Family Based Studies in Complex Disorders: The Use of Bioinformatics Software for Data Analysis in Studies on Osteoporosis

Abstract Background Genetic disposition is considered critical for identifying subjects at high risk for disease development. Investigating disease-causing and high and low expressed genes can support finding the root causes of uncertainties in patient care. However, independent and timely high-throughput next-generation sequencing data analysis is still a challenge for non-computational biologists and geneticists. Results In this manuscript, we present a findable, accessible, interactive, and reusable (FAIR) bioinformatics platform, i.e., GVViZ (visualizing genes with disease-causing variants). GVViZ is a user-friendly, cross-platform, and database application for RNA-seq-driven variable and complex gene-disease data annotation and expression analysis with a dynamic heat map visualization. GVViZ has the potential to find patterns across millions of features and extract actionable information, which can support the early detection of complex disorders and the development of new therapies for personalized patient care. The execution of GVViZ is based on a set of simple instructions that users without a computational background can follow to design and perform customized data analysis. It can assimilate patients’ transcriptomics data with the public, proprietary, and our in-house developed gene-disease databases to query, easily explore, and access information on gene annotation and classified disease phenotypes with greater visibility and customization. To test its performance and understand the clinical and scientific impact of GVViZ, we present GVViZ analysis for different chronic diseases and conditions, including Alzheimer’s disease, arthritis, asthma, diabetes mellitus, heart failure, hypertension, obesity, osteoporosis, and multiple cancer disorders. The results are visualized using GVViZ and can be exported as image (PNF/TIFF) and text (CSV) files that include gene names, Ensembl (ENSG) IDs, quantified abundances, expressed transcript lengths, and annotated oncology and non-oncology diseases. Conclusions We emphasize that automated and interactive visualization should be an indispensable component of modern RNA-seq analysis, which is currently not the case. However, experts in clinics and researchers in life sciences can use GVViZ to visualize and interpret the transcriptomics data, making it a powerful tool to study the dynamics of gene expression and regulation. Furthermore, with successful deployment in clinical settings, GVViZ has the potential to enable high-throughput correlations between patient diagnoses based on clinical and transcriptomics data.

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A realistic review of family-based interventions for children of substance abusing parents.

10.32920/14636277 ◽

2021 ◽

Author(s):

Amelia M. Usher ◽

Kelly E. McShane ◽

Candice Dwyer

Keyword(s):

Data Analysis ◽

Disease Model ◽

Realist Review ◽

Program Theory ◽

Intervention Programs ◽

Substance Abusing ◽

The Family ◽

Prevention Model ◽

Family Based ◽

Family Based Interventions

Background Millions of children across North America and Europe live in families with alcohol or drug abusing parents. These children are at risk for a number of negative social, emotional and developmental outcomes, including an increased likelihood of developing a substance use disorder later in life. Family-based intervention programs for children with substance abusing parents can yield positive outcomes. This study is a realist review of evaluations of family-based interventions aimed at improving psychosocial outcomes for children of substance abusing parents (COSAPs). The primary objectives were to uncover patterns of contextual factors and mechanisms that generate program outcomes, and advance program theory in this field. Methods Realist review methodology was chosen as the most appropriate method of systematic review because it is a theory-driven approach that seeks to explore mechanisms underlying program effectiveness (or lack thereof). A systematic and comprehensive search of academic and grey literature uncovered 32 documents spanning 7 different intervention programs. Data was extracted from the included documents using abstraction templates designed to code for contexts, mechanisms and outcomes of each program. Two candidate program theories of family addiction were used to guide data analysis: the family disease model and the family prevention model. Data analysis was undertaken by a research team using an iterative process of comparison and checking with original documents to determine patterns within the data. Results Programs originating in both the family disease model and the family prevention model were uncovered, along with hybrid programs that successfully included components from each candidate program theory. Four demi-regularities were found to account for the effectiveness of programs included in this review: (1) opportunities for positive parent-child interactions, (2) supportive peer-to-peer relationships, (3) the power of knowledge, and (4) engaging hard to reach families using strategies that are responsive to socio-economic needs and matching services to client lived experience. Conclusions This review yielded new findings that had not otherwise been explored in COSAP program research and are discussed in order to help expand program theory. Implications for practice and evaluation are further discussed.

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TAXONOMIC LEVEL NEEDED TO DETECT SIGNIFICANT CHANGES IN POLYCHAETE COMMUNITIES OVER DIFFERENT MACROPHYTE ASSEMBLAGES ON ROCKY INTERTIDAL SHORES

Marine Research in Indonesia ◽

10.14203/mri.v42i2.189 ◽

2017 ◽

Vol 42 (2) ◽

pp. 93-108

Author(s):

Hadiyanto

Keyword(s):

Data Analysis ◽

Sample Size ◽

Statistical Power ◽

Linear Models ◽

Ecological Monitoring ◽

Rocky Intertidal ◽

Global Changes ◽

Taxonomic Level ◽

Significant Relationships ◽

Family Based

Environmental degradation has more significant impacts on rocky intertidal communities after global changes increase progressively. Thus, ecological monitoring should be conducted properly to analyse potential drivers and their impacts. However, most of the ecological monitoring in rocky intertidal shores is more interested in macroalgae. Polychaetes associated with macrophyte assemblages should be also involved in the monitoring because they are important in determining coastal health and productivity. A successful ecological monitoring should consider three factors: taxonomic level, statistical power, and sample size. In this study, those factors were analysed in the relationships between polychaetes and macrophytes. Four taxonomic levels of polychaetes (i.e. order, family, genus, species) were tested based on 25 samples collected from rocky intertidal shores of Gunung Kidul, Yogyakarta, Indonesia. Relationships between each of taxonomic richness of polychaetes and each of macrophytes variables (i.e. species richness, biomass, species composition) were analysed using a Generalised Linear Models fitted by Poisson Distribution and log link. The statistical power of those relationships and the sample size needed to obtain a strong statistical power (>0.8) were also recorded. Relationships between each of taxonomic composition of polychaetes and each of macrophyte variables were analysed using a distance-based Redundancy Analysis based on Bray-Curtis dissimilarity on log(x+1) transformed abundance data with 999 permutations. Results showed that family-based data analysis was sufficient to detect significant relationships between polychaetes and macrophytes. However, the statistical power of most relationships was relatively weak (<0.8). Hence, the family-based data analysis should select a 44-sample size to gain significant relationships with a strong statistical power.

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Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes

10.1101/310821 ◽

2018 ◽

Cited By ~ 1

Author(s):

Suhas Ganesh ◽

Ahmed P Husayn ◽

Ravi Kumar Nadella ◽

Ravi Prabhakar More ◽

Manasa Sheshadri ◽

...

Keyword(s):

Bipolar Disorder ◽

Exome Sequencing ◽

Rare Variants ◽

Association Studies ◽

Mental Illnesses ◽

Disease Genes ◽

Mendelian Disease ◽

Genome Wide Association Studies ◽

Complex Disorders ◽

Family Based

AbstractIntroductionSevere Mental Illnesses (SMI), such as bipolar disorder and schizophrenia, are highly heritable, and have a complex pattern of inheritance. Genome wide association studies detect a part of the heritability, which can be attributed to common genetic variation. Examination of rare variants with Next Generation Sequencing (NGS) may add to the understanding of genetic architecture of SMIs.MethodsWe analyzed 32 ill subjects (with diagnosis of Bipolar Disorder, n=26; schizophrenia, n=4; schizoaffective disorder, n=1 schizophrenia like psychosis, n=1) from 8 multiplex families; and 33 healthy individuals by whole exome sequencing. Prioritized variants were selected by a 4-step filtering process, which included deleteriousness by 5 in silico algorithms; sharing within families, absence in the controls and rarity in South Asian sample of Exome Aggregation Consortium.ResultsWe identified a total of 42 unique rare, non-synonymous deleterious variants in this study with an average of 5 variants per family. None of the variants were shared across families, indicating a ‘private’ mutational profile. Twenty (47.6%) of the variant harboring genes identified in this sample have been previously reported to contribute to the risk of neuropsychiatric syndromes. These include genes which are related to neurodevelopmental processes, or have been implicated in different monogenic syndromes with a severe neurodevelopmental phenotype.ConclusionNGS approaches in family based studies are useful to identify novel and rare variants in genes for complex disorders like SMI. The study further validates the phenotypic burden of rare variants in Mendelian disease genes, indicating pleiotropic effects in the etiology of severe mental illnesses.

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PENERAPAN DISIPLIN POSITIF DALAM PENGASUHAN ANAK OLEH KELUARGA YANG TELAH DIREUNIFIKASI DI KOTA BANDUNG

Pekerjaan Sosial ◽

10.31595/peksos.v15i2.84 ◽

2017 ◽

Vol 15 (2) ◽

Author(s):

Irniyati Samosir

Keyword(s):

Child Care ◽

Data Analysis ◽

Action Research ◽

Practical Implication ◽

Educational Background ◽

Erik Erikson ◽

Data Display ◽

Positive Discipline ◽

Care Pattern ◽

Family Based

Abstract The formulation of the problems in this research is to identify the model for positive discipline in child care within the reunited families in Bandung. The sub problems is to identify application of positive discipline in reunited families, to identify the result of positive discipline, to identify the reflection of positive discipline by the reunited families and to identify the improved model of positive discipline. The objectives of this research are to identify the child care pattern in reunified families and identify practices of positive discipline in reunified families in order to stregthen child care in the family. This research is using qualitative approach with action research methods. The data collection is collected using depth interview, documentation study, observation and discussions with child, parents and family. Data check was done with 1) Credibility test which covers: observation extension, increasing perseverance, triangulation, professional discussions and member check; 2) Transferability; 3) Dependability; 4) Conformability. For data analysis was done by qualitative data analysis, which covers these steps: data reduction, data display and drawing conclusions and verifications. The participants in this research are children and family which have been reunited, with the parent educational background up to elementary school, most of the parents is working as a laborer and household domestic worker and do not have the knowledge and skill on care. The result of this research has shown the increase knowledge for parents and reunited families on the necessity, the rights and methods of child care. These knowledge and understanding has an impact on the care pattern and parents and family attitude towards the child. The outcome of this research is a practical implication of positive discipline model in family based care for reunited families. In theory, this research confirms various assumption on positive discipline approaches especially on the role of giving warmth during care, and assumption on the child development phases from Erik Erikson which urgently needs to be understood by parents in order for them to give care appropriately with the child’s development. Key words: Positive Discipline; Reunified; Family Based Care Abstrak Rumusan masalah penelitian ini adalah bagaimanakah model penerapan disiplin positif dalam pengasuhan anak oleh keluarga yang telah direunifikasi di kota Bandung. Sub-sub permasalahannya adalah bagaimana karakteristik dan interaksi anak dan keluarga yang telah direunifikasi, bagaimana perencanaan model disiplin positif untuk keluarga yang telah direunifikasi, bagaimana aplikasi disiplin positif oleh keluarga yang telah direunifikasi, bagaimana hasil yang dicapai dari penerapan disiplin positif, bagaiman refleksi terhadap penerapan disiplin positif oleh keluarga yang telah direunifikasi serta bagaimana penyempurnaan model penerapan disiplin positif. Adapun tujuan dari penelitian ini adalah ingin mengetahui bagaimana pola pengasuhan anak dalam keluarga yang telah direunifikasi serta bagaimana penerapan disiplin positif kepada keluarga yang telah direunifikasi dalam rangka memperkuat pengasuhan anak dalam keluarga. Penelitian ini menggunakan pendekatan kualitatif dengan metode penelitian action research. Pengumpulan data diperoleh menggunakan teknik wawancara mendalam, studi dokumentasi, observasi dan diskusi dengan anak, orangtua dan keluarga. Sedangkan pemeriksaan data dilakukan dengan: 1) Uji kredibilitas yang meliputi : perpanjangan pengamatan, peningkatan ketekunan, triangulasi, diskusi teman sejawat dan membercheck; 2) Transferability; 3) Dependability; 4) Konfirmability. Untuk analisis data dilakukan melalui analisis data kualitatif, meliputi tahapan: reduksi data, display data, dan penarikan kesimpulan dan verifikasi. Partisipan dalam penelitian ini adalah anak dan keluarga yang telah direunifikasi, dengan latar belakang pendidikan orangtua tingkat SD, kebanyakan bekerja sebagai buruh dan pembantu rumah tangga serta tidak memiliki cukup pengetahuan dan keterampilan tentang pengasuhan. Hasil penelitian menunjukkan adanya penambahan pengetahuan orangtua dan keluarga yang telah direunifikasi mengenai kebutuhan, hak dan cara pengasuhan anak. Pengetahuan dan pemahaman tersebut berdampak kepada perubahan pada pola pengasuhan dan sikap orangtua dan keluarga terhadap anak. Penelitian ini juga menghasilkan implikasi praktis berupa Model Penerapan Disiplin Positif dalam Pengasuhan oleh Keluarga yang Telah Direunifikasi. Secara teoritik, penelitian juga mengkonfirmasi beberapa asumsi tentang pendekatan disiplin positif khususnya tentang peran pemberian kehangatan dalam pengasuhan, serta asumsi tentang tahapan perkembangan anak dari Erik Erikson yang sangat perlu dipahami oleh orangtua agar dapat memberikan pengasuhan sesuai kebutuhan perkembangan anak.Kata kunci: Disiplin Positif; Reunifikasi; Pengasuhan Berbasis Keluarga

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The Bioconductor channel in F1000Research

F1000Research ◽

10.12688/f1000research.6758.2 ◽

2016 ◽

Vol 4 ◽

pp. 217 ◽

Cited By ~ 1

Author(s):

Wolfgang Huber ◽

Vincent J. Carey ◽

Sean Davis ◽

Kasper Daniel Hansen ◽

Martin Morgan

Keyword(s):

Data Analysis ◽

Genomic Data ◽

Integrative Analysis ◽

Know How ◽

Software Packages ◽

Bioinformatics Software ◽

Task Oriented ◽

Genome Scale ◽

A Current ◽

Scale Data

Bioconductor (bioconductor.org) is a rich source of software and know-how for the integrative analysis of genomic data. The Bioconductor channel in F1000Research provides a forum for task-oriented workflows that cover a solution to a current, important problem in genome-scale data analysis. It also hosts manuscripts describing software packages, package-based vignettes, teaching labs, benchmark studies, methodological reviews and bioinformatics software oriented perspective papers.

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Linkage, case-control association, and family-based association tests for complex disorders

BMC Proceedings ◽

10.1186/1753-6561-1-s1-s43 ◽

2007 ◽

Vol 1 (S1) ◽

Cited By ~ 4

Author(s):

Brian K Suarez ◽

Robert Culverhouse ◽

Carol H Jin ◽

Anthony Hinrichs

Keyword(s):

Case Control ◽

Association Tests ◽

Complex Disorders ◽

Family Based ◽

Control Association

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ANALISIS PERBEDAAN DIVIDEN PADA PERUSAHAAN KELUARGA DAN NON KELUARGA BERDASARKAN KEPEMILIKAN ULTIMAT

MODUS ◽

10.24002/modus.v26i2.584 ◽

2016 ◽

Vol 26 (2) ◽

pp. 133 ◽

Cited By ~ 1

Author(s):

Krisnati Adi Cahyani ◽

I Putu Sugiartha Sanjaya

Keyword(s):

Data Analysis ◽

Ownership Structure ◽

Sampling Method ◽

Stock Exchange ◽

Secondary Data ◽

Family Ownership ◽

Manufacturing Companies ◽

Purposive Sampling ◽

Family Based

This study aims to to analyze whether there is a diference of the dividend shared on family company and non family based on the ultimate ownerships. Sampling method that used in this research was 400 manufacturing companies which are listed at Indonesia Stock Exchange (IDX), with research periods 2009-2012. The sample collected by purposive sampling method. Secondary data obtained from a IDX database and the ownership structure obtained through Sanjayaâ€™s (2010) previous research. The result of data analysis shows there are signifcant and diferencesÂ of the dividend shared between family company and non family. Family company pay dividends lower than non family company.Keywords : Dividend, Agency Teory, Family Ownership, IDX

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A realistic review of family-based interventions for children of substance abusing parents.

10.32920/14636277.v1 ◽

2021 ◽

Author(s):

Amelia M. Usher ◽

Kelly E. McShane ◽

Candice Dwyer

Keyword(s):

Data Analysis ◽

Disease Model ◽

Realist Review ◽

Program Theory ◽

Intervention Programs ◽

Substance Abusing ◽

The Family ◽

Prevention Model ◽

Family Based ◽

Family Based Interventions

Background Millions of children across North America and Europe live in families with alcohol or drug abusing parents. These children are at risk for a number of negative social, emotional and developmental outcomes, including an increased likelihood of developing a substance use disorder later in life. Family-based intervention programs for children with substance abusing parents can yield positive outcomes. This study is a realist review of evaluations of family-based interventions aimed at improving psychosocial outcomes for children of substance abusing parents (COSAPs). The primary objectives were to uncover patterns of contextual factors and mechanisms that generate program outcomes, and advance program theory in this field. Methods Realist review methodology was chosen as the most appropriate method of systematic review because it is a theory-driven approach that seeks to explore mechanisms underlying program effectiveness (or lack thereof). A systematic and comprehensive search of academic and grey literature uncovered 32 documents spanning 7 different intervention programs. Data was extracted from the included documents using abstraction templates designed to code for contexts, mechanisms and outcomes of each program. Two candidate program theories of family addiction were used to guide data analysis: the family disease model and the family prevention model. Data analysis was undertaken by a research team using an iterative process of comparison and checking with original documents to determine patterns within the data. Results Programs originating in both the family disease model and the family prevention model were uncovered, along with hybrid programs that successfully included components from each candidate program theory. Four demi-regularities were found to account for the effectiveness of programs included in this review: (1) opportunities for positive parent-child interactions, (2) supportive peer-to-peer relationships, (3) the power of knowledge, and (4) engaging hard to reach families using strategies that are responsive to socio-economic needs and matching services to client lived experience. Conclusions This review yielded new findings that had not otherwise been explored in COSAP program research and are discussed in order to help expand program theory. Implications for practice and evaluation are further discussed.

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Implementasi Program Parents Course untuk Meningkatkan Pemahaman Orang Tua tentang Auditory Verbal Therapy (AVT) bagi Anak dengan Hambatan Pendengaran di Yayasan Aurica Surabaya

PSIKOLOGI KONSELING ◽

10.24114/konseling.v8i1.5227 ◽

2017 ◽

Vol 8 (1) ◽

Author(s):

Ana Rafikayati

Keyword(s):

Qualitative Research ◽

Data Analysis ◽

Hearing Impairment ◽

Flow Analysis ◽

Test Design ◽

Data Display ◽

Planning Stage ◽

Post Test ◽

Family Based ◽

Auditory Verbal Therapy

Auditory Verbal Therapy (AVT) is a family based rehabilitation approach of hearing. Families, especially parents become the main persons who takes responsibility in child's language development. This study aimed to describe the implementation parents course program to improve the understanding of Auditory Verbal Therapy (AVT) for parents of children with hearing impairment in Aurica Foundation Surabaya. This research used descriptive qualitative research. Research’s subject in this research are the AVT therapists of Aurica foundation, audiologists and parents of children with hearing impairment. Data collection used interviews, observation and documentation techniques. Data analysis used flow analysis of Miles Huberman covering steps of data reduction, data display and verification. The results of this research is known that the implementation of parents course program course to improve the understanding of AVT for parents of children with hearing impairment in Aurica Foundation Surabaya is covering the planning, implementation and evaluation. In planning stage, the trainer analyzed needs of the knowledge AVT. Parents course consists of 4 stages: stage I, II, III, and IV. The program starts from the easy material to complex. The implementation of the parents course program is done in 4 phases. The technique used during training are presentation, discussions and demonstrations. Program evaluation of parents course done by a comparative pre-test and post-test design.

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