When does disruption of meaning in bereavement become debilitating? Screening for deleterious outcomes with the ISLES-SF.

Meaning reconstruction is a central process in bereavement adaptation. However, clinical measures or means for identifying individuals whose struggles with meaning making have become dysfunctional have yet to be developed for clinicians to readily use in practice. Therefore, the objective of this study was to evaluate the diagnostic effectiveness of the Integration of Stressful Life Experiences Scale-Short Form (ISLES-SF) for measuring clinically significant struggles with meaning making of loss. The results of this study of 118 bereaved adults support the diagnostic use of the ISLES-SF (sensitivity of 83% and specificity of 73%), as well as an identified cut-score (≥ 14) that researchers and clinicians can employ to accurately and efficiently identify those whose difficulties with making meaning of loss have become debilitating. The results also showed that those who scored in the clinical range of the ISLES-SF displayed higher levels of anxiety, depression and prolonged grief than those not struggling with meaning making.

Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers.

The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21.2 y) are included. Germline pathogenic/likely pathogenic variants are identified in 12% of participants, of which 60% were not known prior. Therapeutically actionable variants are identified by targeted gene report and whole genome in 32% and 62% of participants, respectively, and increase to 96% after integrating transcriptome analyses. Thirty-two molecularly informed therapies are pursued in 28 participants with 54% achieving a clinical benefit rate; objective response or stable disease ≥6 months. Integrated WGTA identifies therapeutically actionable variants in almost all tumors and are directly translatable to clinical care of children with poor prognosis cancers.

Deathbed experiences and meaning-making: Perspectives of family caregivers of patients who received cancer palliative care.

OBJECTIVES: The deathbed symbolizes a time when the patient is dangerously ill and where death is imminent. The memories of family caregivers during this time can potentially shape their meaning-making of the patient's death and bereavement adjustment. We aimed to understand the experiences of family caregivers at the deathbed of patients receiving palliative care. We also examined caregiver's meaning-making that occurred after the patient's death. METHODS: In this retrospective qualitative study, family caregivers of cancer patients who received palliative care in Singapore were recruited through purposive sampling. In-person, semi-structured interviews were individually conducted with study participants to understand their experiences from a caregiver's perspective before and after the death of the patient. Thematic content analysis method was conducted. RESULTS: A total of 25 bereaved family caregivers were interviewed, with spouses, adult children, and others comprising one-third each of the sample. Six themes emerged from caregivers' recollected experiences around the patient deathbed: Lasting image of the patient, A time of intense emotions, Healthcare providers prepare caregivers, A time for saying goodbye, Rituals provide comfort, and Impact on family ties. Four themes emerged surrounding post-loss meaning-making: An end to the pain and suffering, "Have I done enough?," Significance in the timing of events, and Gaining strength and personal growth. SIGNIFICANCE OF RESULTS: The deathbed is a salient time for family caregivers as they prepare for patient's death. There are opportunities to provide support to the family based on the study findings.

Re-Conceptualizing Bereavement Care Practices: Insights Gained from Service Providers.

The management and delivery of bereavement care and support services present practical challenges. A national-level, qualitative study was conducted to examine the current practices in Singapore. The study's purpose was to inform bereavement care practices by drawing from perspectives of service providers offering death, dying and bereavement-related services. This qualitative study was undertaken using focused group discussion (FGD) with service providers from the health, social and death-related sectors. Ten FGDs were conducted with a total of 69 participants. Thematic analysis yield two themes - identifying challenging circumstances to provide bereavement care and strategies for dealing with the gaps in service delivery. The service providers' experiential knowledge could be borrowed to strengthen the current bereavement care practices for the good of the community. The findings have informed the reconceptualization of a local bereavement care and support service model, with the public health model as the recommended underpinning conceptual framework.

Learning in digital environments: a model for cross-cultural alignment.

This article presents a conceptual model of cross-cultural alignments in education in the digital era. The intention was to explore and respond to urgent questions regarding learners and the learning environments in today's networked society. The model explores the enabling or constraining influences of educational systems, digital environments, learners, and educators on other learners and is based on the concept of social justice. The skills and competencies required for efficient learner development in a digital environment include digital competence, collaboration skills, intercultural competence, and lifelong learning skills. The interrelationship of these components and their influence on learners' skills and competencies are discussed through the lens of cross-cultural alignment by examining three intercultural projects worldwide. The authors recommend that educational systems provide educational institutions with a high-quality infrastructure as well as to support educators and learners in the development of digital skills. Future research may examine the model's components and their interrelationships so that it may serve researchers and practitioners as a basis for the design of future intercultural projects.

Trauma to Transformation: the lived experience of bereaved parents of children with chronic life-threatening illnesses in Singapore.

BACKGROUND: In 2016, over 6.6 million children died globally, and 245 children died in Singapore. Chronic illnesses are prevalent causes of child mortality around the world. Despite growing research that examines the lived experience of parents bereaved by their child's chronic life-threatening illness, there is no such study within the Asian context. METHODS: To bridge this knowledge gap, meaning-oriented, strength-focused interviews were conducted with 25 parental units (i.e. 6 couples, 13 lone mothers, 4 lone fathers, and 2 primary parental figures) who lost their child to chronic life-threatening illness in Singapore (N = 31), including those of Chinese (n = 17), Malay (n = 10) and Indian ethnicities (n = 4), between August 2017 and April 2018. RESULTS: Data analysis adhering to the grounded theory approach revealed 7 themes and 25 sub-themes that were organized into a Trauma-to-Transformation Model of Parental Bereavement. This model shows the major milestones in participants' lived experience of their child's chronic life-threatening illness and death, starting from the diagnosis of their child's chronic life-threatening illness and the subsequent emotional turmoil (Theme 1), the mourning of their child's death and the losses which accompanied the death (Theme 3) and participants' experience of posttraumatic growth through reflection of their journey of caregiving and child loss (Theme 5). The model further describes the deliberate behaviors or 'rituals' that helped participants to regain power over their lives (Theme 2), sustain an intimate bond with their child beyond death (Theme 4), and transcend their loss by deriving positive outcomes from their experience (Theme 6). Finally, the model denotes that the lived experiences and well-being of participants were embedded within the health-and-social-care ecosystem, and in turn impacted by it (Theme 7). CONCLUSION: These themes and their corresponding sub-themes are discussed, with recommendations for enhancing culturally sensitive support services for grieving Asian parents around the globe.

Thematic analysis of spousal interaction patterns among Asian parents of children with chronic life-threatening illness.

OBJECTIVE: This is the first known study which examines the evolutionary nature of spousal interaction patterns among Asian parents of children with chronic life-threatening illness, from the time of providing care to their child through bereavement. This study is informed by earlier findings that when a child is diagnosed with a chronic life-threatening illness, parents are faced with multiple stressors, leaving them with little time to invest in their spousal relationship. PARTICIPANTS AND SETTING: A constructivist-phenomenological research paradigm was adopted and meaning-oriented interviews were conducted with 20 parental units (i.e., 6 couples, 12 lone mothers and 2 lone fathers) of Chinese, Malay and Indian ethnicities who lost their child to chronic life-threatening illness in Singapore. RESULTS: Qualitative thematic analysis of the data revealed four themes, which describe the evolutionary nature of spousal interaction patterns among Asian parents of children with chronic life-threatening illness, from caregiving through bereavement. Findings reveal participants' tendency to concentrate on pragmatic, solution-focused communication during the period of caregiving (pragmatic interaction), avoid discussion about their emotional pain as a means of protecting their spouse (partner-oriented self-regulation), respect and acknowledge their spouse's personal coping strategies (empathic responding) and show greater appreciation and emotional expression within the spousal relationship after their child's death (affective appreciation). CONCLUSION: Engaging in pragmatic discussions, deferring emotion-focused and potentially distressing conversations, and acknowledging their spouse's need for personal space are important coping strategies for Asian couples facing their child's chronic life-threatening illness and in the immediate aftermath of his/her death. Bereaved couples who have processed their grief individually feel ready to share their reflections with their spouse, deriving meaning and greater relational closeness through such disclosure. These findings are discussed from a cultural lens, with recommendations for healthcare professionals working with Asian parents of children with chronic life-threatening illness.

Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis.

We report a case of early-onset pancreatic ductal adenocarcinoma in a patient harboring biallelic MUTYH germline mutations, whose tumor featured somatic mutational signatures consistent with defective MUTYH-mediated base excision repair and the associated driver KRAS transversion mutation p.Gly12Cys. Analysis of an additional 730 advanced cancer cases (N = 731) was undertaken to determine whether the mutational signatures were also present in tumors from germline MUTYH heterozygote carriers or if instead the signatures were only seen in those with biallelic loss of function. We identified two patients with breast cancer each carrying a pathogenic germline MUTYH variant with a somatic MUTYH copy loss leading to the germline variant being homozygous in the tumor and demonstrating the same somatic signatures. Our results suggest that monoallelic inactivation of MUTYH is not sufficient for C:G>A:T transversion signatures previously linked to MUTYH deficiency to arise (N = 9), but that biallelic complete loss of MUTYH function can cause such signatures to arise even in tumors not classically seen in MUTYH-associated polyposis (N = 3). Although defective MUTYH is not the only determinant of these signatures, MUTYH germline variants may be present in a subset of patients with tumors demonstrating elevated somatic signatures possibly suggestive of MUTYH deficiency (e.g., COSMIC Signature 18, SigProfiler SBS18/SBS36, SignatureAnalyzer SBS18/SBS36).

Genomic Classifier for Guiding Treatment of Intermediate-Risk Prostate Cancers to Dose-Escalated Image Guided Radiation Therapy Without Hormone Therapy.

PURPOSE: The National Comprehensive Cancer Network (NCCN) has recently endorsed the stratification of intermediate-risk prostate cancer (IR-PCa) into favorable and unfavorable subgroups and recommend the addition of androgen deprivation therapy (ADT) to radiation therapy (RT) for unfavorable IR-PCa. Recently, more accurate prognostication was demonstrated by integrating a 22-feature genomic classifier (GC) to the NCCN stratification system. Here, we test the utility of the GC to better identify patients with IR-PCa who are sufficiently treated by RT alone. METHODS AND MATERIALS: We identified a novel cohort comprising 121 patients with IR-PCa treated with dose-escalated image guided RT (78 Gy in 39 fractions) without ADT. GC scores were derived from tumors sampled in diagnostic biopsies. Multivariable analyses, including both NCCN subclassification and GC scores, were performed for biochemical failure (prostate-specific antigen nadir + 2 ng/mL) and metastasis occurrence. RESULTS: By NCCN subclassification, 33 (27.3%) and 87 (71.9%) of men were classified as having favorable and unfavorable IR-PCa, respectively (1 case unclassifiable). GC scores were high in 3 favorable IR-PCa and low in 60 unfavorable IR-PCa. Higher GC scores, but not NCCN risk subgroups, were associated with biochemical relapse (hazard ratio, 1.36; 95% confidence interval [CI], 1.09-1.71] per 10% increase; P = .007) and metastasis (hazard ratio, 2.05; 95% CI, 1.24-4.24; P = .004). GC predicted biochemical failure at 5 years (area under the curve, 0.78; 95% CI, 0.59-0.91), and the combinatorial NCCN + GC model significantly outperformed the NCCN alone model for predicting early-onset metastasis (area under the curve for 5-year metastasis of 0.89 vs 0.86 [GC alone] vs 0.54 [NCCN alone]). CONCLUSIONS: We demonstrated the accuracy of the GC for predicting disease recurrence in IR-PCa treated with dose-escalated image guided RT alone. Our findings highlight the need to evaluate this GC in a prospective clinical trial investigating the role of ADT-RT in clinicogenomic-defined IR-PCa subgroups.

Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer.

Purpose: Recent studies have identified mutation signatures of homologous recombination deficiency (HRD) in over 20% of breast cancers, as well as pancreatic, ovarian, and gastric cancers. There is an urgent need to understand the clinical implications of HRD signatures. Whereas BRCA1/2 mutations confer sensitivity to platinum-based chemotherapies, it is not yet clear whether mutation signatures can independently predict platinum response.Experimental Design: In this observational study, we sequenced tumor whole genomes (100× depth) and matched normals (60×) of 93 advanced-stage breast cancers (33 platinum-treated). We computed a published metric called HRDetect, independently trained to predict BRCA1/2 status, and assessed its capacity to predict outcomes on platinum-based chemotherapies. Clinical endpoints were overall survival (OS), total duration on platinum-based therapy (TDT), and radiographic evidence of clinical improvement (CI).Results: HRDetect predicted BRCA1/2 status with an area under the curve (AUC) of 0.94 and optimal threshold of 0.7. Elevated HRDetect was also significantly associated with CI on platinum-based therapy (AUC = 0.89; P = 0.006) with the same optimal threshold, even after adjusting for BRCA1/2 mutation status and treatment timing. HRDetect scores over 0.7 were associated with a 3-month extended median TDT (P = 0.0003) and 1.3-year extended median OS (P = 0.04).Conclusions: Our findings not only independently validate HRDetect, but also provide the first evidence of its association with platinum response in advanced breast cancer. We demonstrate that HRD mutation signatures may offer clinically relevant information independently of BRCA1/2 mutation status and hope this work will guide the development of clinical trials. Clin Cancer Res; 23(24); 7521-30. ©2017 AACR.

Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma.

We describe a woman with the known pathogenic germline variant CHEK2:c.1100delC and synchronous diagnoses of both pelvic genital type leiomyosarcoma (LMS) and metastatic invasive ductal breast carcinoma. CHEK2 (checkpoint kinase 2) is a tumor-suppressor gene encoding a serine/threonine-protein kinase (CHEK2) involved in double-strand DNA break repair and cell cycle arrest. The CHEK2:c.1100delC variant is a moderate penetrance allele resulting in an approximately twofold increase in breast cancer risk. Whole-genome and whole-transcriptome sequencing were performed on the leiomyosarcoma and matched blood-derived DNA. Despite the presence of several genomic hits within the double-strand DNA damage pathway (CHEK2 germline variant and multiple RAD51B somatic structural variants), tumor profiling did not show an obvious DNA repair deficiency signature. However, even though the LMS displayed clear malignant features, its genomic profiling revealed several characteristics classically associated with leiomyomas including a translocation, t(12;14), with one breakpoint disrupting RAD51B and the other breakpoint upstream of HMGA2 with very high expression of HMGA2 and PLAG1 This is the first report of LMS genomic profiling in a patient with the germline CHEK2:c.1100delC variant and an additional diagnosis of metastatic invasive ductal breast carcinoma. We also describe a possible mechanistic relationship between leiomyoma and LMS based on genomic and transcriptome data. Our findings suggest that RAD51B translocation and HMGA2 overexpression may play an important role in LMS oncogenesis.

Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing.

Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of the molecular biology of peritoneal mesothelioma. Translation of the emerging data into better treatments and outcome is needed. From two patients with peritoneal mesothelioma, we derived whole genome sequences, RNA expression profiles, and targeted deep sequencing data. Molecular data were made available for translation into a clinical treatment plan. Treatment responses and outcomes were later examined in the context of molecular findings. Molecular studies presented here provide the first reported whole genome sequences of peritoneal mesothelioma. Mutations in known mesothelioma-related genes NF2, CDKN2A, LATS2, amongst others, were identified. Activation of MET-related signaling pathways was demonstrated in both cases. A hypermutated phenotype was observed in one case (434 vs. 18 single nucleotide variants) and was associated with a favourable outcome despite sarcomatoid histology and multifocal disease. This study represents the first report of whole genome analyses of peritoneal mesothelioma, a key step in the understanding and treatment of this disease.

Meta-Analysis of Gene Expression in Autism Spectrum Disorder.

Autism spectrum disorders (ASD) are clinically heterogeneous and biologically complex. In general it remains unclear, what biological factors lead to changes in the brains of autistic individuals. A considerable number of transcriptome analyses have been performed in attempts to address this question, but their findings lack a clear consensus. As a result, each of these individual studies has not led to any significant advance in understanding the autistic phenotype as a whole. Here, we report a meta-analysis of more than 1000 microarrays across twelve independent studies on expression changes in ASD compared to unaffected individuals, in both blood and brain tissues. We identified a number of known and novel genes that are consistently differentially expressed across three studies of the brain (71 samples in total). A subset of the highly ranked genes is suggestive of effects on mitochondrial function. In blood, consistent changes were more difficult to identify, despite individual studies tending to exhibit larger effects than the brain studies. Our results are the strongest evidence to date of a common transcriptome signature in the brains of individuals with ASD.

Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers.

Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted "panel" sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care. Between June 2012 and August 2014, 100 adult patients with incurable cancers consented to participate in the Personalized OncoGenomics (POG) study. Fresh tumor and blood samples were obtained and used for whole-genome and RNA sequencing. Computational approaches were used to identify candidate driver mutations, genes, and pathways. Diagnostic and drug information were then sought based on these candidate "drivers." Reports were generated and discussed weekly in a multidisciplinary team setting. Other multidisciplinary working groups were assembled to establish guidelines on the interpretation, communication, and integration of individual genomic findings into patient care. Of 78 patients for whom WGA was possible, results were considered actionable in 55 cases. In 23 of these 55 cases, the patients received treatments motivated by WGA. Our experience indicates that a multidisciplinary team of clinicians and scientists can implement a paradigm in which WGA is integrated into the care of late stage cancer patients to inform systemic therapy decisions.

Optimization of human mtDNA control region sequencing for forensic applications.

Sequencing mitochondrial DNA hypervariable regions I and II (HVI and HVII) is useful in forensic missing person and unidentified remains cases. Improvements in ease and sensitivity of testing will yield results from more samples in a timely fashion. Routinely, amplification of HVI and HVII is followed by Sanger sequencing using the BigDye(®) Terminator v3.1 Cycle Sequencing kit (Applied Biosystems) using 4 µL of ready reaction mix (RRM). Each sequencing reaction is then purified through column filtration before capillary electrophoresis. Using lower amounts of RRM (2 µL or 1 µL) and purification using BigDye(®) XTerminator(™) (Applied Biosystems) instead of columns showed no loss of sequence length and increased the quality and the sensitivity of testing, allowing HVI and HVII typing from mitochondrial genome equivalent to 125 fg of nuclear DNA, or 100 pg of HVI/HVII amplicons. Using this methodology, testing can be completed in 1 day, and the cost of testing is reduced.

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences.

BACKGROUND: Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available through online public resources and, when available, it is scattered across multiple access tools. DESCRIPTION: Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 7,000 genes to 2,000 different phenotypes. CONCLUSIONS: Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.