPB (n =16) or VVB (n=5). We retrospectively reviewed our study population for complication rates and perioperative characteristics.

Results:

Our results are reported using the validated Dindo-Clavien Classification system comparing the VVB and CPB cohorts. No significant difference was noted in minor complication rate (60.0% versus 68.7%, P=1.0), major complication rate (40.0% versus 31.3%, P=1.0), or overall complication rate (60.0% versus 62.5%, P=1.0) comparing VVB versus CPB. We also demonstrated a trend towards decreased time on bypass (P=0.09) in the VVB cohort.

Conclusion:

The use of VVB over CPB provides no decrease in minor, major, or overall complication rate. The use of VVB however, can be employed on an individualized basis with final decision on vascular bypass selection left to the discretion of the surgeon based on specifics of the individual case.

Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics

PURPOSE

Targeted therapies in renal cell carcinoma (RCC) are limited by acquired resistance. Novel therapeutic targets are needed to combat resistance and, ideally, target the unique biology of RCC subtypes.

EXPERIMENTAL DESIGN

Tyrosine kinases provide critical oncogenic signaling and their inhibition has significantly impacted cancer care. To describe a landscape of tyrosine kinase activity in RCC that could inform novel therapeutic strategies, we performed a mass spectrometry-based system-wide survey of tyrosine phosphorylation in 10 RCC cell lines as well as 15 clear cell and 15 papillary RCC human tumors. To prioritize identified tyrosine kinases for further analysis, a 63 tyrosine kinase inhibitor (TKI) drug screen was performed.

RESULTS

Among the cell lines, 28 unique tyrosine phosphosites were identified across 19 kinases and phosphatases including EGFR, MET, JAK2, and FAK in nearly all samples. Multiple FAK TKIs decreased cell viability by at least 50% and inhibited RCC cell line adhesion, invasion, and proliferation. Among the tumors, 49 unique tyrosine phosphosites were identified across 44 kinases and phosphatases. FAK pY576/7 was found in all tumors and many cell lines, whereas DDR1 pY792/6 was preferentially enriched in the papillary RCC tumors. Both tyrosine kinases are capable of transmitting signals from the extracellular matrix and emerged as novel RCC therapeutic targets.

CONCLUSIONS

Tyrosine kinase profiling informs novel therapeutic strategies in RCC and highlights the unique biology among kidney cancer subtypes. Clin Cancer Res; 22(22); 5605-16. ©2016 AACR.

Clinical role of additional adjuvant chemotherapy in patients with locally advanced urothelial carcinoma following neoadjuvant chemotherapy and cystectomy

PURPOSE

Neoadjuvant chemotherapy (NAC) can downstage invasive bladder cancers prior to radical cystectomy (RC) and improve overall survival. However, the optimal management in patients with persistent non-organ confined disease (pT3-T4 and/or pN+) following RC has not been completely defined. The aim of this study was to describe outcomes associated with the use of adjuvant chemotherapy (AC) in patients with residual non-organ confined cancer at RC following NAC.

MATERIALS AND METHODS

Using data from a high-volume referral institution, pT3-T4 and/or pN+ patients who received NAC and then also RC were identified. Recurrence-free survival (RFS) and cancer-specific survival (CSS) were assessed with Kaplan-Meier analysis.

RESULTS

From 2001 to 2013, 161 patients received NAC and then RC. Eighty-eight pT3-T4 and/or pN+ patients were identified. Twenty-nine (33 %) received AC. Adjuvant chemotherapy in the majority of patients was carboplatin-based (16), followed by cisplatin (8) and other, mainly taxane-containing regimens (5). The median RFS was 17.5 months in the AC and 13.7 months in the non-AC group (p = 0.78). AC remained an insignificant predictor for RFS after adjusting for pT, pN and margin status (HR 0.89, 95 % CI 0.48-1.68]). CSS was 23 and 22 months (p = 0.65) and remained insignificant after adjusting for pathologic confounders.

CONCLUSIONS

In our current study population, adjuvant conventional cytotoxic chemotherapy was not associated with significant improvements in RFS or CSS. The choice of AC regimens, and incorporation of newer treatments, may be the key for improving outcomes in this high-risk patient group.

Long term survival and predictors of disease reclassification in patients on an active surveillance protocol for prostate cancer

INTRODUCTION

Up to 50% of patients will have disease reclassification while on active surveillance (AS) for their prostate cancer. Determining which patients will have reclassification that will impact their survival is difficult. We investigated clinicopathologic factors associated with disease reclassification and differences in both overall and metastasis free survival between those treated and those remaining on AS.

MATERIALS AND METHODS

We performed a retrospective review of patients who were enrolled in an AS protocol between 1994 and 2000. Inclusion criteria for AS were: < cT2a disease, PSA < 10 ng/mL, < 50% of single core involvement, and Gleason score < 7, as well as sufficient follow up for evaluation (at least 1 subsequent transrectal ultrasound guided biopsy after initial diagnosis).

RESULTS

There were 102 patients that met the inclusion criteria with median age of 70 years (IQR 68-73), follow up of 9.25 years (IQR 6.1-12.2) and time to disease reclassification of 4.7 years (IQR 2.8-7.9). Only prostate-specific antigen (PSA) density ≥ 0.15 was a significant predictor of disease reclassification with a hazard ratio of 5.5 (95% confidence interval 2.3-13.4, p < 0.01). There was no significant difference in metastasis free and overall survival between patients who received treatment and those that continued on AS despite reclassification of disease; this remained true even while stratifying patients by age ≥ 70 compared to those < 70 years old.

CONCLUSIONS

PSA density is a significant predictor of disease reclassification and AS remains a safe option for patients with low risk prostate cancer with up to 10 years of follow up.

Is percent seminoma associated with intraoperative morbidity during post-chemotherapy RPLND?

INTRODUCTION

To evaluate whether varying degrees of seminomatous elements in the primary orchiectomy specimen would be predictive of patient morbidity during post-chemotherapy retroperitoneal lymph node dissection (PC-RPLND) since the desmoplastic reaction with seminoma is associated with increased intraoperative complexity.

MATERIALS AND METHODS

We retrospectively identified 127 patients who underwent PC-RPLND for residual retroperitoneal masses. Clinicodemographic, intraoperative, and 30 day postoperative outcomes were compared for patients with pure seminoma (SEM), mixed germ cell tumors (GCT) containing seminoma elements (NS+SEM), and tumors with no seminoma elements (NS). Multivariate logistic regression was used to determine independent predictors of intraoperative and postoperative 30 day complications.

RESULTS

We excluded 19 patients who received chemotherapy prior to orchiectomy, 2 patients with primary extragonadal GCT, and 3 patients who underwent re-do RPLND, leaving 103 patients for analysis. Fourteen patients (13.6%) had SEM, 18 (17.5%) had NS+SEM, and 71 (68.9%) had only NS elements. SEM patients were older (p = 0.03), had more intraoperative blood loss (p = 0.03), and were more likely to have residual seminomatous components in their post-chemotherapy lymph node (LN) histology (p = 0.01). Percent seminoma in the orchiectomy specimen was an independent predictor of estimated blood loss > 1.5 liters (odds ratio: 1.04, 95% confidence interval: 1.01-1.07; p = 0.013) after adjusting for age, stage, IGCCC risk category, preop chemotherapy, number and largest LN removed, need for vascular or adjacent organ resection (including nephrectomy), and LN histology.

CONCLUSIONS

Higher percentage of seminoma in the orchiectomy specimen is associated with increased estimated blood loss during PC-RPLND. Percent seminoma, therefore, may be a useful prognostic tool for appropriate pre-surgical planning prior to PC-RPLND.

Predictors of Postoperative Complications in Patients Who Undergo Radical Nephrectomy and IVC Thrombectomy: A Large Contemporary Tertiary Center Analysis

In an analysis of a large single-institution experience in the surgical management of renal cell carcinoma (RCC) and inferior vena cava (IVC) thrombus, the authors present the effect of RCC characteristics on survival, and aim to identify potential preoperative variables predictive of intraoperative complexity with regard to estimated blood loss, transfusion volume, surgical time, length of stay, and postoperative complication rates. Age, American Society of Anesthesiologists score, Charlson Comorbidity Index, preoperative calcium, preoperative creatinine, and IVC wall invasion were significantly related to complication rates.

INTRODUCTION

Preoperative laboratory values are commonly used as markers of health and potential disease burden, however, their effect on perioperative complexity has not previously been assessed. The authors aimed to evaluate the effect of renal cell carcinoma and inferior vena cava (IVC) thrombus characteristics on cancer-specific survival (CSS), and identify potential preoperative variables predictive of intraoperative complexity.

MATERIALS AND METHODS

In a retrospective chart review we identified 144 patients who underwent nephrectomy and IVC thrombectomy. Univariate and multivariate analyses were used to assess the effect of disease characteristics on CSS and postoperative complications. Linear regression analysis was used to determine the association between preoperative laboratory values and intraoperative complexity characterized by estimated blood loss (EBL), transfusion volume (TV), operative time, and length of hospital stay (LOS).

RESULTS

Analysis of intraoperative complexity revealed a significant correlation between preoperative creatinine (Cr) and EBL (P = .022), TV (P = .041), and LOS (P = .005), and preoperative hemoglobin (Hgb) was associated with increased EBL (P < .001) and TV (P < .001). Multivariate analyses showed a significant relationship between overall complication rates and preoperative calcium (Ca; P = .012), American Society of Anesthesiologists (ASA) score (P = .003), and IVC wall invasion (P = .005), and a significant association between major complications and preoperative Ca (P = .011), preoperative Cr (P = .041), age (P = .050), and Charlson Comorbidity Index (CCI; P = .002).

CONCLUSION

With regard to intraoperative complexity and postoperative complications, preoperative Cr and Hgb were significantly associated with increased EBL, TV, and LOS, and ASA score, preoperative Ca, preoperative Cr, IVC wall invasion, age, and CCI were found to have significant relationships with complication rates.

Clinical Outcomes After Neoadjuvant Chemotherapy and Radical Cystectomy in the Presence of Urothelial Carcinoma of the Bladder With Squamous or Glandular Differentiation

We assessed 126 patients with cT1-4, N0-2 urothelial carcinoma of the bladder who were treated with neoadjuvant chemotherapy followed by radical cystectomy. Twenty patients (16%) had squamous or glandular histological variation (HV). Significant pathologic downstaging (pT<2, N0) was seen in the HV patients (60% vs. 32%; P [ .02) and this difference remained significant after controlling for other clinical and pathological confounders.

BACKGROUND

To assess the pathological response rates and survival outcomes in patients with squamous or glandular histological variation (HV) treated with neoadjuvant chemotherapy (nCT) and radical cystectomy (RC), and compare these with patients with pure urothelial carcinoma of the bladder (PUCB).

PATIENTS AND METHODS

We performed a retrospective review of patients with clinical stage T1-4, N0-2 urothelial cancer treated with cisplatin-based nCT and RC in a single institution setting. Patients who received neoadjuvant carboplatin-based regimens were excluded. The primary end point was pathological response. Overall survival (OS) was a secondary end point. Logistic regression and Cox proportional hazard models were used for multivariate analyses.

RESULTS

We evaluated 126 patients, including 20 (16%) with HV. Median estimated glomerular filtration rate (79.6 vs. 73.6 mL/min; P = .07) and the rate of complete endoscopic resection (75% vs. 40%; P = .01) were higher in the HV patients. Complete pathological response was similar between the groups (21% PUCB vs. 25% HV; P = .77). However, a significantly higher rate of pathologic downstaging (pT<2, N0 [pDS]) was seen in the HV patients (60% vs. 32%; P = .02). In a logistic regression model to predict pDS, in which clinically relevant confounding variables were included, HV (odds ratio, 4.01; 95% confidence interval, 1.16-13.9) remained an independent predictor of pDS. OS was similar between the 2 groups (HV: 45.7 vs. PUCB: 48.3 months; P = .73).

CONCLUSION

When controlling for confounding factors, improved pDS rates were seen in the HV patients although there were no significant differences in the OS stratified according to histology. These results support the continued use of systemic nCT for this subgroup of patients.

Minimally invasive post-chemotherapy retroperitoneal lymph node dissection for nonseminoma

INTRODUCTION

We present our experience with minimally-invasive retroperitoneal lymph node dissection (MI-RPLND) in the post-chemotherapy (PC) setting for residual masses in patients with nonseminoma.

MATERIALS AND METHODS

Nineteen men who underwent PC MI-RPLND (14--laparoscopic, 5--robotic) for low-volume residual disease (no more than 5 clinically enlarged retroperitoneal masses, size < 5 cm, no adjacent organ or vascular invasion) between 2006 and 2011 were identified. Clinicodemographic information and pathological outcomes were reported.

RESULTS

Median age of our study population was 32 (interquartile range [IQR]: 28-39). Most patients presented with clinical stage II disease (63%) and were categorized as good risk (90%) by the International Germ Cell Consensus Classification. Median size of residual masses on PC imaging was 2.1 cm (IQR: 1.7-3). Full-template bilateral RPLND was completed in 53% of cases, and modified left-sided RPLND in 47%. Median operative time was 370 minutes (IQR: 320-420), and median estimated blood loss was 300 cc (IQR: 150-450). Median length of stay was 3 days (IQR: 2-3). Five patients (26%) experienced a postoperative 30 day complication, but none were higher than Clavien grade II. On final pathology, median number of lymph nodes removed was 12 (IQR: 8-23), and 8 patients (42%) had residual teratoma. No patient experienced a recurrence at median follow up of 24 months (IQR: 5-76).

CONCLUSIONS

PC MI-RPLND is a feasible option in a select group of patients with acceptable patient morbidity and short-term outcomes. Longer follow up is required to determine the oncologic efficacy of this approach.

Predicting postoperative complications of inguinal lymph node dissection for penile cancer in an international multicentre cohort

OBJECTIVES

To assess the potential complications associated with inguinal lymph node dissection (ILND) across international tertiary care referral centres, and to determine the prognostic factors that best predict the development of these complications.

MATERIALS AND METHODS

A retrospective chart review was conducted across four international cancer centres. The study population of 327 patients underwent diagnostic/therapeutic ILND. The endpoint was the overall incidence of complications and their respective severity (major/minor). The Clavien-Dindo classification system was used to standardize the reporting of complications.

RESULTS

A total of 181 patients (55.4%) had a postoperative complication, with minor complications in 119 cases (65.7%) and major in 62 (34.3%). The total number of lymph nodes removed was an independent predictor of experiencing any complication, while the median number of lymph nodes removed was an independent predictor of major complications. The American Joint Committee on Cancer stage was an independent predictor of all wound infections, while the patient's age, ILND with Sartorius flap transposition, and surgery performed before the year 2008 were independent predictors of major wound infections.

CONCLUSIONS

This is the largest report of complication rates after ILND for squamous cell carcinoma of the penis and it shows that the majority of complications associated with ILND are minor and resolve without prolonged morbidity. Variables pertaining to the extent of disease burden have been found to be prognostic of increased postoperative morbidity.