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Book ; Online: Innamincka Talk: A grammar of the Innamincka dialect of Yandruwandha with notes on other dialects

Breen, Gavan

2015

Abstract: Innamincka Talk: A grammar of the Innamincka dialect of Yandruwandha with notes on other dialects is one of a pair of companion volumes on Yandruwandha, a dialect of the language formerly spoken on the Cooper and Strzelecki Creeks and the country to the ... ...

Abstract	Innamincka Talk: A grammar of the Innamincka dialect of Yandruwandha with notes on other dialects is one of a pair of companion volumes on Yandruwandha, a dialect of the language formerly spoken on the Cooper and Strzelecki Creeks and the country to the north of the Cooper, in the northeast corner of South Australia and a neighbouring strip of Queensland. The other volume is entitledInnamincka Words. Innamincka Talk is the more technical work of the two and is intended for specialists and for interested readers who are willing to put some time and effort into studying the language.Innamincka Words is for readers, especially descendants of the original people of the area, who are interested in the language, but not necessarily interested in its more technical aspects. It is also a necessary resource for users of Innamincka Talk. These volumes document all that could be learnt from the last speakers of the language in the last years of their lives by a linguist who was involved with other languages at the same time. These were people who did not have a full knowledge of the culture of their forebears, but were highly competent, indeed brilliant, in the way they could teach what they knew to the linguist student
Keywords	Mathematics
Size	1 electronic resource ( p.)
Publisher	ANU Press
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT020091509
ISBN	9781921934193 ; 1921934190
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Book ; Online: Innamincka Words: Yandruwandha dictionary and stories

Breen, Gavan

2015

Abstract: Innamincka Words: Yandruwandha dictionary and stories is one of a pair of companion volumes on Yandruwandha, a dialect of the language formerly spoken on the Cooper and Strzelecki Creeks and the country to the north of the Cooper, in the northeast corner ...

Abstract	Innamincka Words: Yandruwandha dictionary and stories is one of a pair of companion volumes on Yandruwandha, a dialect of the language formerly spoken on the Cooper and Strzelecki Creeks and the country to the north of the Cooper, in the northeast corner of South Australia and a neighbouring strip of Queensland. The other volume is entitled Innamincka Talk: a grammar of the Innamincka dialect of Yandruwandha with notes on other dialects. Innamincka Words is for readers, especially descendants of the original people of the area, who are interested in the language. It is also a necessary resource for users of the more technical Innamincka Talk. These volumes document all that could be learnt from the last speakers of the language in the last years of their lives by a linguist who was involved with other languages at the same time. These were people who did not have a full knowledge of the culture of their forebears, but were highly competent, indeed brilliant, in the way they could teach what they knew to the linguist student
Keywords	Mathematics
Size	1 electronic resource ( p.)
Publisher	ANU Press
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT020091513
ISBN	9781921934216 ; 1921934212
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Drug enrichment and discovery from schizophrenia genome-wide association results: an analysis and visualisation approach.

Gaspar, H A / Breen, G

Scientific reports

2017 Volume 7, Issue 1, Page(s) 12460

Abstract: Using successful genome-wide association results in psychiatry for drug repurposing is an ongoing challenge. Databases collecting drug targets and gene annotations are growing and can be harnessed to shed a new light on psychiatric disorders. We used ... ...

Abstract	Using successful genome-wide association results in psychiatry for drug repurposing is an ongoing challenge. Databases collecting drug targets and gene annotations are growing and can be harnessed to shed a new light on psychiatric disorders. We used genome-wide association study (GWAS) summary statistics from the Psychiatric Genetics Consortium (PGC) Schizophrenia working group to build a drug repositioning model for schizophrenia. As sample size increases, schizophrenia GWAS results show increasing enrichment for known antipsychotic drugs, selective calcium channel blockers, and antiepileptics. Each of these therapeutical classes targets different gene subnetworks. We identify 123 Bonferroni-significant druggable genes outside the MHC, and 128 FDR-significant biological pathways related to neurons, synapses, genic intolerance, membrane transport, epilepsy, and mental disorders. These results suggest that, in schizophrenia, current well-powered GWAS results can reliably detect known schizophrenia drugs and thus may hold considerable potential for the identification of new therapeutic leads. Moreover, antiepileptics and calcium channel blockers may provide repurposing opportunities. This study also reveals significant pathways in schizophrenia that were not identified previously, and provides a workflow for pathway analysis and drug repurposing using GWAS results.
MeSH term(s)	Anticonvulsants/therapeutic use ; Antipsychotic Agents/therapeutic use ; Biological Transport/drug effects ; Biological Transport/genetics ; Calcium Channel Blockers/therapeutic use ; Drug Repositioning ; Gene Regulatory Networks/drug effects ; Genome-Wide Association Study ; Humans ; Metabolic Networks and Pathways/drug effects ; Metabolic Networks and Pathways/genetics ; Molecular Targeted Therapy ; Nerve Tissue Proteins/agonists ; Nerve Tissue Proteins/antagonists & inhibitors ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Neurons/drug effects ; Neurons/metabolism ; Neurons/pathology ; Pharmacogenetics/methods ; Protein Interaction Mapping ; Sample Size ; Schizophrenia/drug therapy ; Schizophrenia/genetics ; Schizophrenia/metabolism ; Schizophrenia/physiopathology ; Synapses/drug effects ; Synapses/metabolism ; Synapses/pathology
Chemical Substances	Anticonvulsants ; Antipsychotic Agents ; Calcium Channel Blockers ; Nerve Tissue Proteins
Language	English
Publishing date	2017-09-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-12325-3
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Article ; Online: Introducing the Fear Learning and Anxiety Response (FLARe) app and web portal for the remote delivery of fear conditioning experiments.

McGregor, T / Purves, K L / Barry, T / Constantinou, E / Craske, M G / Breen, G / Young, K S / Eley, T C

Behavior research methods

2022 Volume 55, Issue 6, Page(s) 3164–3178

Abstract: Experimental paradigms measuring key psychological constructs can enhance our understanding of mechanisms underlying human psychological well-being and mental health. Delivering such paradigms remotely affords opportunities to reach larger, more ... ...

Abstract	Experimental paradigms measuring key psychological constructs can enhance our understanding of mechanisms underlying human psychological well-being and mental health. Delivering such paradigms remotely affords opportunities to reach larger, more representative samples than is typically possible with in-person research. The efficiency gained from remote delivery makes it easier to test replication of previously established effects in well-powered samples. There are several challenges to the successful development and delivery of remote experimental paradigms, including use of an appropriate delivery platform, identifying feasible outcome measures, and metrics of participant compliance. In this paper, we present FLARe (Fear Learning and Anxiety Response), open-source software in the form of a smartphone app and web portal for the creation and delivery of remote fear conditioning experiments. We describe the benefits and challenges associated with the creation of a remote delivery platform for fear conditioning, before presenting in detail the resultant software suite, and one instance of deploying this using the FLARe Research infrastructure. We provide examples of the application of FLARe to several research questions which illustrate the benefits of the remote approach to experiment delivery. The FLARe smartphone app and web portal are available for use by other researchers and have been designed to be user-friendly and intuitive. We hope that FLARe will be a useful tool for those interested in conducting well-powered fear conditioning studies to inform our understanding of the development and treatment of anxiety disorders.
MeSH term(s)	Humans ; Mobile Applications ; Anxiety/psychology ; Fear/psychology ; Learning ; Anxiety Disorders/psychology ; Anxiety Disorders/therapy ; Extinction, Psychological/physiology
Language	English
Publishing date	2022-09-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	231560-9
ISSN	1554-3528 ; 0743-3808 ; 1554-351X
ISSN (online)	1554-3528
ISSN	0743-3808 ; 1554-351X
DOI	10.3758/s13428-022-01952-y
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Article ; Online: Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics.

Gaspar, Héléna A / Breen, Gerome

BMC bioinformatics

2019 Volume 20, Issue 1, Page(s) 116

Abstract: Background: Principal component analysis (PCA) is a standard method to correct for population stratification in ancestry-specific genome-wide association studies (GWASs) and is used to cluster individuals by ancestry. Using the 1000 genomes project data, ...

Abstract	Background: Principal component analysis (PCA) is a standard method to correct for population stratification in ancestry-specific genome-wide association studies (GWASs) and is used to cluster individuals by ancestry. Using the 1000 genomes project data, we examine how non-linear dimensionality reduction methods such as t-distributed stochastic neighbor embedding (t-SNE) or generative topographic mapping (GTM) can be used to provide improved ancestry maps by accounting for a higher percentage of explained variance in ancestry, and how they can help to estimate the number of principal components necessary to account for population stratification. GTM generates posterior probabilities of class membership which can be used to assess the probability of an individual to belong to a given population - as opposed to t-SNE, GTM can be used for both clustering and classification. Results: PCA only partially identifies population clusters and does not separate most populations within a given continent, such as Japanese and Han Chinese in East Asia, or Mende and Yoruba in Africa. t-SNE and GTM, taking into account more data variance, can identify more fine-grained population clusters. GTM can be used to build probabilistic classification models, and is as efficient as support vector machine (SVM) for classifying 1000 Genomes Project populations. Conclusion: The main interest of probabilistic GTM maps is to attain two objectives with only one map: provide a better visualization that separates populations efficiently, and infer genetic ancestry for individuals or populations. This paper is a first application of GTM for ancestry classification models. Our code ( https://github.com/hagax8/ancestry_viz ) and interactive visualizations ( https://lovingscience.com/ancestries ) are available online.
MeSH term(s)	African Continental Ancestry Group/genetics ; Arabidopsis/genetics ; Asian Continental Ancestry Group/genetics ; Cluster Analysis ; Genetics, Population ; Genome-Wide Association Study ; Humans ; Models, Statistical ; Principal Component Analysis ; Stochastic Processes
Language	English
Publishing date	2019-03-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-019-2680-1
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Article ; Online: From awareness to action: an urgent call to reduce mortality and improve outcomes in eating disorders.

Ayton, Agnes / Ibrahim, Ali / Downs, James / Baker, Suzanne / Kumar, Ashish / Virgo, Hope / Breen, Gerome

The British journal of psychiatry : the journal of mental science

2023 Volume 224, Issue 1, Page(s) 3–5

Abstract: High mortality rates and poor outcomes from eating disorders, especially anorexia nervosa, are largely preventable and require urgent action. A national strategy to address this should include prevention; early detection; timely access to integrated ... ...

Abstract	High mortality rates and poor outcomes from eating disorders, especially anorexia nervosa, are largely preventable and require urgent action. A national strategy to address this should include prevention; early detection; timely access to integrated physical and psychological treatments; safe management of emergencies; suicide prevention; and investment in training, services and research.
MeSH term(s)	Humans ; Feeding and Eating Disorders/therapy ; Anorexia Nervosa/psychology ; Suicide Prevention ; Bulimia Nervosa/psychology
Language	English
Publishing date	2023-07-31
Publishing country	England
Document type	Journal Article
ZDB-ID	218103-4
ISSN	1472-1465 ; 0007-1250
ISSN (online)	1472-1465
ISSN	0007-1250
DOI	10.1192/bjp.2023.133
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Article ; Online: A formant study of the alveolar versus retroflex contrast in three Central Australian languages: Stop, nasal, and lateral manners of articulation.

Tabain, Marija / Butcher, Andrew / Breen, Gavan / Beare, Richard

The Journal of the Acoustical Society of America

2020 Volume 147, Issue 4, Page(s) 2745

Abstract: This study presents formant transition data from 21 speakers for the apical alveolar∼retroflex contrast in three neighbouring Central Australian languages: Arrernte, Pitjantjatjara, and Warlpiri. The contrast is examined for three manners of articulation: ...

Abstract	This study presents formant transition data from 21 speakers for the apical alveolar∼retroflex contrast in three neighbouring Central Australian languages: Arrernte, Pitjantjatjara, and Warlpiri. The contrast is examined for three manners of articulation: stop, nasal, and lateral /t ∼ ʈ/ /n ∼ ɳ/, and /l ∼ ɭ/, and three vowel contexts /a i u/. As expected, results show that a lower F3 and F4 in the preceding vowel signal a retroflex consonant; and that the alveolar∼retroflex contrast is most clearly realized in the context of an /a/ vowel, and least clearly realized in the context of an /i/ vowel. Results also show that the contrast is most clearly realized for the stop manner of articulation. These results provide an acoustic basis for the greater typological rarity of retroflex nasals and laterals as compared to stops. It is suggested that possible nasalization of the preceding vowel accounts for the poorer nasal consonant results, and that articulatory constraints on lateral consonant production account for the poorer lateral consonant results. Importantly, differences are noticed between speakers, and it is suggested that literacy plays a major role in maintenance of this marginal phonemic contrast.
MeSH term(s)	Acoustics ; Australia ; Language ; Phonetics ; Speech Acoustics
Language	English
Publishing date	2020-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0001012
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Article ; Online: Association Between Genetic Risk for Psychiatric Disorders and the Probability of Living in Urban Settings.

Maxwell, Jessye M / Coleman, Jonathan R I / Breen, Gerome / Vassos, Evangelos

JAMA psychiatry

2021 Volume 78, Issue 12, Page(s) 1355–1364

Abstract: Importance: Urban residence has been highlighted as an environmental risk factor for schizophrenia and, to a lesser extent, several other psychiatric disorders. However, few studies have explored genetic effects on the choice of residence.: Objective!# ...

Abstract	Importance: Urban residence has been highlighted as an environmental risk factor for schizophrenia and, to a lesser extent, several other psychiatric disorders. However, few studies have explored genetic effects on the choice of residence. Objective: To investigate whether individuals with genetic predisposition to a range of psychiatric disorders have an increased likelihood to live in urban areas. Design, setting, and participants: A cross-sectional retrospective cohort study including genotypes, address history, and geographic distribution of population density in the UK based on census data from 1931-2011 was conducted. Polygenic risk score (PRS) analyses, genome-wide association studies, genetic correlation, and 2-sample mendelian randomization analyses were applied to 385 793 UK Biobank participants with self-reported or general practitioner registration-based address history. The study was conducted from February 2018 to May 2021, and data analysis was performed from April 2018 to May 2021. Main outcomes and measures: Population density of residence at different ages and movement during the life span between urban and rural environments. Results: In this cohort study of 385 793 unrelated UK Biobank participants (207 963 [54%] were women; age, 37-73 years; mean [SD], 56.7 [8] years), PRS analyses showed significant associations with higher population density across adult life (age 25 to >65 years) reaching highest significance at the 45- to 55-year age group for schizophrenia (88 people/km2; 95% CI, 65-98 people/km2), bipolar disorder (44 people/km2; 95% CI, 34-54 people/km2), anorexia nervosa (36 people/km2; 95% CI, 22-50 people/km2), and autism spectrum disorder (35 people/km2; 95% CI, 25-45 people/km2). The schizophrenia PRS was also significantly associated with higher birthplace population density (37 people/km2; 95% CI, 19-55 people/km2; P = 8 × 10-5). Attention-deficit/hyperactivity disorder PRS was significantly associated with reduced population density in adult life (-31 people/km2; 95% CI, -42 to -20 people/km2 at age 35-45 years). Individuals with higher PRS for schizophrenia, bipolar disorder, anorexia nervosa, and autism spectrum disorder and lower PRS for attention-deficit/hyperactivity disorder preferentially moved from rural environments to cities (difference in PRS with Tukey pairwise comparisons for schizophrenia: 0.05; 95% CI, 0.03 to 0.60; bipolar disorder: 0.10; 95% CI, 0.08 to 0.13; anorexia nervosa: 0.05; 95% CI, 0.03 to 0.07; autism spectrum disorder: 0.04; 95% CI 0.03 to 0.06; and attention-deficit/hyperactivity disorder: -0.09, 95% CI, -0.12 to -0.06). Genetic correlation results were largely consistent with PRS analyses, whereas mendelian randomization provided support for associations between schizophrenia and bipolar disorder and living in high population-density areas. Conclusions and relevance: These findings suggest that a high genetic risk for a variety of psychiatric disorders may affect an individual's choice of residence. This result supports the hypothesis of genetic selection of an individual's environment, which intersects the traditional gene-environment dichotomy.
MeSH term(s)	Adult ; Aged ; Cross-Sectional Studies ; Databases, Genetic ; Female ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Humans ; Male ; Mendelian Randomization Analysis ; Mental Disorders/epidemiology ; Mental Disorders/genetics ; Middle Aged ; Multifactorial Inheritance ; Neighborhood Characteristics/statistics & numerical data ; Retrospective Studies ; Risk ; United Kingdom/epidemiology ; Urban Population/statistics & numerical data
Language	English
Publishing date	2021-10-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701203-7
ISSN	2168-6238 ; 2168-622X
ISSN (online)	2168-6238
ISSN	2168-622X
DOI	10.1001/jamapsychiatry.2021.2983
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Article ; Online: Genetic and Geographical Associations With Six Dimensions of Psychotic Experiences in Adolesence.

Maxwell, Jessye / Ronald, Angelica / Cardno, Alastair G / Breen, Gerome / Rimfeld, Kaili / Vassos, Evangelos

Schizophrenia bulletin

2022 Volume 49, Issue 2, Page(s) 319–328

Abstract: Background and hypothesis: Large-scale epidemiological and genetic research have shown that psychotic experiences in the community are risk factors for adverse physical and psychiatric outcomes. We investigated the associations of six types of specific ... ...

Abstract	Background and hypothesis: Large-scale epidemiological and genetic research have shown that psychotic experiences in the community are risk factors for adverse physical and psychiatric outcomes. We investigated the associations of six types of specific psychotic experiences and negative symptoms assessed in mid-adolescence with well-established environmental and genetic risk factors for psychosis. Study design: Fourteen polygenic risk scores (PRS) and nine geographical environmental variables from 3590 participants of the Twins Early Development Study (mean age 16) were associated with paranoia, hallucinations, cognitive disorganization, grandiosity, anhedonia, and negative symptoms scales. The predictors were modeled using LASSO regularization separately (Genetic and Environmental models) and jointly (GE model). Study results: In joint GE models, we found significant genetic associations of negative symptoms with educational attainment PRS (β = -.07; 95% CI = -0.12 to -0.04); cognitive disorganization with neuroticism PRS (β = .05; 95% CI = 0.03-0.08); paranoia with MDD (β = .07; 95% CI = 0.04-0.1), BMI (β = .05; 95% CI = 0.02-0.08), and neuroticism PRS (β = .05; 95% CI = 0.02-0.08). From the environmental measures only family SES (β = -.07, 95% CI = -0.10 to -0.03) and regional education levels (β = -.06; 95% CI = -0.09 to -0.02) were associated with negative symptoms. Conclusions: Our findings advance understanding of how genetic propensity for psychiatric, cognitive, and anthropometric traits, as well as environmental factors, together play a role in creating vulnerability for specific psychotic experiences and negative symptoms in mid-adolescence.
MeSH term(s)	Adolescent ; Humans ; Genetic Predisposition to Disease ; Psychotic Disorders/epidemiology ; Psychotic Disorders/genetics ; Hallucinations/etiology ; Paranoid Disorders/psychology ; Delusions
Language	English
Publishing date	2022-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	439173-1
ISSN	1745-1701 ; 0586-7614
ISSN (online)	1745-1701
ISSN	0586-7614
DOI	10.1093/schbul/sbac149
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Article ; Online: The COPILOT Raw Illumina Genotyping QC Protocol.

Patel, Hamel / Lee, Sang-Hyuck / Breen, Gerome / Menzel, Stephen / Ojewunmi, Oyesola / Dobson, Richard J B

Current protocols

2022 Volume 2, Issue 4, Page(s) e373

Abstract: The Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses that rely on various software, different programming languages, ... ...

Abstract	The Illumina genotyping microarrays generate data in image format, which is processed by the platform-specific software GenomeStudio, followed by an array of complex bioinformatics analyses that rely on various software, different programming languages, and numerous dependencies to be installed and configured correctly. The entire process can be time-consuming, can lead to reproducibility errors, and can be a daunting task for bioinformaticians. To address this, we introduce the COPILOT protocol, which has been successfully used to transform raw Illumina genotype intensity data into high-quality analysis-ready data on tens of thousands of human patient samples that have been genotyped on a variety of Illumina genotyping arrays. This includes processing both mainstream and custom content genotyping chips with over 4 million markers per sample. The COPILOT QC protocol consists of two distinct tandem procedures to process raw Illumina genotyping data. The first protocol is an up-to-date process to systematically QC raw Illumina microarray genotyping data using the Illumina-specific GenomeStudio software. The second protocol takes the output from the first protocol and further processes the data through the COPILOT (Containerised wOrkflow for Processing ILlumina genOtyping daTa) containerized QC pipeline, to automate an array of complex bioinformatics analyses to improve data quality through a secondary clustering algorithm and to automatically identify typical Genome-Wide Association Study (GWAS) data issues, including gender discrepancies, heterozygosity outliers, related individuals, and population outliers, through ancestry estimation. The data is returned to the user in analysis-ready PLINK binary format and is accompanied by a comprehensive and interactive HTML summary report file which quickly helps the user understand the data and guides the user for further data analyses. The COPILOT protocol and containerized pipeline are also available at https://khp-informatics.github.io/COPILOT/index.html. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing raw Illumina genotyping data using GenomeStudio Basic Protocol 2: COPILOT: A containerised workflow for processing Illumina genotyping data.
MeSH term(s)	Genome-Wide Association Study ; Genotype ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Polymorphism, Single Nucleotide ; Reproducibility of Results
Language	English
Publishing date	2022-04-22
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.373
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