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1.
BMC Genomics ; 25(1): 122, 2024 Jan 29.
Article in English | MEDLINE | ID: mdl-38287261

ABSTRACT

BACKGROUND: Cancers exhibit complex transcriptomes with aberrant splicing that induces isoform-level differential expression compared to non-diseased tissues. Transcriptomic profiling using short-read sequencing has utility in providing a cost-effective approach for evaluating isoform expression, although short-read assembly displays limitations in the accurate inference of full-length transcripts. Long-read RNA sequencing (Iso-Seq), using the Pacific Biosciences (PacBio) platform, can overcome such limitations by providing full-length isoform sequence resolution which requires no read assembly and represents native expressed transcripts. A constraint of the Iso-Seq protocol is due to fewer reads output per instrument run, which, as an example, can consequently affect the detection of lowly expressed transcripts. To address these deficiencies, we developed a concatenation workflow, PacBio Full-Length Isoform Concatemer Sequencing (PB_FLIC-Seq), designed to increase the number of unique, sequenced PacBio long-reads thereby improving overall detection of unique isoforms. In addition, we anticipate that the increase in read depth will help improve the detection of moderate to low-level expressed isoforms. RESULTS: In sequencing a commercial reference (Spike-In RNA Variants; SIRV) with known isoform complexity we demonstrated a 3.4-fold increase in read output per run and improved SIRV recall when using the PB_FLIC-Seq method compared to the same samples processed with the Iso-Seq protocol. We applied this protocol to a translational cancer case, also demonstrating the utility of the PB_FLIC-Seq method for identifying differential full-length isoform expression in a pediatric diffuse midline glioma compared to its adjacent non-malignant tissue. Our data analysis revealed increased expression of extracellular matrix (ECM) genes within the tumor sample, including an isoform of the Secreted Protein Acidic and Cysteine Rich (SPARC) gene that was expressed 11,676-fold higher than in the adjacent non-malignant tissue. Finally, by using the PB_FLIC-Seq method, we detected several cancer-specific novel isoforms. CONCLUSION: This work describes a concatenation-based methodology for increasing the number of sequenced full-length isoform reads on the PacBio platform, yielding improved discovery of expressed isoforms. We applied this workflow to profile the transcriptome of a pediatric diffuse midline glioma and adjacent non-malignant tissue. Our findings of cancer-specific novel isoform expression further highlight the importance of long-read sequencing for characterization of complex tumor transcriptomes.


Subject(s)
Glioma , Transcriptome , Humans , Child , Gene Expression Profiling/methods , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA Splicing , Sequence Analysis, RNA , High-Throughput Nucleotide Sequencing/methods
2.
Brain ; 146(1): 387-404, 2023 01 05.
Article in English | MEDLINE | ID: mdl-35802027

ABSTRACT

Variants in the AUTS2 gene are associated with a broad spectrum of neurological conditions characterized by intellectual disability, microcephaly, and congenital brain malformations. Here, we use a human cerebral organoid model to investigate the pathophysiology of a heterozygous de novo missense AUTS2 variant identified in a patient with multiple neurological impairments including primary microcephaly and profound intellectual disability. Proband cerebral organoids exhibit reduced growth, deficits in neural progenitor cell (NPC) proliferation and disrupted NPC polarity within ventricular zone-like regions compared to control cerebral organoids. We used CRISPR-Cas9-mediated gene editing to correct this variant and demonstrate rescue of impaired organoid growth and NPC proliferative deficits. Single-cell RNA sequencing revealed a marked reduction of G1/S transition gene expression and alterations in WNT-ß-catenin signalling within proband NPCs, uncovering a novel role for AUTS2 in NPCs during human cortical development. Collectively, these results underscore the value of cerebral organoids to investigate molecular mechanisms underlying AUTS2 syndrome.


Subject(s)
Autistic Disorder , Intellectual Disability , Microcephaly , Neural Stem Cells , Humans , Microcephaly/genetics , Microcephaly/metabolism , Intellectual Disability/genetics , Organoids/metabolism , Cytoskeletal Proteins , Transcription Factors/metabolism
3.
Demography ; 61(3): 829-847, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38785364

ABSTRACT

A growing proportion of individuals adopt family caregiving roles. Family caregivers are the primary providers of long-term care in the United States yet limited federal policy supports exist, despite the known negative impacts of caregiving. There is also limited information about the prevalence of youth/young adult caregivers and the impacts of caregiving at formative ages in the United States. Our objective is to estimate the prevalence of youth caregivers and examine the association of caregiving with educational investments. We use the American Time Use Survey (2013-2019) to identify and describe youth caregivers (aged 15-18) and young adult caregivers (aged 19-22) and compare them with non-caregiving peers. We estimate that there are approximately 1,623,000 youth caregivers and 1,986,000 young adult caregivers, corresponding to 9.2% and 12.7% of these age groups, respectively. However, there is a wide range in the estimated prevalence per year, from approximately 364,000 to 2.8 million youth caregivers and from 353,000 to 2.2 million young adult caregivers, depending on caregiver definition. Unlike adult caregivers, we find that young men and women were nearly equally likely to provide care. We also find that non-White individuals are disproportionately represented as youth caregivers. Compared with non-caregiving peers, both youth and young adult caregivers are less likely to be enrolled in school and, among those enrolled in school, spend significantly less time on educational activities. Considering the association of caregiving among youth/young adults and education, policies supporting youth and young adult caregivers are critical.


Subject(s)
Caregivers , Educational Status , Humans , Caregivers/statistics & numerical data , Adolescent , United States , Male , Female , Young Adult , Prevalence , Socioeconomic Factors , Sociodemographic Factors , Adult , Age Factors
4.
Genes Chromosomes Cancer ; 62(1): 39-46, 2023 01.
Article in English | MEDLINE | ID: mdl-35716171

ABSTRACT

Ependymal tumors are the third most common brain tumor under 14 years old. Even though metastatic disease is a rare event, it affects mostly young children and carries an adverse prognosis. The factors associated with dissemination and the best treatment approach have not yet been established and there is limited published data on how to manage metastatic disease, especially in patients under 3 years of age. We provide a review of the literature on clinical characteristics and radiation-sparing treatments for metastatic ependymoma in children under 3 years of age treated. The majority (73%) of the identified cases were above 12 months old and had the PF as the primary site at diagnosis. Chemotherapy-based approaches, in different regimens, were used with radiation reserved for progression or relapse. The prognosis varied among the studies, with an average of 50%-58% overall survival. This study also describes the case of a 7-month-old boy with metastatic posterior fossa (PF) ependymoma, for whom we identified a novel SPECC1L-RAF1 gene fusion using a patient-centric comprehensive molecular profiling protocol. The patient was successfully treated with intensive induction chemotherapy followed by high-dose chemotherapy and autologous hematopoietic progenitor cell rescue (AuHSCR). Currently, the patient is in continuous remission 5 years after his diagnosis, without radiation therapy. The understanding of the available therapeutic approaches may assist physicians in their management of such patients. This report also opens the perspective of newly identified molecular alterations in metastatic ependymomas that might drive more chemo-sensitive tumors.


Subject(s)
Brain Neoplasms , Ependymoma , Hematopoietic Stem Cell Transplantation , Child , Male , Humans , Child, Preschool , Infant , Adolescent , Neoplasm Recurrence, Local , Ependymoma/drug therapy , Ependymoma/genetics , Ependymoma/radiotherapy , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Brain Neoplasms/diagnosis
5.
Ann Rheum Dis ; 82(2): 235-245, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36171069

ABSTRACT

BACKGROUND: Idiopathic inflammatory myopathies (IIM) are a group of autoimmune diseases characterised by myositis-related autoantibodies plus infiltration of leucocytes into muscles and/or the skin, leading to the destruction of blood vessels and muscle fibres, chronic weakness and fatigue. While complement-mediated destruction of capillary endothelia is implicated in paediatric and adult dermatomyositis, the complex diversity of complement C4 in IIM pathology was unknown. METHODS: We elucidated the gene copy number (GCN) variations of total C4, C4A and C4B, long and short genes in 1644 Caucasian patients with IIM, plus 3526 matched healthy controls using real-time PCR or Southern blot analyses. Plasma complement levels were determined by single radial immunodiffusion. RESULTS: The large study populations helped establish the distribution patterns of various C4 GCN groups. Low GCNs of C4T (C4T=2+3) and C4A deficiency (C4A=0+1) were strongly correlated with increased risk of IIM with OR equalled to 2.58 (2.28-2.91), p=5.0×10-53 for C4T, and 2.82 (2.48-3.21), p=7.0×10-57 for C4A deficiency. Contingency and regression analyses showed that among patients with C4A deficiency, the presence of HLA-DR3 became insignificant as a risk factor in IIM except for inclusion body myositis (IBM), by which 98.2% had HLA-DR3 with an OR of 11.02 (1.44-84.4). Intragroup analyses of patients with IIM for C4 protein levels and IIM-related autoantibodies showed that those with anti-Jo-1 or with anti-PM/Scl had significantly lower C4 plasma concentrations than those without these autoantibodies. CONCLUSIONS: C4A deficiency is relevant in dermatomyositis, HLA-DRB1*03 is important in IBM and both C4A deficiency and HLA-DRB1*03 contribute interactively to risk of polymyositis.


Subject(s)
Dermatomyositis , Myositis , Adult , Humans , Child , Complement C4 , DNA Copy Number Variations , HLA-DRB1 Chains/genetics , Autoantibodies/genetics , HLA-DR3 Antigen/genetics , Genetic Predisposition to Disease , Risk Factors , Complement C4a/genetics
6.
Psychiatr Ann ; 53(11): 491-495, 2023 Nov 01.
Article in English | MEDLINE | ID: mdl-38293647

ABSTRACT

Sleep disturbances, namely insomnia and recurrent nightmares, are ubiquitous following trauma exposure and are considered hallmarks of posttraumatic stress disorder (PTSD). Other sleep disorders frequently co-occur with PTSD. This article describes research examining sleep problems most common in PTSD, including prevalence and clinical characteristics. Sleep disturbances are often robust to trauma-focused treatment; thus, evidence for psychological and pharmacological interventions for insomnia and nightmares in PTSD are discussed. Given the high prevalence of sleep problems in PTSD, more work is needed to empirically study putative mechanisms linking trauma exposure and sleep, as well as how to best target these symptoms in patients with PTSD.

7.
Ann Surg Oncol ; 29(12): 7354-7367, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35780216

ABSTRACT

INTRODUCTION: Sarcoma clinical outcomes have been stagnant for decades due to heterogeneity of primaries, lack of comprehensive preclinical models, and rarity of disease. We hypothesized that engineering hydrogel-based sarcoma organoids directly from the patient without xenogeneic extracellular matrices (ECMs) or growth factors is routinely feasible and allows rare tumors to remain viable as avatars for personalized research. METHODS: Surgically resected sarcomas (angiosarcomas, leiomyosarcoma, gastrointestinal stromal tumor, liposarcoma, myxofibrosarcoma, dermatofibrosarcoma protuberans [DFSP], and pleiomorphic abdominal sarcoma) were dissociated and incorporated into a hyaluronic acid and collagen-based ECM hydrogel and screened for chemotherapy efficacy. A subset of organoids was enriched with a patient-matched immune system for screening of immunotherapy efficacy (iPTOs). Response to treatment was assessed using LIVE/DEAD staining and metabolic assays. RESULTS: Sixteen sarcomas were biofabricated into three-dimensional (3D) patient-specific sarcoma organoids with a 100% success rate. Average time from organoid development to initiation of drug testing was 7 days. Enrichment of organoids with immune system components derived from either peripheral blood mononuclear cells or lymph node cells was performed in 10/16 (62.5%) patients; 4/12 (33%) organoids did not respond to chemotherapy, while response to immunotherapy was observed in 2/10 (20%) iPTOs. CONCLUSIONS: A large subset of sarcoma organoids does not exhibit response to chemotherapy or immunotherapy, as currently seen in clinical practice. Routine development of sarcoma hydrogel-based organoids directly from the operating room is a feasible platform, allowing for such rare tumors to remain viable for personalized translational research.


Subject(s)
Sarcoma , Soft Tissue Neoplasms , Adult , Humans , Hyaluronic Acid/metabolism , Hydrogels , Leukocytes, Mononuclear , Operating Rooms , Organoids/pathology , Sarcoma/pathology , Soft Tissue Neoplasms/pathology , Translational Research, Biomedical
8.
Med Care ; 60(7): 530-537, 2022 07 01.
Article in English | MEDLINE | ID: mdl-35471419

ABSTRACT

BACKGROUND: Of the 26.4 million family caregivers in the United States, nearly 40% report high levels of emotional strain and subjective burden. However, for the 5 million caregivers of Veterans, little is known about the experiences of caregivers of Veterans during the coronavirus disease 2019 (COVID-19) pandemic. OBJECTIVE: The aim was to examine pandemic-related changes of caregiver well-being outcomes. RESEARCH DESIGN, SUBJECTS, AND MEASURES: Using a pre/post design and longitudinal data of individual caregivers captured pre-COVID-19 and during COVID-19, we use multilevel generalized linear mixed models to examine pandemic-related changes to caregiver well-being (n=903). The primary outcome measures include Zarit Subjective Burden, Center for Epidemiologic Studies Short Depression Scale, perceived financial strain, life chaos, and loneliness. RESULTS: During the pandemic, we observe slight improvements for caregivers across well-being measures except for perceived financial strain. Before the pandemic, we observed that caregivers screened positive for clinically significant caregiver burden and probable depression. While we do not observe worsening indicators of caregiver well-being during the COVID-19 pandemic, the average predicted values of indicators of caregiver well-being remain clinically significant for caregiving subjective burden and depression. CONCLUSIONS: These findings illuminate pandemic-related impacts of caregivers receiving support through the Veterans Affairs (VA) pre-COVID and during the COVID-19 pandemic while caring for a population of frail, older care-recipients with a high burden of mental illness and other chronic conditions. Considering the long-term impacts of the pandemic to increase morbidity and the expected increased demand for caregivers in an aging population, these consistently high levels of distress despite receiving support highlight the need for interventions and policy reform to systematically support caregivers more broadly.


Subject(s)
COVID-19 , Veterans , Aged , COVID-19/epidemiology , Caregivers/psychology , Chronic Disease , Humans , Pandemics , Veterans/psychology
9.
Milbank Q ; 100(3): 854-878, 2022 09.
Article in English | MEDLINE | ID: mdl-35579187

ABSTRACT

Policy Points In the absence of federal policy, states adopted policies to support family caregivers, but availability and level of support varies. We describe, compare, and rank state policies to support family caregivers as aligned with National Academy of Medicine recommendations. Although the landscape of state policies supporting caregivers has improved over time, few states provide financial supports as recommended, and benefit restrictions hinder accessibility for all types of family caregivers. Implementing policies supporting family caregivers will become more critical over time, as the reliance on family caregivers as essential providers of long-term care is only expected to grow as the population ages. CONTEXT: In the United States in 2020, approximately 26 million individuals provided unpaid care to a family member or friend. On average, 60% of caregivers were employed, and they provided 20.4 hours of care per week on top of employment. Although a handful of patchwork laws exist to aid family caregivers, systematic supports, including comprehensive training, respite, and financial support, remain limited. In the absence of federal supports, states have adopted policies to provide assistance, but they vary in availability and level of support provided. Our objectives were to describe, compare, and rank state policies to support family caregivers over time. METHODS: We used publicly available data from the AARP Long-Term Services and Supports State Scorecard, the National Academy for State Health Policy, and Tax Credits for Workers and Families for all 50 states and the District of Columbia (2015-2019). FINDINGS: We found that states had increased supports to family caregivers over this five-year period, although significant variability in adoption and implementation of policies persists. Approximately 20% of states had enacted policies that exceed the federal Family and Medical Leave Act requirements, and 18% offered paid family leave. However, most states had not improved spousal impoverishment protections for Medicaid beneficiaries. For example, from 2016 to 2019, 24% of states provided fewer or no protections, while 71% of states did not improve spousal impoverishment protections over time. Access to training for caregivers varied based on eligibility criteria (e.g., select populations and/or only co-residing caregivers). CONCLUSIONS: Overall, state approaches to support family caregivers vary by eligibility and scope of services. Substantial gaps in support of caregivers, particularly economic supports, persist. Although the landscape of state policies supporting caregivers has improved over time, few states provide financial supports as recommended by the National Academy of Medicine, and benefit restrictions hinder accessibility for all family caregivers.


Subject(s)
Caregivers , Medicaid , Health Policy , Humans , Long-Term Care , National Academies of Science, Engineering, and Medicine, U.S., Health and Medicine Division , United States
10.
Epilepsia ; 63(8): 1981-1997, 2022 08.
Article in English | MEDLINE | ID: mdl-35687047

ABSTRACT

OBJECTIVE: Epilepsy-associated developmental lesions, including malformations of cortical development and low-grade developmental tumors, represent a major cause of drug-resistant seizures requiring surgical intervention in children. Brain-restricted somatic mosaicism has been implicated in the genetic etiology of these lesions; however, many contributory genes remain unidentified. METHODS: We enrolled 50 children who were undergoing epilepsy surgery into a translational research study. Resected tissue was divided for clinical neuropathologic evaluation and genomic analysis. We performed exome and RNA sequencing to identify somatic variation and we confirmed our findings using high-depth targeted DNA sequencing. RESULTS: We uncovered candidate disease-causing somatic variation affecting 28 patients (56%), as well as candidate germline variants affecting 4 patients (8%). In agreement with previous studies, we identified somatic variation affecting solute carrier family 35 member A2 (SLC35A2) and mechanistic target of rapamycin kinase (MTOR) pathway genes in patients with focal cortical dysplasia. Somatic gains of chromosome 1q were detected in 30% (3 of 10) of patients with Type I focal cortical dysplasia (FCD)s. Somatic variation in mitogen-activated protein kinase (MAPK) pathway genes (i.e., fibroblast growth factor receptor 1 [FGFR1], FGFR2, B-raf proto-oncogene, serine/threonine kinase [BRAF], and KRAS proto-oncogene, GTPase [KRAS]) was associated with low-grade epilepsy-associated developmental tumors. RNA sequencing enabled the detection of somatic structural variation that would have otherwise been missed, and which accounted for more than one-half of epilepsy-associated tumor diagnoses. Sampling across multiple anatomic regions revealed that somatic variant allele fractions vary widely within epileptogenic tissue. Finally, we identified putative disease-causing variants in genes not yet associated with focal cortical dysplasia. SIGNIFICANCE: These results further elucidate the genetic basis of structural brain abnormalities leading to focal epilepsy in children and point to new candidate disease genes.


Subject(s)
Epilepsy , Malformations of Cortical Development , Brain/pathology , Child , Epilepsy/pathology , Humans , Malformations of Cortical Development/complications , Malformations of Cortical Development/genetics , Malformations of Cortical Development/metabolism , Mutation , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , TOR Serine-Threonine Kinases/genetics , TOR Serine-Threonine Kinases/metabolism
11.
Brain ; 144(10): 2971-2978, 2021 11 29.
Article in English | MEDLINE | ID: mdl-34048549

ABSTRACT

Phosphatase and tensin homologue (PTEN) regulates cell growth and survival through inhibition of the mammalian target of rapamycin (MTOR) signalling pathway. Germline genetic variation of PTEN is associated with autism, macrocephaly and PTEN hamartoma tumour syndromes. The effect of developmental PTEN somatic mutations on nervous system phenotypes is not well understood, although brain somatic mosaicism of MTOR pathway genes is an emerging cause of cortical dysplasia and epilepsy in the paediatric population. Here we report two somatic variants of PTEN affecting a single patient presenting with intractable epilepsy and hemimegalencephaly that varied in clinical severity throughout the left cerebral hemisphere. High-throughput sequencing analysis of affected brain tissue identified two somatic variants in PTEN. The first variant was present in multiple cell lineages throughout the entire hemisphere and associated with mild cerebral overgrowth. The second variant was restricted to posterior brain regions and affected the opposite PTEN allele, resulting in a segmental region of more severe malformation, and the only neurons in which it was found by single-nuclei RNA-sequencing had a unique disease-related expression profile. This study reveals brain mosaicism of PTEN as a disease mechanism of hemimegalencephaly and furthermore demonstrates the varying effects of single- or bi-allelic disruption of PTEN on cortical phenotypes.


Subject(s)
Cerebral Cortex/diagnostic imaging , Genetic Variation/genetics , Hemimegalencephaly/diagnostic imaging , Hemimegalencephaly/genetics , Mutation/genetics , PTEN Phosphohydrolase/genetics , Cerebral Cortex/surgery , Hemimegalencephaly/surgery , Humans , Infant , Male
12.
J Med Internet Res ; 24(12): e36729, 2022 12 30.
Article in English | MEDLINE | ID: mdl-36583929

ABSTRACT

BACKGROUND: Reddit is a popular social media platform that has faced scrutiny for inflammatory language against those with obesity, yet there has been no comprehensive analysis of its obesity-related content. OBJECTIVE: We aimed to quantify the presence of 4 types of obesity-related content on Reddit (misinformation, facts, stigma, and positivity) and identify psycholinguistic features that may be enriched within each one. METHODS: All sentences (N=764,179) containing "obese" or "obesity" from top-level comments (n=689,447) made on non-age-restricted subreddits (ie, smaller communities within Reddit) between 2011 and 2019 that contained one of a series of keywords were evaluated. Four types of common natural language processing features were extracted: bigram term frequency-inverse document frequency, word embeddings derived from Bidirectional Encoder Representations from Transformers, sentiment from the Valence Aware Dictionary for Sentiment Reasoning, and psycholinguistic features from the Linguistic Inquiry and Word Count Program. These features were used to train an Extreme Gradient Boosting machine learning classifier to label each sentence as 1 of the 4 content categories or other. Two-part hurdle models for semicontinuous data (which use logistic regression to assess the odds of a 0 result and linear regression for continuous data) were used to evaluate whether select psycholinguistic features presented differently in misinformation (compared with facts) or stigma (compared with positivity). RESULTS: After removing ambiguous sentences, 0.47% (3610/764,179) of the sentences were labeled as misinformation, 1.88% (14,366/764,179) were labeled as stigma, 1.94% (14,799/764,179) were labeled as positivity, and 8.93% (68,276/764,179) were labeled as facts. Each category had markers that distinguished it from other categories within the data as well as an external corpus. For example, misinformation had a higher average percent of negations (ß=3.71, 95% CI 3.53-3.90; P<.001) but a lower average number of words >6 letters (ß=-1.47, 95% CI -1.85 to -1.10; P<.001) relative to facts. Stigma had a higher proportion of swear words (ß=1.83, 95% CI 1.62-2.04; P<.001) but a lower proportion of first-person singular pronouns (ß=-5.30, 95% CI -5.44 to -5.16; P<.001) relative to positivity. CONCLUSIONS: There are distinct psycholinguistic properties between types of obesity-related content on Reddit that can be leveraged to rapidly identify deleterious content with minimal human intervention and provide insights into how the Reddit population perceives patients with obesity. Future work should assess whether these properties are shared across languages and other social media platforms.


Subject(s)
Social Media , Humans , Prevalence , Infodemiology , Psycholinguistics , Communication
13.
Genes Chromosomes Cancer ; 60(9): 640-646, 2021 09.
Article in English | MEDLINE | ID: mdl-34041825

ABSTRACT

Gastroblastomas are rare tumors with a biphasic epithelioid/spindle cell morphology that typically present in early adulthood and have recurrent MALAT1-GLI1 fusions. We describe an adolescent patient with Wiskott-Aldrich syndrome who presented with a large submucosal gastric tumor with biphasic morphology. Despite histologic features consistent with gastroblastoma, a MALAT1-GLI1 fusion was not found in this patient's tumor; instead, comprehensive molecular profiling identified a novel EWSR1-CTBP1 fusion and no other significant genetic alterations. The tumor also overexpressed NOTCH and FGFR by RNA profiling. The novel fusion and expression profile suggest a role for epithelial-mesenchymal transition in this tumor, with potential implications for the pathogenesis of biphasic gastric tumors such as gastroblastoma.


Subject(s)
Alcohol Oxidoreductases/genetics , Carcinoma/genetics , DNA-Binding Proteins/genetics , Oncogene Proteins, Fusion/genetics , RNA-Binding Protein EWS/genetics , Stomach Neoplasms/genetics , Adolescent , Age of Onset , Carcinoma/pathology , Humans , Male , Stomach Neoplasms/pathology
14.
BMC Genomics ; 22(1): 872, 2021 Dec 04.
Article in English | MEDLINE | ID: mdl-34863095

ABSTRACT

BACKGROUND: Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and specific detection of gene fusions through the analysis of next-generation-based RNA sequencing (RNA-Seq) data is computationally challenging and may be confounded by low tumor cellularity or underlying genomic complexity. Furthermore, numerous computational tools are available to identify fusions from supporting RNA-Seq reads, yet each algorithm demonstrates unique variability in sensitivity and precision, and no clearly superior approach currently exists. To overcome these challenges, we have developed an ensemble fusion calling approach to increase the accuracy of identifying fusions. RESULTS: Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless technology. This method uses paired end RNA-Seq sequence reads as input, and the output from each algorithm is examined to identify fusions detected by a consensus of at least three algorithms. These consensus fusion results are filtered by comparison to an internal database to remove likely artifactual fusions occurring at high frequencies in our internal cohort, while a "known fusion list" prevents failure to report known pathogenic events. We have employed the EnFusion pipeline on RNA-Seq data from 229 patients with pediatric cancer or blood disorders studied under an IRB-approved protocol. The samples consist of 138 central nervous system tumors, 73 solid tumors, and 18 hematologic malignancies or disorders. The combination of an ensemble fusion-calling pipeline and a knowledge-based filtering strategy identified 67 clinically relevant fusions among our cohort (diagnostic yield of 29.3%), including RBPMS-MET, BCAN-NTRK1, and TRIM22-BRAF fusions. Following clinical confirmation and reporting in the patient's medical record, both known and novel fusions provided medically meaningful information. CONCLUSIONS: The EnFusion pipeline offers a streamlined approach to discover fusions in cancer, at higher levels of sensitivity and accuracy than single algorithm methods. Furthermore, this method accurately identifies driver fusions in pediatric cancer, providing clinical impact by contributing evidence to diagnosis and, when appropriate, indicating targeted therapies.


Subject(s)
Genome , Neoplasms , Child , Genomics , Humans , Neoplasms/genetics , Sequence Analysis, DNA , Sequence Analysis, RNA
15.
Clin Psychol Psychother ; 28(1): 251-260, 2021 Jan.
Article in English | MEDLINE | ID: mdl-32822516

ABSTRACT

In adult populations, bipolar disorders (BDs) and posttraumatic stress disorder (PTSD) have overlapping symptoms, potentially leading to misdiagnosis. This misdiagnosis or failure to diagnose both co-occurring disorders can result in individuals not receiving the proper treatment to address their symptoms. This article highlights how trauma-informed psychological assessment can assist in differential diagnosis and improve the timely delivery of appropriate treatments. The overlapping symptoms of PTSD and BD are discussed to assist in differential diagnosis, and we suggest guidelines for conducting trauma-informed, evidence-based assessments to help clarify these diagnoses.


Subject(s)
Bipolar Disorder/diagnosis , Bipolar Disorder/psychology , Stress Disorders, Post-Traumatic/diagnosis , Stress Disorders, Post-Traumatic/psychology , Adult , Diagnosis, Differential , Humans
16.
Dreaming ; 31(2): 117-127, 2021 Jun.
Article in English | MEDLINE | ID: mdl-37363340

ABSTRACT

A previous study in military veterans with posttraumatic stress disorder (PTSD) and recurrent nightmares found a high prevalence of lucid dreaming (LD), the awareness while a dream continues that one is dreaming, and an "LD profile" characterized by frequent dream awareness and rare dream content control. Given the importance of the nightmare disturbance in PTSD, this study assessed with questionnaires the prevalence and characteristics of lucid nightmares, specifically, in a sample of 54 veterans with PTSD. Over half the sample endorsed experiencing LD, with nearly all of these individuals explicitly reporting lucidity in nightmares. The lucid nightmare profile was characterized by high awareness and low content control. Veterans reported feeling stuck and anxious, trying unsuccessfully to awaken from lucid nightmares. We conclude that lucid nightmares may occur commonly in veterans with PTSD, with a profile resembling that previously reported for LD experiences generally in this group.

17.
Behav Sleep Med ; 17(4): 481-491, 2019.
Article in English | MEDLINE | ID: mdl-29120247

ABSTRACT

Objective: Clinicians' perceptions of CBT-I Coach, a patient-facing mobile app for cognitive-behavioral therapy for insomnia (CBT-I), are critical to its adoption and integration into practice. Diffusion of innovations theory emphasizes the influence of perceptions, including the relative advantage to current practice, the compatibility to clinicians' needs, the complexity, the innovation's trialability, and observability. This study intended to evaluate the use and perceptions of CBT-I Coach among Veterans Affairs (VA)-trained CBT-I clinicians. Participants and Methods: Clinicians (N = 108) were surveyed about their use, feedback, and perceptions of CBT-I Coach a year after the app became available. Results: Overall perceptions of CBT-I Coach were favorable. Fifty percent of clinicians reported using CBT-I Coach, with 98% intending to continue use. The app was perceived to increase sleep diary completion and homework compliance. Clinicians viewed the app as providing accessibility to helpful tools and improving patient engagement. Of those not using the app, 83% endorsed intention to use it. Reasons for nonuse were lack of patient access to smart phones, not being aware of the app, not having time to learn it, and inability to directly access app data. Those who reported using CBT-I Coach had more favorable perceptions across all constructs (p < .01 - p < .001), except relative advantage, compared to nonusers. Users perceived it as less complex and more compatible with their practice than nonusers. Conclusions: Continued efforts are needed to increase adoption and enhance use of CBT-I Coach, as well as study if reported benefits can be evidenced more directly.


Subject(s)
Attitude of Health Personnel , Cognitive Behavioral Therapy , Equipment and Supplies Utilization , Mobile Applications/statistics & numerical data , Physicians , Sleep Initiation and Maintenance Disorders/psychology , Sleep Initiation and Maintenance Disorders/therapy , Surveys and Questionnaires , Humans , Middle Aged , Patient Compliance/statistics & numerical data , Physicians/psychology , United States , United States Department of Veterans Affairs
18.
J Clin Psychol Med Settings ; 26(2): 166-172, 2019 06.
Article in English | MEDLINE | ID: mdl-30043244

ABSTRACT

Sleep disorders are frequently under assessed and not well understood by medical practitioners. This study investigated medical practitioners' knowledge of, experience with, and treatment considerations for sleep disorders, with a particular emphasis on nightmares. Eighty-eight individuals practicing medicine in the United States completed a survey eliciting information in three domains: (a) professional experience with nightmares, (b) knowledge of nightmares, and (c) attitudes about treatment of sleep disturbances. Seventy percent of participants reported a lack of professional experience with nightmares, 78% endorsed inaccurate definitions of a nightmares, and 82% considered sleep disorders to be a secondary problem, with 75% considering nightmares a secondary problem. Seventy-two percent of participants reported they would be likely to consider psychological treatment for nightmares. Results suggest that medical practitioners may not be receiving updated and/or adequate education about sleep disorders, including nightmares. This lack of information may contribute to sleep disorders being under assessed and untreated.


Subject(s)
Attitude of Health Personnel , Clinical Competence/statistics & numerical data , Dreams , Health Personnel/statistics & numerical data , Sleep Wake Disorders/therapy , Adult , Female , Humans , Male , United States
19.
Inquiry ; 55: 46958018762914, 2018.
Article in English | MEDLINE | ID: mdl-29591540

ABSTRACT

Family caregivers are an important component of the long-term services and supports (LTSS) system. However, caregiving may have negative consequences for caregiver physical and emotional health. Connecting caregivers to formal short-term home- and community-based services (HCBS), through information resources and referrals, might alleviate family caregiver burden and delay nursing home entry for the patient. The aim of this study was to evaluate the early impact of the Program of Comprehensive Assistance for Family Caregivers (PCAFC) (established by P.L. 111-163 for family caregivers of seriously injured post-9/11 Veterans) on Veteran use of LTSS. A two-cohort pre-post design with a nonequivalent comparison group (treated n = 15 650; comparison n = 8339) was used to (1) examine the association between caregiver enrollment in PCAFC and any VA-purchased or VA-provided LTSS use among Veterans and (2) describe program-related trends in HCBS and institutional LTSS use. The comparison group was an inverse-propensity-score weighted sample of Veterans whose caregivers applied for, but were not accepted into, the program. From baseline through 24 months post application, use of any LTSS ranged from 13.1% to 17.8% for Veterans whose caregivers were enrolled in PCAFC versus from 3.8% to 5.3% for Veterans in the comparison group. Participation in PCAFC was associated with a statistically significant increased use of any LTSS from 1 to 24 months post application (over time odds ratios ranged from 2.71 [95% confidence interval: 2.31-3.17] to 4.86 [3.93-6.02]). Support for family caregivers may enhance utilization of LTSS for Veterans with physical, emotional, and/or cognitive conditions.


Subject(s)
Adaptation, Psychological , Caregivers/psychology , United States Department of Veterans Affairs/organization & administration , Adult , Caregivers/education , Family , Female , Health Status , Humans , Male , Mental Health , Middle Aged , Propensity Score , Respite Care/organization & administration , Retrospective Studies , United States
20.
Adm Policy Ment Health ; 45(4): 550-564, 2018 07.
Article in English | MEDLINE | ID: mdl-29374821

ABSTRACT

The VA Program of Comprehensive Assistance for Family Caregivers (PCAFC) provides landmark support for family caregivers of post-9/11 veterans. This study examines PCAFC support for veterans with and without PTSD and assesses whether program effect differs by PTSD status using a pre-post, non-equivalent, propensity score weighted comparison group design (n = 24,280). Veterans with and without PTSD in PCAFC accessed more mental health, primary, and specialty care services than weighted comparisons. PCAFC participation had stronger effects on access to primary care for veterans with PTSD than for veterans without PTSD. For veterans with PTSD, PCAFC support might enhance health service use.


Subject(s)
Ambulatory Care , Caregivers/education , Family , Health Services Accessibility , Mental Health Services , Primary Health Care , Social Support , Stress Disorders, Post-Traumatic/nursing , Veterans , Adult , Female , Humans , Male , Middle Aged , Propensity Score , Retrospective Studies , Stress Disorders, Post-Traumatic/therapy , United States , United States Department of Veterans Affairs
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