Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples

BACKGROUND

Next-generation sequencing (NGS) of tumour samples is a critical component of personalised cancer treatment, but it requires high-quality DNA samples. Routine neutral-buffered formalin (NBF) fixation has detrimental effects on nucleic acids, causing low yields, as well as fragmentation and DNA base changes, leading to significant artefacts.

PATIENTS AND METHODS

We have carried out a detailed comparison of DNA quality from matched samples isolated from high-grade serous ovarian cancers from 16 patients fixed in methanol and NBF. These experiments use tumour fragments and mock biopsies to simulate routine practice, ensuring that results are applicable to standard clinical biopsies.

RESULTS

Using matched snap-frozen tissue as gold standard comparator, we show that methanol-based fixation has significant benefits over NBF, with greater DNA yield, longer fragment size and more accurate copy-number calling using shallow whole-genome sequencing (WGS). These data also provide a new approach to understand and quantify artefactual effects of fixation using non-negative matrix factorisation to analyse mutational spectra from targeted and WGS data.

CONCLUSION

We strongly recommend the adoption of methanol fixation for sample collection strategies in new clinical trials. This approach is immediately available, is logistically simple and can offer cheaper and more reliable mutation calling than traditional NBF fixation.

Periconception HIV Risk Behavior Among Men and Women Reporting HIV-Serodiscordant Partners in KwaZulu-Natal, South Africa

HIV-infected men and women who choose to conceive risk infecting their partners. To inform safer conception programs we surveyed HIV risk behavior prior to recent pregnancy amongst South African, HIV-infected women (N = 209) and men (N = 82) recruited from antenatal and antiretroviral clinics, respectively, and reporting an uninfected or unknown-HIV-serostatus pregnancy partner. All participants knew their HIV-positive serostatus prior to the referent pregnancy. Only 11 % of women and 5 % of men had planned the pregnancy; 40 % of women and 27 % of men reported serostatus disclosure to their partner before conception. Knowledge of safer conception strategies was low. Around two-thirds reported consistent condom use, 41 % of women and 88 % of men reported antiretroviral therapy, and a third of women reported male partner circumcision prior to the referent pregnancy. Seven women (3 %) and two men (2 %) reported limiting sex without condoms to peak fertility. None reported sperm washing or manual insemination. Safer conception behaviors including HIV-serostatus disclosure, condom use, and ART at the time of conception were not associated with desired pregnancy. In light of low pregnancy planning and HIV-serostatus disclosure, interventions to improve understandings of serodiscordance and motivate mutual HIV-serostatus disclosure and pregnancy planning are necessary first steps before couples or individuals can implement specific safer conception strategies.

Changes from 1986 to 2006 in reasons for liking leisure-time physical activity among adolescents

Reasons for participating in physical activity (PA) may have changed in accordance with the general modernization of society. The aim is to examine changes in self-reported reasons for liking leisure-time physical activity (LTPA) and their association with self-reported LTPA over a 20-year period. Data were collected among nationally representative samples of 13-year-olds in Finland, Norway, and Wales in 1986 and 2006 (N = 9252) as part of the WHO cross-national Health Behaviour in School-aged Children (HBSC) study. Univariate ANOVAs to establish differences according to gender, year, and country were conducted. In all countries, 13-year-olds in 2006 tended to report higher importance in terms of achievement and social reasons than their counterparts in 1986, while changes in health reasons were minor. These reasons were associated with LTPA in a similar way at both time points. Health reasons for liking LTPA were considered most important, and were the strongest predictor of LTPA. The findings seem robust as they were consistent across countries and genders. Health education constitutes the most viable strategy for promoting adolescents' motivation for PA, and interventions and educational efforts could be improved by an increased focus on LTPA and sport as a social activity.

Exploring child dental service use among migrant families in metropolitan Melbourne, Australia

BACKGROUND

This study describes and explores factors related to dental service use among migrant children.

METHODS

A cross-sectional analysis of baseline data from Teeth Tales, an exploratory trial implementing a community based child oral health promotion intervention. The sample size and target population was 600 families with 1-4 year old children from Iraqi, Lebanese and Pakistani backgrounds residing in metropolitan Melbourne. Participants were recruited into the study using purposive and snowball sampling techniques.

RESULTS

Most (88%; 550/625) children had never visited the dentist (mean (SD) age 3.06 years (1.11)). In the fully adjusted model the variable most significantly associated with child dental visiting was parent reported 'no reason for child to visit the dentist' (OR = 0.07, p < 0.001). Of those children whose parents reported their child had no reason to visit the dentist, 22% (37/165) experienced dental caries with 8% (13/165) at the level of cavitation.

CONCLUSIONS

Dental service use by migrant preschool children was very low. The relationship between perceived dental need and dental service use is currently not aligned. One in 10 children of select migrant background had visited a dentist, which is in the context of 1 in 3 with dental caries. To improve utilization, health services should consider organizational cultural competence, outreach and increased engagement with the migrant community.

Comparison of the hybrid capture test and polymerase chain reaction in identifying women who have an atypical squamous cell of undetermined significance papanicolaou smear and need colposcopy

OBJECTIVES

The objective of this study was to detect human papillomavirus (HPV) in women with a newly diagnosed atypical squamous cells of undetermined significance (ASCUS) using the hybrid capture (HC) test and the polymerase chain reaction (PCR). We sought to evaluate the accuracy of both tests in identifying women with a concomitant cervical intraepithelial neoplasia (CIN).

MATERIALS AND METHODS

We studied 360 women who had a diagnosis of ASCUS and were referred to the colposcopy clinic. Subjects were between 18 and 50 years, had newly diagnosed ASCUS, had no history of cervical biopsies or treatment, and were not pregnant. A cell sample for HPV testing and colposcopically directed biopsies of lesions were obtained. HPV was detected using the Digene HC and PCR systems (Digene, Silver Spring, MD).

RESULTS

Biopsies showed concomitant CIN in 80 patients (22.2%). Of these, 19 had CIN2 or CIN3. HPV-DNA was detected in 76 of the 360 women (21.1%) using HC and in 166 of 348 women (47.7%) using PCR. The concordance between HC and PCR for detecting HPV was 65%. The sensitivity, specificity, and positive and negative predictive values of HC for detecting CIN were 48%, 86%, 50%, and 85%, respectively. The sensitivity, specificity, and positive and negative predictive values of PCR for detecting CIN were 67%, 58%, 31%, and 86%, respectively. Focusing on CIN2 and CIN3 alone, these values were 79%, 82%, 20%, and 99% for HC, respectively, and 89%, 55%, 10%, and 99% for PCR, respectively.

CONCLUSION

The specificity of HC was higher than the specificity of PCR. For this reason, the HC might be more useful than PCR as a secondary triage method for detecting CIN in women who have incident ASCUS and need colposcopy.

An ontology approach to comparative phenomics in plants

BACKGROUND

Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a small scale, comprehensive queries and analyses that span a broad set of reference species, research disciplines, and knowledge domains continue to be severely limited by the absence of a common semantic framework.

RESULTS

We developed a workflow to curate and standardize existing phenotype datasets for six plant species, encompassing both model species and crop plants with established genetic resources. Our effort focused on mutant phenotypes associated with genes of known sequence in Arabidopsis thaliana (L.) Heynh. (Arabidopsis), Zea mays L. subsp. mays (maize), Medicago truncatula Gaertn. (barrel medic or Medicago), Oryza sativa L. (rice), Glycine max (L.) Merr. (soybean), and Solanum lycopersicum L. (tomato). We applied the same ontologies, annotation standards, formats, and best practices across all six species, thereby ensuring that the shared dataset could be used for cross-species querying and semantic similarity analyses. Curated phenotypes were first converted into a common format using taxonomically broad ontologies such as the Plant Ontology, Gene Ontology, and Phenotype and Trait Ontology. We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions of gene families, protein functions, and shared metabolic pathways that underlie informative plant phenotypes.

CONCLUSIONS

The use of ontologies, annotation standards, shared formats, and best practices for cross-taxon phenotype data analyses represents a novel approach to plant phenomics that enhances the utility of model genetic organisms and can be readily applied to species with fewer genetic resources and less well-characterized genomes. In addition, these tools should enhance future efforts to explore the relationships among phenotypic similarity, gene function, and sequence similarity in plants, and to make genotype-to-phenotype predictions relevant to plant biology, crop improvement, and potentially even human health.

AISO: Annotation of Image Segments with Ontologies

Background

Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors under which the organisms were sampled. At present, most of these annotations are described in free text, may involve limited use of non-standard vocabularies, and rarely specify precise coordinates of features on the image plane such that a computer vision algorithm could identify, extract and annotate them. Therefore, researchers and curators need a tool that can identify and demarcate features in an image plane and allow their annotation with semantically contextual ontology terms. Such a tool would generate data useful for inter and intra-specific comparison and encourage the integration of curation standards. In the future, quality annotated image segments may provide training data sets for developing machine learning applications for automated image annotation.

Results

We developed a novel image segmentation and annotation software application, “Annotation of Image Segments with Ontologies” (AISO). The tool enables researchers and curators to delineate portions of an image into multiple highlighted segments and annotate them with an ontology-based controlled vocabulary. AISO is a freely available Java-based desktop application and runs on multiple platforms. It can be downloaded at http://www.plantontology.org/software/AISO.

Conclusions

AISO enables curators and researchers to annotate digital images with ontology terms in a manner which ensures the future computational value of the annotated images. We foresee uses for such data-encoded image annotations in biological data mining, machine learning, predictive annotation, semantic inference, and comparative analyses.

Comprehensive interrogation of the cellular response to fluorescent, detonation and functionalized nanodiamonds

Nanodiamonds (NDs) are versatile nanoparticles that are currently being investigated for a variety of applications in drug delivery, biomedical imaging and nanoscale sensing. Although initial studies indicate that these small gems are biocompatible, there is a great deal of variability in synthesis methods and surface functionalization that has yet to be evaluated. Here we present a comprehensive analysis of the cellular compatibility of an array of nanodiamond subtypes and surface functionalization strategies. These results demonstrate that NDs are well tolerated by multiple cell types at both functional and gene expression levels. In addition, ND-mediated delivery of daunorubicin is less toxic to multiple cell types than treatment with daunorubicin alone, thus demonstrating the ability of the ND agent to improve drug tolerance and decrease therapeutic toxicity. Overall, the results here indicate that ND biocompatibility serves as a promising foundation for continued preclinical investigation.

Oncology nursing support for safe and effective use of eribulin in metastatic breast cancer

Nurse practitioners play important roles in breast cancer prevention, early detection, therapeutic efficacy, and surveillance. Assessment of a patient's health status is part of the nine nurse practitioner core competencies updated in 2012 by the National Organization of Nurse Practitioner Faculties. Although adverse events are common in treatment for metastatic breast cancer (MBC), proactive management strategies can limit the number and/or severity of adverse events. Additionally, knowledge of common metastatic sites and clinical signs/symptoms of recurrence provides one of the first-line strategies for successful treatment. We review five case studies of women with MBC who were managed successfully with eribulin mesylate in late lines of therapy after at least two chemotherapeutic regimens for advanced breast cancer that included both an anthracycline and a taxane in either the adjuvant or metastatic setting.

Diamond nanogel-embedded contact lenses mediate lysozyme-dependent therapeutic release

Temporarily implanted devices, such as drug-loaded contact lenses, are emerging as the preferred treatment method for ocular diseases like glaucoma. Localizing the delivery of glaucoma drugs, such as timolol maleate (TM), can minimize adverse effects caused by systemic administration. Although eye drops and drug-soaked lenses allow for local treatment, their utility is limited by burst release and a lack of sustained therapeutic delivery. Additionally, wet transportation and storage of drug-soaked lenses result in drug loss due to elution from the lenses. Here we present a nanodiamond (ND)-embedded contact lens capable of lysozyme-triggered release of TM for sustained therapy. We find that ND-embedded lenses composed of enzyme-cleavable polymers allow for controlled and sustained release of TM in the presence of lysozyme. Retention of drug activity is verified in primary human trabecular meshwork cells. These results demonstrate the translational potential of an ND-embedded lens capable of drug sequestration and enzyme activation.

Multi-protein delivery by nanodiamonds promotes bone formation

Bone morphogenetic proteins (BMPs) are well-studied regulators of cartilage and bone development that have been Food and Drug Administration (FDA)-approved for the promotion of bone formation in certain procedures. BMPs are seeing more use in oral and maxillofacial surgeries because of recent FDA approval of InFUSE(®) for sinus augmentation and localized alveolar ridge augmentation. However, the utility of BMPs in medical and dental applications is limited by the delivery method. Currently, BMPs are delivered to the surgical site by the implantation of bulky collagen sponges. Here we evaluate the potential of detonation nanodiamonds (NDs) as a delivery vehicle for BMP-2 and basic fibroblast growth factor (bFGF). Nanodiamonds are biocompatible, 4- to 5-nm carbon nanoparticles that have previously been used to deliver a wide variety of molecules, including proteins and peptides. We find that both BMP-2 and bFGF are readily loaded onto NDs by physisorption, forming a stable colloidal solution, and are triggered to release in slightly acidic conditions. Simultaneous delivery of BMP-2 and bFGF by ND induces differentiation and proliferation in osteoblast progenitor cells. Overall, we find that NDs provide an effective injectable alternative for the delivery of BMP-2 and bFGF to promote bone formation.