Exome sequencing in multiplex families with left-sided cardiac defects has high yield for disease gene discovery.

Congenital heart disease (CHD) is a common group of birth defects with a strong genetic contribution to their etiology, but historically the diagnostic yield from exome studies of isolated CHD has been low. Pleiotropy, variable expressivity, and the difficulty of accurately phenotyping newborns contribute to this problem. We hypothesized that performing exome sequencing on selected individuals in families with multiple members affected by left-sided CHD, then filtering variants by population frequency, in silico predictive algorithms, and phenotypic annotations from publicly available databases would increase this yield and generate a list of candidate disease-causing variants that would show a high validation rate. In eight of the nineteen families in our study (42%), we established a well-known gene/phenotype link for a candidate variant or performed confirmation of a candidate variant's effect on protein function, including variants in genes not previously described or firmly established as disease genes in the body of CHD literature: BMP10, CASZ1, ROCK1 and SMYD1. Two plausible variants in different genes were found to segregate in the same family in two instances suggesting oligogenic inheritance. These results highlight the need for functional validation and demonstrate that in the era of next-generation sequencing, multiplex families with isolated CHD can still bring high yield to the discovery of novel disease genes.

Long-term efficacy and safety of addition of carboplatin with or without veliparib to standard neoadjuvant chemotherapy in triple-negative breast cancer: 4-year follow-up data from BrighTNess, a randomized phase III trial.

BACKGROUND: Primary analyses of the phase III BrighTNess trial showed addition of carboplatin with/without veliparib to neoadjuvant chemotherapy significantly improved pathological complete response (pCR) rates with manageable acute toxicity in patients with triple-negative breast cancer (TNBC). Here, we report 4.5-year follow-up data from the trial. PATIENTS AND METHODS: Women with untreated stage II-III TNBC were randomized (2 : 1 : 1) to paclitaxel (weekly for 12 doses) plus: (i) carboplatin (every 3 weeks for four cycles) plus veliparib (twice daily); (ii) carboplatin plus veliparib placebo; or (iii) carboplatin placebo plus veliparib placebo. All patients then received doxorubicin and cyclophosphamide every 2-3 weeks for four cycles. The primary endpoint was pCR. Secondary endpoints included event-free survival (EFS), overall survival (OS), and safety. Since the co-primary endpoint of increased pCR with carboplatin plus veliparib with paclitaxel versus carboplatin with paclitaxel was not met, secondary analyses are descriptive. RESULTS: Of 634 patients, 316 were randomized to carboplatin plus veliparib with paclitaxel, 160 to carboplatin with paclitaxel, and 158 to paclitaxel. With median follow-up of 4.5 years, the hazard ratio for EFS for carboplatin plus veliparib with paclitaxel versus paclitaxel was 0.63 [95% confidence interval (CI) 0.43-0.92, P = 0.02], but 1.12 (95% CI 0.72-1.72, P = 0.62) for carboplatin plus veliparib with paclitaxel versus carboplatin with paclitaxel. In post hoc analysis, the hazard ratio for EFS was 0.57 (95% CI 0.36-0.91, P = 0.02) for carboplatin with paclitaxel versus paclitaxel. OS did not differ significantly between treatment arms, nor did rates of myelodysplastic syndromes, acute myeloid leukemia, or other secondary malignancies. CONCLUSIONS: Improvement in pCR with the addition of carboplatin was associated with long-term EFS benefit with a manageable safety profile, and without increasing the risk of second malignancies, whereas adding veliparib did not impact EFS. These findings support the addition of carboplatin to weekly paclitaxel followed by doxorubicin and cyclophosphamide neoadjuvant chemotherapy for early-stage TNBC.

Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population.

BACKGROUND: The role of synonymous single-nucleotide variants in human health and disease is poorly understood, yet evidence suggests that this class of "silent" genetic variation plays multiple regulatory roles in both transcription and translation. One mechanism by which synonymous codons direct and modulate the translational process is through alteration of the elaborate structure formed by single-stranded mRNA molecules. While tools to computationally predict the effect of non-synonymous variants on protein structure are plentiful, analogous tools to systematically assess how synonymous variants might disrupt mRNA structure are lacking. RESULTS: We developed novel software using a parallel processing framework for large-scale generation of secondary RNA structures and folding statistics for the transcriptome of any species. Focusing our analysis on the human transcriptome, we calculated 5 billion RNA-folding statistics for 469 million single-nucleotide variants in 45,800 transcripts. By considering the impact of all possible synonymous variants globally, we discover that synonymous variants predicted to disrupt mRNA structure have significantly lower rates of incidence in the human population. CONCLUSIONS: These findings support the hypothesis that synonymous variants may play a role in genetic disorders due to their effects on mRNA structure. To evaluate the potential pathogenic impact of synonymous variants, we provide RNA stability, edge distance, and diversity metrics for every nucleotide in the human transcriptome and introduce a "Structural Predictivity Index" (SPI) to quantify structural constraint operating on any synonymous variant. Because no single RNA-folding metric can capture the diversity of mechanisms by which a variant could alter secondary mRNA structure, we generated a SUmmarized RNA Folding (SURF) metric to provide a single measurement to predict the impact of secondary structure altering variants in human genetic studies.

A phase II evaluation of Temozolomide in patients with recurrent epithelial ovarian cancer.

OBJECTIVES: To assess the antitumor activity of Temozolomide, a novel alkylating agent, in patients with persistent or recurrent ovarian or primary peritoneal carcinoma who have failed other second-line chemotherapy agents. To identify the nature and degree of toxicity of Temozolomide in this group of patients. METHODS: Temozolomide was administered orally at an initial dose of 150 mg/m(2) daily for 5 days, every 4 weeks. If the initial course was tolerated without dose-limiting toxicity, then the dose was increased to 200 mg/m(2). Patients were evaluated for response and toxicity. RESULTS: Fifteen patients were enrolled and evaluated. The median number of prior treatment regimens was 3. Hematologic toxicity was encountered in 26% of patients and was manageable. There were no complete or partial responses. One patient had stable disease with significant improvement in her performance status while on treatment. CONCLUSION: This dose and schedule of Temozolomide had insignificant activity in this heavily pretreated group of patients with persistent or recurrent ovarian or primary peritoneal carcinoma.

Papanicolaou and thin-layer cervical cytology with colposcopic biopsy control. A comparison.

OBJECTIVE: To compare the accuracy of conventional Papanicolaou and fluid-based, thin-layer cervical cytology. STUDY DESIGN: Cervical cytology was performed in duplicate on women who presented for cervical screening. Papanicolaou and thin-layer (ThinPrep, Cytyc Corp., Boxborough, Massachusetts) cytologic samples were collected simultaneously using a split-sample method. Cytologic slides were read and reported independently. Clinical follow-up was based on the most abnormal result. Colposcopy was performed as clinically indicated, and biopsy results were compared with cytologic diagnoses. RESULTS: Three thousand samples were compared. Papanicolaou and thin-layer results were significantly different (P = .0001), with identical diagnoses in 1,844 (61%) of patients. Eighty thin-layer (2.7%) and 177 Papanicolaou (5.9%) samples were read as limited or unsatisfactory (P < .0001). The rates of atypical squamous cells of undetermined significance (ASCUS) were not statistically different (P = .06). Thin-layer cytology was read more often as low grade squamous intraepithelial lesion (P = .001) or high grade squamous intraepithelial lesion (P = .006). Colposcopy with biopsy was performed on 291 patients. With ASCUS considered an abnormal result, thin-layer cytology was more sensitive (91% vs. 85%) but had lower positive predictive value (69% vs. 74%) than Papanicolaou cytology for the presence of cervical neoplasia. CONCLUSION: Papanicolaou and thin-layer cervical cytology yielded significantly different information. Thin-layer cytology yielded significantly fewer unsatisfactory results and was more sensitive for identifying cervical intraepithelial neoplasia.

Educational and support needs of patients and their families awaiting cardiac surgery.

OBJECTIVE: To identify and explore the learning and support needs of patients and families during the waiting period before cardiac surgery. DESIGN: Prospective, cross-sectional cohort survey design. SETTING: University-affiliated tertiary cardiovascular care center in mideastern Canada. SUBJECTS: One hundred forty-seven patients currently on the cardiac surgery waiting list, and 125 family members of these patients. OUTCOME MEASURES: Needs Inventory for Patients who Wait. INTERVENTION: All patients were sent a survey for themselves and one for a family member that included: a demographic profile, subjective questionnaire, and the Needs Inventory for Patients who Wait. The survey was to be completed and returned to the investigators. RESULTS: The return rates were 77% (113) for patients, and 70% (87) for family members. For patients and their family members, item rankings were highly correlated for areas in which they wanted information (r = 0.84), and for areas that caused them the most concern (r = 0.91). Family members were also concerned about caring for the patient before and after surgery. The number of weeks on the waiting list (< 1 month to > 6 months) did not change the concerns of patients and family. CONCLUSIONS: This survey identifies some of the educational and support needs of patients undergoing cardiac surgery and their family members. Patients are concerned about their health and survival until the surgical procedure, as well as about the success of the procedure. Families share patients' concerns and have an additional concern regarding how to support the patient during the perioperative stage. The needs identified by patients and their families in this survey were found to be stable over time, and within the realm of nursing practice to address.

Gas chromatographic determination of methylcyclopentadienylmanganesetricarbonyl in biological tissues and fluids.

The procedure described for quantitating methylcyclopentadienylmanganese-tricarbonyl (MMT, a fuel additive) in small samples of biological fluids and tissues is based on extracting the MMT into hexane containing biphenyl as internal standard, followed by gas chromatographic analysis. With flame ionisation detection, as little as 1-2 ppm of MMT in tissue can be determined relatively easily. The method is also applicable to in vitro investigations of MMT metabolism, and it has been used to show that the enzymic oxidation of MMT by rat-liver microsomes is a cytochrome P-450-dependent process.