Silent mutations reveal therapeutic vulnerability in RAS Q61 cancers.

RAS family members are the most frequently mutated oncogenes in human cancers. Although KRAS(G12C)-specific inhibitors show clinical activity in patients with cancer1-3, there are no direct inhibitors of NRAS, HRAS or non-G12C KRAS variants. Here we uncover the requirement of the silent KRASG60G mutation for cells to produce a functional KRAS(Q61K). In the absence of this G60G mutation in KRASQ61K, a cryptic splice donor site is formed, promoting alternative splicing and premature protein termination. A G60G silent mutation eliminates the splice donor site, yielding a functional KRAS(Q61K) variant. We detected a concordance of KRASQ61K and a G60G/A59A silent mutation in three independent pan-cancer cohorts. The region around RAS Q61 is enriched in exonic splicing enhancer (ESE) motifs and we designed mutant-specific oligonucleotides to interfere with ESE-mediated splicing, rendering the RAS(Q61) protein non-functional in a mutant-selective manner. The induction of aberrant splicing by antisense oligonucleotides demonstrated therapeutic effects in vitro and in vivo. By studying the splicing necessary for a functional KRAS(Q61K), we uncover a mutant-selective treatment strategy for RASQ61 cancer and expose a mutant-specific vulnerability, which could potentially be exploited for therapy in other genetic contexts.

Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants.

Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, branching is inhibited, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance responses. Here we describe TAA1, an aminotransferase, and show that TAA1 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway is rapidly deployed to synthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance.

How does patient-centered communication in ovarian cancer care enhance patient well-being? A mixed methods study.

OBJECTIVE: Greater perceived patient-centered communication (PCC) is associated with better health-related quality of life (HRQoL) in patients with ovarian cancer. Quantitative measures of PCC and HRQoL do little to explain this association. We interviewed patients with high and low ratings of PCC to understand how it is associated with HRQoL. METHODS: Explanatory sequential mixed methods study. Participants were English-speaking U.S. adults with ovarian cancer. We assessed PCC with the Patient-Centered Communication - Cancer (PCC-Ca)-36 (possible score range 1-5; higher scores represent greater patient-centeredness), and purposively sampled 14 participants with total scores in the top and bottom quartiles. Participants completed individual, semi-structured interviews about their communication experiences. Guided by the National Cancer Institute Framework for PCC in Cancer Care, we analyzed interview transcripts using directed content analysis. We integrated survey and interview findings in a joint display. RESULTS: Among 176 survey respondents, PCC-Ca-36 total scores ranged from 1.7 to 5.0. Participants with scores in the top quartile (4.8-5.0) perceived clinicians as proactive and attentive to psychosocial concerns. Those with scores in the bottom quartile (1.7-3.5) described not feeling known as an individual and receiving limited support for self-management. CONCLUSIONS: The association between PCC and QoL may be partially explained by differences in perceived support for psychosocial concerns and self-management. PCC may facilitate receipt of proactive, personalized care.

Concordance between influential adverse treatment outcomes and localized prostate cancer treatment decisions.

BACKGROUND: Although treatment decisions for localized prostate cancer (LPC) are preference-sensitive, the extent to which individuals with LPC receive preference-concordant treatment is unclear. In a sample of individuals with LPC, the purpose of this study was to (a) assess concordance between the influence of potential adverse treatment outcomes and treatment choice; (b) determine whether receipt of a decision aid predicts higher odds of concordance; and (c) identify predictors of concordance from a set of participant characteristics and influential personal factors. METHODS: Participants reported the influence of potential adverse treatment outcomes and personal factors on treatment decisions at baseline. Preference-concordant treatment was defined as (a) any treatment if risk of adverse outcomes did not have a lot of influence, (b) active surveillance if risk of adverse outcomes had a lot of influence, or (c) radical prostatectomy or active surveillance if risk of adverse bowel outcomes had a lot of influence and risk of other adverse outcomes did not have a lot of influence. Data were analyzed using descriptive statistics and logistic regression. RESULTS: Of 224 participants, 137 (61%) pursued treatment concordant with preferences related to adverse treatment outcomes. Receipt of a decision aid did not predict higher odds of concordance. Low tumor risk and age ≥ 60 years predicted higher odds of concordance, while attributing a lot of influence to the impact of treatment on recreation predicted lower odds of concordance. CONCLUSIONS: Risk of potential adverse treatment outcomes may not be the foremost consideration of some patients with LPC. Assessment of the relative importance of patients' stated values and preferences is warranted in the setting of LPC treatment decision making. CLINICAL TRIAL REGISTRATION: NCT01844999 ( www. CLINICALTRIALS: gov ).

Self-Reported Severity, Characteristics, and Functional Limitations of Chemotherapy-Induced Peripheral Neuropathy.

BACKGROUND: The early identification of chemotherapy-induced peripheral neuropathy (CIPN) (e.g., numbness or tingling in the fingers or toes) is important due to its frequency and the few effective treatment options available. The identification of common patient-reported CIPN characteristics and associated functional limitations may help to facilitate patient-clinician discussions of CIPN in practice. AIMS: To quantify the severity, duration, location, characteristics, and associated functional limitations of chemotherapy-induced peripheral neuropathy (CIPN) in patients receiving neurotoxic chemotherapy. DESIGN: Exploratory secondary analysis of a prospective, two-phase study SETTING: Breast, gastrointestinal, and multiple myeloma clinics at Dana-Farber Cancer Institute. PARTICIPANTS: 142 individuals who planned to receive at least three more cycles of neurotoxic chemotherapy after consent. METHODS: Participants self-reported CIPN using standardized measures (i.e., PRO-CTCAE™ Numbness and Tingling Items or 0-10 numerical rating scale of worst CIPN pain intensity) and/or study team generated follow up questions about CIPN location, duration, characteristics, and functional limitations prior to three consecutive clinic visits (T1, T2, T3). Participants' responses to the CIPN self-report questionnaires were described by chemotherapy type and age. RESULTS: Over approximately 36.5 days (T1-T3), the percentage of participants reporting at least mild CIPN increased from 59.3% to 71%. At T3, patients with non-painful (n = 98) or painful neuropathy (n = 34) frequently reported symptoms in the fingers (non-painful = 83.5%, painful = 76.5%) or toes (non-painful = 49.5%, painful = 41.2%) and characterized symptoms as numbness (non-painful = 54.1%, painful = 50%) or tingling (non-painful = 68.4%, painful = 82.4%). Self-reported CIPN functional limitations (n = 55) included difficulties with buttoning a shirt (38.2%) or walking (25.5%). Paclitaxel-related CIPN (n = 33) was frequently characterized as "continuous" (30.3%), whereas oxaliplatin-related CIPN (n = 51) was frequently characterized as "intermittent" (41.2%). Young adults (15-39 years old, n = 15) frequently reported moderate-severe non-painful CIPN (46.7%), painful CIPN (40%), and CIPN interference (33.3%). CONCLUSIONS: Consistent with qualitative research, participants frequently described CIPN as numbness and/or tingling in the fingers and/or toes.

Transitioning from heparin to saline locks for central venous access devices in oncology: An evidence-based practice approach.

Central vascular access devices (CVADs) are often essential to the care of patients undergoing long-term cancer treatment. CVAD maintenance is an essential oncology nurse competency. Evidence-based practice (EBP) in flushing and locking help to prevent intraluminal occlusion, a common complication. Heparinized saline (HS) has been the standard locking solution for CVADs. However, research indicates no superiority of HS over normal saline (NS). The objectives of this EBP project were 1) to evaluate whether a significant difference in intraluminal occlusion was associated with the change from HS to NS use for locking CVADs in ambulatory oncology care, and 2) to evaluate the effects of peer nurse mentoring on nurses' and patients' perspectives about the practice change. Analysis of data revealed decreases in alteplase usage after transitioning to NS locking. Patient and nurse surveys indicated that peer nurse mentoring increased nurse and patient confidence and competence in making the practice transition.

Decision support for men with prostate cancer: Concordance between treatment choice and tumor risk.

BACKGROUND: Decision support tools improve decisional conflict and elicit patient preferences related to prostate cancer treatment. It was hypothesized that men using the Personal Patient Profile-Prostate (P3P) would be more likely to pursue guideline-concordant treatment. METHODS: Men from a trial assessing the P3P decision support intervention were identified. The primary exposure was allocation to P3P (vs usual care), and the outcome was appropriate treatment per guidelines (eg, low risk = active surveillance). It was assessed whether providers recommended against any treatment options (ie, restricted). A multivariable model was fit for men with low-risk cancer that estimated the odds of the outcome of interest. RESULTS: This study identified 295 men in the cohort: 113 (38%) had low-risk disease, 119 (40%) had favorable intermediate-risk disease, and 63 (21%) had unfavorable intermediate-risk disease. Among low-risk patients, more men pursued active surveillance after using P3P whether they were given unrestricted (62% vs 54% with usual care; P = .54) or restricted options (71% vs 59% with usual care; P = .34). After adjustments, only Black race (odds ratio [OR], 0.31; 95% CI, 0.11-0.89) and restricted options (OR, 0.23; 95% CI, 0.08-0.65) had an inverse association with the receipt of surveillance for patients with low-risk prostate cancer. An impact associated with P3P versus usual care (OR, 0.89; 95% CI, 0.36-2.20) was not observed. CONCLUSIONS: Among men in a trial assessing a decision support tool, Black race and restricted treatment options were associated with less use of active surveillance for low-risk prostate cancer. Although the P3P instrument ameliorates decisional conflict, its use was not associated with more appropriate alignment of treatment with disease risk.

Exploring the impact of a decision support algorithm to improve clinicians' chemotherapy-induced peripheral neuropathy assessment and management practices: a two-phase, longitudinal study.

BACKGROUND: Chemotherapy-induced peripheral neuropathy (CIPN) negatively affects physical function and chemotherapy dosing, yet, clinicians infrequently document CIPN assessment and/or adhere to evidence-based CIPN management in practice. The primary aims of this two-phase, pre-posttest study were to explore the impact of a CIPN clinician decision support algorithm on clinicians' frequency of CIPN assessment documentation and adherence to evidence-based management. METHODS: One hundred sixty-two patients receiving neurotoxic chemotherapy (e.g., taxanes, platinums, or bortezomib) answered patient-reported outcome measures on CIPN severity and interference prior to three clinic visits at breast, gastrointestinal, or multiple myeloma outpatient clinics (n = 81 usual care phase [UCP], n = 81 algorithm phase [AP]). During the AP, study staff delivered a copy of the CIPN assessment and management algorithm to clinicians (N = 53) prior to each clinic visit. Changes in clinicians' CIPN assessment documentation (i.e., index of numbness, tingling, and/or CIPN pain documentation) and adherence to evidence-based management at the third clinic visit were compared between the AP and UCP using Pearson's chi-squared test. RESULTS: Clinicians' frequency of adherence to evidence-based CIPN management was higher in the AP (29/52 [56%]) than the UCP (20/46 [43%]), but the change was not statistically significant (p = 0.31). There were no improvements in clinicians' CIPN assessment frequency during the AP (assessment index = 0.5440) in comparison to during the UCP (assessment index = 0.6468). CONCLUSIONS: Implementation of a clinician-decision support algorithm did not significantly improve clinicians' CIPN assessment documentation or adherence to evidence-based management. Further research is needed to develop theory-based implementation interventions to bolster the frequency of CIPN assessment and use of evidence-based management strategies in practice. TRIAL REGISTRATION: ClinicalTrials.Gov, NCT03514680 . Registered 21 April 2018.

Perceived patient-centered communication, quality of life, and symptom burden in individuals with ovarian cancer.

OBJECTIVE: To describe perceptions of patient-centered communication (PCC); assess whether physician specialty, patient characteristics, or health system characteristics are associated with PCC; and identify associations between PCC, health-related quality of life (HRQoL), and symptom burden among individuals with ovarian cancer. METHODS: Cross-sectional, descriptive survey of English-speaking adults with ovarian cancer. PCC, HRQoL, and ovarian cancer symptom burden were assessed with the PCC-Ca-36, the FACT-G, and the FOSI-18, respectively. PCC-Ca-36 scores were summarized using descriptive statistics. Predictors of PCC-Ca-36, FACT-G, and FOSI-18 scores were identified using multiple linear regression. RESULTS: Participants (n = 176) had a mean age of 59.4 years (SD = 12.1). The majority (65.9%) had advanced-stage disease, while 42.0% were receiving treatment. The mean PCC-Ca-36 total score was 4.09 (SD = 0.78) out of a possible 5, indicating participants often perceived that clinicians engaged in PCC. Among the PCC functions, participants reported that clinicians least often enabled patient self-management (M = 3.65, SD = 0.99), responded to emotions (M = 3.84, SD = 1.04), and managed uncertainty (M = 3.91, SD = 0.93). In multivariable analyses, neither physician specialty nor patient and health system characteristics were significantly associated with overall PCC. Greater overall PCC predicted better overall HRQoL; better social/family, emotional, and functional well-being; and lower overall and physical symptom burden (all p ≤ 0.05). CONCLUSION: Greater PCC is significantly associated with better HRQoL and lower symptom burden among individuals with ovarian cancer. PRACTICE IMPLICATIONS: Promotion of PCC is a promising strategy to improve patient-reported outcomes in the ovarian cancer care setting.

Informing models of cancer genetics care in the era of multigene panel testing with patient-led recommendations.

The study describes patient-reported experiences and recommendations to improve the genetic counseling and multigene panel testing (MGPT) process. A descriptive mixed-method study with concurrently collected and integrated qualitative and quantitative data was conducted. Eligible participants were English-speaking adults with a breast or gynecologic cancer diagnosis who had received genetic counseling and testing with a MGPT from one Comprehensive Cancer Center. Satisfaction with the genetic counseling, genetic knowledge using a recently validated scale (KnowGene), the multidimensional impact of cancer risk assessment (MICRA), family communication, and the association with demographic factors were evaluated. To supplement the large quantitative data set, qualitative focus group responses and open-ended text items were collected. Univariate and multivariable associations between each outcome of interest and personal characteristics were assessed. Qualitative data were content-analyzed. 603 participants completed the survey (48% response rate) and 10 individuals participated in the focus groups. Participants were mostly Caucasian, educated with a college degree or more, and female with median age 58 (24-91), and 78% of participants had a breast cancer diagnosis. Of all individuals undergoing genetic testing using a MGPT, 13% had a pathogenic variant identified, and 30% had a variant of uncertain significance (VUS). Overall, participants reported satisfaction with the genetic counseling and testing process (mean 36.9 [SD 4.7]). On average, participants had 7 incorrect answers out of 19 on the genetic knowledge scale (mean 12.3 [SD 3.4]). MICRA scores showed overall low levels of distress and uncertainty, as well as positive experiences, with wide variability (median 17 [0-84]). Age, marital status, education level, type of cancer diagnosis, and genetic testing results were significantly associated with outcomes. Most participants communicated genetic testing results to mainly female first-degree relatives. A wide range of individual preferences affecting overall satisfaction, or suggestions for improvement were shared. As new models of streamlined cancer genetic services are being clinically implemented, approaches should continue to assess and tailor the process based on patients' informational and emotional needs.

The Jacki Jacket after mastectomy with reconstruction: a randomized pilot study.

BACKGROUND: Breast cancer patients undergoing mastectomy with reconstruction (TM + R) often experience post-operative discomfort from surgical drains. Despite a variety of garment options for use in the post-operative period, high-quality data assessing the impact of specific garments on post-operative pain are lacking. We report the results of a prospective randomized trial assessing the impact of the Jacki Jacket (JJ), a long-sleeve jacket with inner drain receptacle pockets, on post-discharge pain and quality of life (QOL) after TM + R. METHODS: Breast cancer patients undergoing TM + R at a single institution were randomized post-operatively to receive a JJ or usual care (UC). Participant-reported demographics, pain intensity, and QOL were collected on post-operative day 1 (T1). Following discharge, participants completed a daily pain and medication dairy (T2); on day of drain(s) removal (T3), participants again completed pain and QOL questionnaires. Linear models were used to evaluate associations between JJ use, post-operative pain, and QOL. RESULTS: From 3/8/17 to 12/20/17, 139 women were randomized. All participants completed T1 measures, 102 returned the T2 diary, and 118 (84.9%) completed T3 questionnaires. There was no significant difference in pain scores between JJ and UC arms at any timepoint. Adjusting for surgery type, age, marital status, depression, and obesity, participants randomized to JJ reported significantly better body image scores (estimate = 12.94, p = 0.009). There were no adverse events. CONCLUSIONS: Although JJ garment use did not impact post-operative pain intensity scores, the significant impact of JJ use on body image supports consideration for inclusion of such garments in post-operative care for patients undergoing TM + R. CLINICAL TRIAL REGISTRATION INFORMATION: Registered with ClinicalTrials.gov, NCT number NCT02976103, November 18, 2016.

Threats of Bots and Other Bad Actors to Data Quality Following Research Participant Recruitment Through Social Media: Cross-Sectional Questionnaire.

BACKGROUND: Recruitment of health research participants through social media is becoming more common. In the United States, 80% of adults use at least one social media platform. Social media platforms may allow researchers to reach potential participants efficiently. However, online research methods may be associated with unique threats to sample validity and data integrity. Limited research has described issues of data quality and authenticity associated with the recruitment of health research participants through social media, and sources of low-quality and fraudulent data in this context are poorly understood. OBJECTIVE: The goal of the research was to describe and explain threats to sample validity and data integrity following recruitment of health research participants through social media and summarize recommended strategies to mitigate these threats. Our experience designing and implementing a research study using social media recruitment and online data collection serves as a case study. METHODS: Using published strategies to preserve data integrity, we recruited participants to complete an online survey through the social media platforms Twitter and Facebook. Participants were to receive $15 upon survey completion. Prior to manually issuing remuneration, we reviewed completed surveys for indicators of fraudulent or low-quality data. Indicators attributable to respondent error were labeled suspicious, while those suggesting misrepresentation were labeled fraudulent. We planned to remove cases with 1 fraudulent indicator or at least 3 suspicious indicators. RESULTS: Within 7 hours of survey activation, we received 271 completed surveys. We classified 94.5% (256/271) of cases as fraudulent and 5.5% (15/271) as suspicious. In total, 86.7% (235/271) provided inconsistent responses to verifiable items and 16.2% (44/271) exhibited evidence of bot automation. Of the fraudulent cases, 53.9% (138/256) provided a duplicate or unusual response to one or more open-ended items and 52.0% (133/256) exhibited evidence of inattention. CONCLUSIONS: Research findings from several disciplines suggest studies in which research participants are recruited through social media are susceptible to data quality issues. Opportunistic individuals who use virtual private servers to fraudulently complete research surveys for profit may contribute to low-quality data. Strategies to preserve data integrity following research participant recruitment through social media are limited. Development and testing of novel strategies to prevent and detect fraud is a research priority.

Item response theory analysis and properties of decisional conflict scales: findings from two multi-site trials of men with localized prostate cancer.

BACKGROUND: Decisional conflict is associated with decision quality and may affect decision outcomes. In the health sciences literature, the Decisional Conflict Scale is widely used to measure decisional conflict, yet limited research has described the psychometric properties of the Decisional Conflict Scale subscales and of the low literacy version of the scale. The purpose of this secondary data analysis was therefore to examine properties of the original (DCS-12) and low literacy (LL DCS-10) Decisional Conflict Scales using Classical Measurement Theory and Item Response Theory. METHODS: Data from two multi-site trials of men with prostate cancer were used to analyze the DCS-12, LL DCS-10, and an aggregated DCS-12 dataset in which five response options were aggregated into three. Internal consistency was estimated with Cronbach's alphas. Subscale correlations were evaluated with Pearson's correlation coefficient. Item difficulty, item discrimination, and test information were evaluated using Graded Response Modeling (GRM). The likelihood ratio test guided model selection. RESULTS: Cronbach's alphas for the total scales and three of four subscales were ≥ 0.85. Alphas ranged from 0.34-0.57 for the support subscales. Subscale correlations ranged from 0.42-0.71 (P < 0.001). Items on the DCS-12 exhibited the widest range of difficulty. Two items on the support subscale had low to moderate discrimination and contributed little information. Only the DCS-12 was informative across the full range of decisional conflict values. CONCLUSIONS: Lack of precision in the support subscale raises concerns about subscale validity. The DCS-12 is most capable of discriminating between respondents with high and low decisional conflict. Evaluation of interventions to reduce decisional conflict must consider the above findings.

Assigning value to preparation for prostate cancer decision making: a willingness to pay analysis.

BACKGROUND: The Personal Patient Profile-Prostate (P3P) is a web-based decision support system for men newly diagnosed with localized prostate cancer that has demonstrated efficacy in reducing decisional conflict. Our objective was to estimate willingness-to-pay (WTP) for men's decisional preparation activities. METHODS: In a multicenter, randomized trial of P3P, usual care group participants received typical preparation for decision making plus referral to publicly-available, educational websites. Intervention group participants received the same, plus online P3P educational media specific to the user's personal preferences and values, and a communication coaching component tailored to race\ethnicity, age and language. WTP data were collected one week after physician consultation. An iterative bidding direct contingent valuation survey format was used, randomly assigning participants to high or low starting values (SV). Tobit models were used to explore associations between SV-adjusted WTP and age, education, marital and work-status, insurance, decision-control preference and decision-making stage. RESULTS: Of 392 participants enrolled, 141 P3P and 107 usual care (UC) provided a WTP value. Men were willing to pay a median $25 (IQR $10-100) for P3P in addition to usual care preparation materials. In the final multivariable tobit regression model, SV, marital status, stage of decision making and income were significantly associated with WTP for P3P. Decision control preference was considered marginally significant (p = 0.11). Men were WTP a median $30 (IQR $10-$200) for usual care material alone. In the final multivariable model, SV, education, and stage of decision making were significantly associated with WTP in usual care. CONCLUSION: WTP was similar for UC and for the addition of P3P to UC decision preparation. The WTP values were associated with demographic and preference variables. Findings can help focus decision support on future patients who would benefit most: those without strong support systems, at earlier stages of decision making, and open to a shared-decision style. TRIAL REGISTRATION: NCT NCT01844999 . Registered May 3, 2013.

Outcomes in adolescents and young adults with Hodgkin lymphoma treated on US cooperative group protocols: An adult intergroup (E2496) and Children's Oncology Group (COG AHOD0031) comparative analysis.

BACKGROUND: There is no clear consensus between pediatric and adult providers about the treatment of adolescents and young adults (AYAs) with Hodgkin lymphoma (HL). METHODS: Failure-free survival (FFS) and overall survival (OS) were compared between 114 patients ages 17 to 21 years with HL who were treated on the Eastern Cooperative Oncology Group-American College of Radiology Imaging Network Intergroup adult E2496 study and 391 similarly patients ages 17 to 21 years with HL who were treated on the pediatric Children's Oncology Group (COG) AHOD0031 study. RESULTS: Comparing AYAs from the COG and E2496 studies, there were no significant differences in extralymphatic disease, anemia, or hypoalbuminemia. More AYAs in the E2496 trial had stage III and IV disease (63% vs 29%; P < .001) and B symptoms (63% vs 27%; P < .001), and fewer had bulk disease (33% vs 77%; P < .001). More AYAs on the COG trial received radiotherapy (76% vs 66%; P = .03), although in smaller doses. E2496 AYA The 5-year FFS and OS rates were 68% and 89%, respectively in the E2496 AYAs and 81% and 97%, respectively, in the COG AYAs, indicating a statistically superior compared in the COG AYAs (P = .001). In stratified multivariable analyses, E2496 AYAs had worse FFS than COG AYAs in all strata except patients who had stage I and II HL without anemia. Propensity score analysis (based on stage, anemia, and bulk disease) confirmed inferior FFS for E2496 AYAs compared with COG AYAs (P = .004). On the E2496 study, FFS was significantly divergent across age groups (P = .005), with inferior outcomes for those ages 17 to 21 years versus 22-44 years. There was no difference across age on the COG study. CONCLUSIONS: Younger AYA patients with HL appear to have better outcomes when treated on a pediatric trial than patients of similar age on an adult trial. Prospective studies examining these differences are warranted. Cancer 2018;124:136-44. © 2017 American Cancer Society.

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.

MOTIVATION: The Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable. RESULTS: We implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results. AVAILABILITY AND IMPLEMENTATION: RankProd 2.0 is available at Bioconductor ( https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ) and as part of the mzMatch pipeline ( http://www.mzmatch.sourceforge.net ). CONTACT: rainer.breitling@manchester.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Decision Support with the Personal Patient Profile-Prostate: A Multicenter Randomized Trial.

PURPOSE: We evaluated the efficacy of the web based P3P (Personal Patient Profile-Prostate) decision aid vs usual care with regard to decisional conflict in men with localized prostate cancer. MATERIALS AND METHODS: A randomized (1:1), controlled, parallel group, nonblinded trial was performed in 4 regions of the United States. Eligible men had clinically localized prostate cancer and an upcoming consultation, and they spoke and read English or Spanish. Participants answered questionnaires to report decision making stage, personal characteristics, concerns and preferences plus baseline symptoms and decisional conflict. A randomization algorithm allocated participants to receive tailored education and communication coaching, generic teaching sheets and external websites plus a 1-page summary to clinicians (intervention) or the links plus materials provided in clinic (usual care). Conflict outcomes and the number of consultations were measured at 1 month. Univariate and multivariable models were used to analyze outcomes. RESULTS: A total of 392 men were randomized, including 198 to intervention and 194 to usual care, of whom 152 and 153, respectively, returned 1-month outcomes. The mean ± SD 1-month decisional conflict scale (score range 0 to 100) was 10.9 ± 16.7 for intervention and 9.9 ± 18.0 for usual care. The multivariable model revealed significantly reduced conflict in the intervention group (-5.00, 95% CI -9.40--0.59). Other predictors of conflict included income, marital or partner status, decision status, number of consultations, clinical site and D'Amico risk classification. CONCLUSIONS: In this multicenter trial the decision aid significantly reduced decisional conflict. Other variables impacted conflict and modified the effect of the decision aid, notably risk classification, consultations and resources. P3P is an effective adjunct for shared decision making in men with localized prostate cancer.

Relationship between individual and family characteristics and psychosocial factors in persons with familial pancreatic cancer.

OBJECTIVE: Describe relationships between self-reported personal demographics or familial characteristics and psychosocial outcomes (Patient Reported Outcome Measurement Information System Global Health, Impact of Event Scale-Revised [pancreatic cancer risk-related distress], cancer risk perception, and cancer worry) in participants with inherited or familial pancreatic cancer risk. METHODS: A multisite cross sectional survey of adults with elevated pancreatic cancer risk based on family history. All variables were summarized with descriptive statistics. To assess univariate associations, t test and chi-square/Fisher's exact test were used, and backward model selection was used in multivariable analysis. RESULTS: Respondents (N = 132) reported moderate to high frequency of cancer worry and 59.3% perceived a 50% or more perceived lifetime risk for pancreatic cancer, which far exceeds objective risk estimates. Cancer worry was associated with female gender (P = .03) and pancreatic cancer risk specific distress (P = .05). Higher-risk perception was associated with having a high school education or less (P = .001), higher distress (P = .02), and cancer worry (P = .008) and family cancer death experience (P = .02). Higher distress was associated with experience as a caregiver to a seriously ill family member in the past 5 years (P = .006). CONCLUSIONS: Individuals with inherited or familial pancreatic cancer risk experience cancer worry, distress, and have increased risk perception, particularly in the period following caring for a loved one with cancer. Routine evaluation of distress in this setting, as well as the development of supportive care resources, will help support patients living with risk for pancreatic cancer.

Psychosocial outcomes of an electronic self-report assessment and self-care intervention for patients with cancer: a randomized controlled trial.

BACKGROUND: The use of Web-based technology to facilitate self-care and communication with health care providers has the potential to improve psychosocial outcomes for patients undergoing cancer treatment. This study reports an analysis of psychosocial outcomes of the electronic self-report assessment for cancer study. METHODS: Adult patients starting cancer therapy were randomized to receive usual education about symptoms and quality of life topics (control) or usual education plus self-care instruction for symptoms and quality of life issues, communication coaching, and the opportunity to track symptoms and quality of life between clinic visits (intervention). Depression (Patient Health Questionnaire-9) and social, emotional, and role functioning (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 subscales) were measured before treatment (T1), 3 to 6 weeks after starting treatment (T2), 2 weeks later (T3), and 2 to 4 weeks after treatment ended or at the next restaging visit for participants who continued to receive treatment (T4). Clinicians received summaries of participant reports at each time point in both groups. RESULTS: In multivariable analysis, the depression scores were significantly lower (P = .04) and there was a trend to higher social and role functioning (P = .07) in the intervention group compared with the control. Working status was significantly associated with lower depression and better social and role functioning. CONCLUSIONS: A patient-centered, Web-based intervention that facilitates self-care and communication can improve psychosocial outcomes in the cancer setting.