scholarly journals A likelihood ratio approach for identifying three-quarter siblings in genetic databases

Heredity ◽  
2021 ◽  
Author(s):  
Iván Galván-Femenía ◽  
Carles Barceló-Vidal ◽  
Lauro Sumoy ◽  
Victor Moreno ◽  
Rafael de Cid ◽  
...  
Keyword(s):  
Likelihood Ratio ◽  
Family Relationships ◽  
Genetic Research ◽  
Data Set ◽  
Scientific Disciplines ◽  
Genome Wide ◽  
Standard Quality ◽  
Control Procedures ◽  
Identity By State ◽  
Second Degree

AbstractThe detection of family relationships in genetic databases is of interest in various scientific disciplines such as genetic epidemiology, population and conservation genetics, forensic science, and genealogical research. Nowadays, screening genetic databases for related individuals forms an important aspect of standard quality control procedures. Relatedness research is usually based on an allele sharing analysis of identity by state (IBS) or identity by descent (IBD) alleles. Existing IBS/IBD methods mainly aim to identify first-degree relationships (parent–offspring or full siblings) and second degree (half-siblings, avuncular, or grandparent–grandchild) pairs. Little attention has been paid to the detection of in-between first and second-degree relationships such as three-quarter siblings (3/4S) who share fewer alleles than first-degree relationships but more alleles than second-degree relationships. With the progressively increasing sample sizes used in genetic research, it becomes more likely that such relationships are present in the database under study. In this paper, we extend existing likelihood ratio (LR) methodology to accurately infer the existence of 3/4S, distinguishing them from full siblings and second-degree relatives. We use bootstrap confidence intervals to express uncertainty in the LRs. Our proposal accounts for linkage disequilibrium (LD) by using marker pruning, and we validate our methodology with a pedigree-based simulation study accounting for both LD and recombination. An empirical genome-wide array data set from the GCAT Genomes for Life cohort project is used to illustrate the method.

Mining Social Media Data to Study the Consequences of Dementia Diagnosis on Caregivers and Relatives (Preprint)

2018 ◽  
Author(s):  
Anika Oellrich ◽  
George Gkotsis ◽  
Richard James Butler Dobson ◽  
Tim JP Hubbard ◽  
Rina Dutta
Keyword(s):  
Social Media ◽  
Family Relationships ◽  
Text Processing ◽  
Automated Analysis ◽  
Health Concern ◽  
Dementia Diagnosis ◽  
Data Set ◽  
Social Media Data ◽  
Real Time Processing ◽  
Media Data

BACKGROUND Dementia is a growing public health concern with approximately 50 million people affected worldwide in 2017 and this number is expected to reach more than 131 million by 2050. The toll on caregivers and relatives cannot be underestimated as dementia changes family relationships, leaves people socially isolated, and affects the finances of all those involved. OBJECTIVE The aim of this study was to explore using automated analysis (i) the age and gender of people who post to the social media forum Reddit about dementia diagnoses, (ii) the affected person and their diagnosis, (iii) relevant subreddits authors are posting to, (iv) the types of messages posted and (v) the content of these posts. METHODS We analysed Reddit posts concerning dementia diagnoses. We used a previously developed text analysis pipeline to determine attributes of the posts as well as their authors to characterise online communications about dementia diagnoses. The posts were also examined by manual curation for the diagnosis provided and the person affected. Furthermore, we investigated the communities these people engage in and assessed the contents of the posts with an automated topic gathering technique. RESULTS Our results indicate that the majority of posters in our data set are women, and it is mostly close relatives such as parents and grandparents that are mentioned. Both the communities frequented and topics gathered reflect not only the sufferer's diagnosis but also potential outcomes, e.g. hardships experienced by the caregiver. The trends observed from this dataset are consistent with findings based on qualitative review, validating the robustness of social media automated text processing. CONCLUSIONS This work demonstrates the value of social media data sources as a resource for in-depth studies of those affected by a dementia diagnosis and the potential to develop novel support systems based on their real time processing in line with the increasing digitalisation of medical care.

Parent and Grandparent Relationships in Emerging Adulthood

2018 ◽  
Author(s):  
Michael W. Pratt ◽  
M. Kyle Matsuba
Keyword(s):  
Emerging Adulthood ◽  
Attachment Theory ◽  
Emerging Adults ◽  
Family Relationships ◽  
Longitudinal Research ◽  
Study Data ◽  
Family Development ◽  
Data Set ◽  
Theory Framework

Chapter 7 begins with an overview of Erikson’s ideas about intimacy and its place in the life cycle, followed by a summary of Bowlby and Ainsworth’s attachment theory framework and its relation to family development. The authors review existing longitudinal research on the development of family relationships in adolescence and emerging adulthood, focusing on evidence with regard to links to McAdams and Pals’ personality model. They discuss the evidence, both questionnaire and narrative, from the Futures Study data set on family relationships, including emerging adults’ relations with parents and, separately, with grandparents, as well as their anticipations of their own parenthood. As a way of illustrating the key personality concepts from this family chapter, the authors end with a case study of Jane Fonda in youth and her father, Henry Fonda, to illustrate these issues through the lives of a 20th-century Hollywood dynasty of actors.

scholarly journals Eyes of Africa: The Genetics of Blindness: Study Design and Methodology

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Olusola Olawoye ◽  
Chimdi Chuka-Okosa ◽  
Onoja Akpa ◽  
Tony Realini ◽  
Michael Hauser ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Case Control Study ◽  
African Ancestry ◽  
Collaborative Study ◽  
Data Set ◽  
Human Heredity ◽  
Genome Wide ◽  
A Genome ◽  
Multiplex Families ◽  
Control Study

Abstract Background This report describes the design and methodology of the “Eyes of Africa: The Genetics of Blindness,” a collaborative study funded through the Human Heredity and Health in Africa (H3Africa) program of the National Institute of Health. Methods This is a case control study that is collecting a large well phenotyped data set among glaucoma patients and controls for a genome wide association study. (GWAS). Multiplex families segregating Mendelian forms of early-onset glaucoma will also be collected for exome sequencing. Discussion A total of 4500 cases/controls have been recruited into the study at the end of the 3rd funded year of the study. All these participants have been appropriately phenotyped and blood samples have been received from these participants. Recent GWAS of POAG in African individuals demonstrated genome-wide significant association with the APBB2 locus which is an association that is unique to individuals of African ancestry. This study will add to the existing knowledge and understanding of POAG in the African population.

scholarly journals CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Philipp Rentzsch ◽  
Max Schubach ◽  
Jay Shendure ◽  
Martin Kircher
Keyword(s):  
Prediction Models ◽  
Splice Variants ◽  
Superior Performance ◽  
Data Set ◽  
Pathogenic Variants ◽  
Genome Wide ◽  
Donor And Acceptor ◽  
Human Proteins ◽  
Variant Effect ◽  
Variant Effect Prediction

Abstract Background Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond those occurring at donor and acceptor dinucleotides. To address this, various methods aim to predict variant effects on splicing. Recently, deep neural networks (DNNs) have been shown to achieve better results in predicting splice variants than other strategies. Methods It has been unclear how best to integrate such process-specific scores into genome-wide variant effect predictors. Here, we use a recently published experimental data set to compare several machine learning methods that score variant effects on splicing. We integrate the best of those approaches into general variant effect prediction models and observe the effect on classification of known pathogenic variants. Results We integrate two specialized splicing scores into CADD (Combined Annotation Dependent Depletion; cadd.gs.washington.edu), a widely used tool for genome-wide variant effect prediction that we previously developed to weight and integrate diverse collections of genomic annotations. With this new model, CADD-Splice, we show that inclusion of splicing DNN effect scores substantially improves predictions across multiple variant categories, without compromising overall performance. Conclusions While splice effect scores show superior performance on splice variants, specialized predictors cannot compete with other variant scores in general variant interpretation, as the latter account for nonsense and missense effects that do not alter splicing. Although only shown here for splice scores, we believe that the applied approach will generalize to other specific molecular processes, providing a path for the further improvement of genome-wide variant effect prediction.

scholarly journals Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias

2021 ◽  
Author(s):  
Anne-Marie Galow ◽  
Sophie Kussauer ◽  
Markus Wolfien ◽  
Ronald M. Brunner ◽  
Tom Goldammer ◽  
...  
Keyword(s):  
Quality Control ◽  
Cardiac Tissue ◽  
High Energy ◽  
Tissue Type ◽  
Pacemaker Cells ◽  
Data Set ◽  
Public Data ◽  
Standard Quality ◽  
Mitochondrial Transcripts

AbstractSingle-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to “low quality” potentially leading to data misinterpretation. Common standard quality control parameters involve the number of detected genes, transcripts per cell, and the fraction of transcripts from mitochondrial genes. While cutoffs for transcripts and genes per cell are usually user-defined for each experiment or individually calculated, a fixed threshold of 5% mitochondrial transcripts is standard and often set as default in scRNA-seq software. However, this parameter is highly dependent on the tissue type. In the heart, mitochondrial transcripts comprise almost 30% of total mRNA due to high energy demands. Here, we demonstrate that a 5%-threshold not only causes an unacceptable exclusion of cardiomyocytes but also introduces a bias that particularly discriminates pacemaker cells. This effect is apparent for our in vitro generated induced-sinoatrial-bodies (iSABs; highly enriched physiologically functional pacemaker cells), and also evident in a public data set of cells isolated from embryonal murine sinoatrial node tissue (Goodyer William et al. in Circ Res 125:379–397, 2019). Taken together, we recommend omitting this filtering parameter for scRNA-seq in cardiovascular applications whenever possible.

scholarly journals Influence of the Generator in-Growth Time on the Final Radiochemical Purity and Stability of Radiopharmaceuticals

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
L. Uccelli ◽  
A. Boschi ◽  
M. Pasquali ◽  
A. Duatti ◽  
G. Di Domenico ◽  
...  
Keyword(s):  
Nuclear Physics ◽  
Radiochemical Purity ◽  
Specific Activity ◽  
Growth Time ◽  
Direct Production ◽  
Theoretical Investigations ◽  
Standard Quality ◽  
Control Procedures ◽  
Italian National Institute ◽  
Preliminary Irradiation

At Legnaro laboratories of the Italian National Institute for Nuclear Physics (INFN), a feasibility study has started since 2011 related to accelerated-based direct production of by the100Mo(p,2n) reaction. Both theoretical investigations and some recent preliminary irradiation tests on100Mo-enriched samples have pointed out that both the / ratio and the specific activity will be basically different in the final accelerator-produced Tc with respect to generator-produced one, which might affect the radiopharmaceutical procedures. The aim of this work was to evaluate the possible impact of different / isomeric ratios on the preparation of different Tc-labeled pharmaceutical kits. A set of measurements with , eluted from a standard99Mo/ generator, was performed, and results on both radiochemical purity and stability studies (following the standard quality control procedures) are reported for a set of widely used pharmaceuticals (i.e., -Sestamibi, -ECD, -MAG3, -DTPA, -MDP, -HMDP, -nanocolloids, and -DMSA). These pharmaceuticals have been all reconstituted with either the first [O4]−eluate obtained from a99Mo/ generator (coming from two different companies) or eluates after 24, 36, 48, and 72 hours from last elution. Results show that the radiochemical purity and stability of these radiopharmaceuticals were not affected up to the value of 11.84 for the / ratio.

scholarly journals Open access resources for genome-wide association mapping in rice

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Susan R. McCouch ◽  
Mark H. Wright ◽  
Chih-Wei Tung ◽  
Lyza G. Maron ◽  
Kenneth L. McNally ◽  
...  
Keyword(s):  
Open Access ◽  
Association Mapping ◽  
High Density ◽  
Genome Wide Association ◽  
Minor Effect ◽  
Data Set ◽  
Genome Wide ◽  
Analytical Strategies ◽  
Biological Interpretation ◽  
Rice Improvement

Abstract Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

scholarly journals A genome-wide scan for a simulated data set using two newly developed methods

1999 ◽  
Vol 17 (S1) ◽  
pp. S621-S626
Author(s):  
Li Hsu ◽  
Corinne Aragaki ◽  
Filemon Quiaoit ◽  
Xiangjing Wang ◽  
Xiubin Xu ◽  
...  
Keyword(s):  
Simulated Data ◽  
Data Set ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Scan
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