Improved detection of gene fusions by applying statistical methods reveals oncogenic RNA cancer drivers.

The extent to which gene fusions function as drivers of cancer remains a critical open question. Current algorithms do not sufficiently identify false-positive fusions arising during library preparation, sequencing, and alignment. Here, we introduce Data-Enriched Efficient PrEcise STatistical fusion detection (DEEPEST), an algorithm that uses statistical modeling to minimize false-positives while increasing the sensitivity of fusion detection. In 9,946 tumor RNA-sequencing datasets from The Cancer Genome Atlas (TCGA) across 33 tumor types, DEEPEST identifies 31,007 fusions, 30% more than identified by other methods, while calling 10-fold fewer false-positive fusions in nontransformed human tissues. We leverage the increased precision of DEEPEST to discover fundamental cancer biology. Namely, 888 candidate oncogenes are identified based on overrepresentation in DEEPEST calls, and 1,078 previously unreported fusions involving long intergenic noncoding RNAs, demonstrating a previously unappreciated prevalence and potential for function. DEEPEST also reveals a high enrichment for fusions involving oncogenes in cancers, including ovarian cancer, which has had minimal treatment advances in recent decades, finding that more than 50% of tumors harbor gene fusions predicted to be oncogenic. Specific protein domains are enriched in DEEPEST calls, indicating a global selection for fusion functionality: kinase domains are nearly 2-fold more enriched in DEEPEST calls than expected by chance, as are domains involved in (anaerobic) metabolism and DNA binding. The statistical algorithms, population-level analytic framework, and the biological conclusions of DEEPEST call for increased attention to gene fusions as drivers of cancer and for future research into using fusions for targeted therapy.

Statistical algorithms improve accuracy of gene fusion detection.

Gene fusions are known to play critical roles in tumor pathogenesis. Yet, sensitive and specific algorithms to detect gene fusions in cancer do not currently exist. In this paper, we present a new statistical algorithm, MACHETE (Mismatched Alignment CHimEra Tracking Engine), which achieves highly sensitive and specific detection of gene fusions from RNA-Seq data, including the highest Positive Predictive Value (PPV) compared to the current state-of-the-art, as assessed in simulated data. We show that the best performing published algorithms either find large numbers of fusions in negative control data or suffer from low sensitivity detecting known driving fusions in gold standard settings, such as EWSR1-FLI1. As proof of principle that MACHETE discovers novel gene fusions with high accuracy in vivo, we mined public data to discover and subsequently PCR validate novel gene fusions missed by other algorithms in the ovarian cancer cell line OVCAR3. These results highlight the gains in accuracy achieved by introducing statistical models into fusion detection, and pave the way for unbiased discovery of potentially driving and druggable gene fusions in primary tumors.

Treatment Compliance and Outcomes for Women With Locoregionally Advanced Cervical Cancer Treated in a Safety Net Health System.

OBJECTIVE: This study aims to assess treatment compliance among women undergoing definitive chemoradiation with weekly cisplatin for cervical cancer within a safety net health system and to quantify the impact of chemotherapy compliance on outcomes. MATERIALS AND METHODS: All women who were treated for International Federation of Gynecology and Obstetrics stage IB2 to stage IVA cervical cancer between April 2008 and May 2014 were identified. Treatment delays were attributed to toxicity, comorbid conditions, or system issues, or categorized as patient-initiated. Disease-free survival and overall survival of women who received fewer than 6 versus 6 or more doses of weekly cisplatin 40 mg/m were compared using Kaplan-Meier analyses. RESULTS: One hundred nineteen women (mean [SD] age, 48.5 [11.8] years) were identified. Most women (n = 112; 94.1%) completed definitive radiotherapy, requiring a mean (SD) of 56.5 (20.1) days. Sixty-four women (57.1%) completed definitive radiotherapy in 56 days or less. Only 44 women (36.4%) received 6 or more cycles of cisplatin. Of 122 delayed cycles, reasons for delay were as follows: grade 2 or higher toxicity (n = 70; 57.4%), medical comorbidity (n = 12; 9.8%), system issues (n = 9; 7.4%), and patient-initiated (n = 14; 11.5%). Multiple issues complicated treatment for 3 doses (2.5%). Reasons for delay were not documented in 14 doses (11.5%). Among patients who received 6 or more cycles, disease-free survival improved by 17.4 months (mean [SD], 61.1 [3.7] vs 43.7 [4.3] months, P = 0.002) and overall survival improved by 8.6 months (mean [SD], 68.7 [2.3] vs 60.1 [3.7] months, P = 0.011). CONCLUSIONS: Higher rates of toxicity and psychosocial barriers to chemotherapy compliance adversely impact survival among women who seek care in low-resource settings. In our population, administration of all 6 cycles of cisplatin was necessary for optimal survival benefit. Future efforts to improve cervical cancer outcomes should address preventable reasons for treatment delays among underinsured or uninsured individuals.

Intraoperative ear bleeding with bilateral otorrhagia during laparoscopic sacrocolpopexy.

BACKGROUND: Spontaneous perioperative otorrhagia is an extremely rare entity with only 4 cases reported in the literature to date, all of which were recognized after the termination of the procedure. CASE: We describe the first reported case of otorrhagia recognized intraoperatively causing abortion of the procedure in a 60-year-old woman undergoing laparoscopic sacrocolpopexy. Otoscopy by the otolaryngology service revealed multiple intracutaneous hematomas and bleeding in bilateral external auditory canals. Computed tomography scan of the head revealed no intracranial hemorrhage. She underwent postoperative drainage by the otolaryngology service with no permanent ear-related sequelae. CONCLUSIONS: We present the fifth reported case of spontaneous perioperative otorrhagia, the first of which to be noticed intraoperatively and cause premature termination of the procedure. The etiology is postulated to be increased arterial and venous pressures causing rupture of subcutaneous capillaries. In our case, several factors may have contributed to this event, including steep Trendelenburg patient positioning, intraperitoneal carbon dioxide insufflation from laparoscopy, and an intraoperative hypertensive episode.

Knowledge of sexually transmitted infections among adolescents in the Houston area presenting for reproductive healthcare at Texas Children's Hospital.

OBJECTIVE: Studies indicate a deficiency in knowledge of sexually transmitted infections (STIs) among adolescents, yet adolescents comprise 25% of the sexually active (SA) population and account for 48% of STIs acquired annually. This survey assesses knowledge of STIs among adolescent females. The goal of this study was to assess knowledge of STIs and how it relates to safe sex behaviors and educational access. DESIGN: A confidential 10-question STI survey was administered to a convenience sample of female adolescents. Data analysis included descriptive statistics, chi-square analysis, and linear regression analysis. SETTING: Texas Children's Hospital Pediatric and Adolescent Gynecology Clinic. INTERVENTIONS: None. PARTICIPANTS: Seventy-five female participants between the ages of 10-21 years. MAIN OUTCOME MEASURES: Age, sexual activity, educational access, preferred methods of risk reduction and questions answered correctly on the STI survey. RESULTS: The mean age of participants was 14.9 ± 2.4 years; mean age of menarche was 10.9 ± 2.9 years. Based on survey responses, all adolescents demonstrated similar knowledge of specific STIs regardless of demographic factors. However, middle and late adolescent groups had increased awareness of STIs. SA participants (36%) were more likely to choose 2 or more methods of risk reduction compared to non-SA participants (P = 0.014). There was no correlation between educational access and preferred methods of risk reduction even though 92% of respondents reported receiving STI education from school, parents, or peers. CONCLUSIONS: Current efforts at STI education are not effective. Different approaches to STI education are necessary to increase knowledge and motivate adolescents to reduce high risk behaviors.