Dataset Information

Meta-analysis of repository data: impact of data regularization on NIMH schizophrenia linkage results.

ABSTRACT: Human geneticists are increasingly turning to study designs based on very large sample sizes to overcome difficulties in studying complex disorders. This in turn almost always requires multi-site data collection and processing of data through centralized repositories. While such repositories offer many advantages, including the ability to return to previously collected data to apply new analytic techniques, they also have some limitations. To illustrate, we reviewed data from seven older schizophrenia studies available from the NIMH-funded Center for Collaborative Genomic Studies on Mental Disorders, also known as the Human Genetics Initiative (HGI), and assessed the impact of data cleaning and regularization on linkage analyses. Extensive data regularization protocols were developed and applied to both genotypic and phenotypic data. Genome-wide nonparametric linkage (NPL) statistics were computed for each study, over various stages of data processing. To assess the impact of data processing on aggregate results, Genome-Scan Meta-Analysis (GSMA) was performed. Examples of increased, reduced and shifted linkage peaks were found when comparing linkage results based on original HGI data to results using post-processed data within the same set of pedigrees. Interestingly, reducing the number of affected individuals tended to increase rather than decrease linkage peaks. But most importantly, while the effects of data regularization within individual data sets were small, GSMA applied to the data in aggregate yielded a substantially different picture after data regularization. These results have implications for analyses based on other types of data (e.g., case-control GWAS or sequencing data) as well as data obtained from other repositories.

SUBMITTER: Walters KA

PROVIDER: S-EPMC3891773 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Meta-analysis of repository data: impact of data regularization on NIMH schizophrenia linkage results.

Walters Kimberly A KA Huang Yungui Y Azaro Marco M Tobin Kathleen K Lehner Thomas T Brzustowicz Linda M LM Vieland Veronica J VJ

PloS one 20140114 1

Human geneticists are increasingly turning to study designs based on very large sample sizes to overcome difficulties in studying complex disorders. This in turn almost always requires multi-site data collection and processing of data through centralized repositories. While such repositories offer many advantages, including the ability to return to previously collected data to apply new analytic techniques, they also have some limitations. To illustrate, we reviewed data from seven older schizop ...[more]

PMID: 24454738

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Project description:BackgroundIndividuals with schizophrenia are at higher risk of physical illnesses, which are a major contributor to their 20-year reduced life expectancy. It is currently unknown what causes the increased risk of physical illness in schizophrenia.AimsTo link genetic data from a clinically ascertained sample of individuals with schizophrenia to anonymised National Health Service (NHS) records. To assess (a) rates of physical illness in those with schizophrenia, and (b) whether physical illness in schizophrenia is associated with genetic liability.MethodWe linked genetic data from a clinically ascertained sample of individuals with schizophrenia (Cardiff Cognition in Schizophrenia participants, n = 896) to anonymised NHS records held in the Secure Anonymised Information Linkage (SAIL) databank. Physical illnesses were defined from the General Practice Database and Patient Episode Database for Wales. Genetic liability for schizophrenia was indexed by (a) rare copy number variants (CNVs), and (b) polygenic risk scores.ResultsIndividuals with schizophrenia in SAIL had increased rates of epilepsy (standardised rate ratio (SRR) = 5.34), intellectual disability (SRR = 3.11), type 2 diabetes (SRR = 2.45), congenital disorders (SRR = 1.77), ischaemic heart disease (SRR = 1.57) and smoking (SRR = 1.44) in comparison with the general SAIL population. In those with schizophrenia, carrier status for schizophrenia-associated CNVs and neurodevelopmental disorder-associated CNVs was associated with height (P = 0.015-0.017), with carriers being 7.5-7.7 cm shorter than non-carriers. We did not find evidence that the increased rates of poor physical health outcomes in schizophrenia were associated with genetic liability for the disorder.ConclusionsThis study demonstrates the value of and potential for linking genetic data from clinically ascertained research studies to anonymised health records. The increased risk for physical illness in schizophrenia is not caused by genetic liability for the disorder.

Project description:BACKGROUND:Newborn screening (NBS) aims to achieve early identification and treatment of affected infants prior to onset of symptoms. The timely completion of each step (i.e., specimen collection, transport, testing, result reporting), is critical for early diagnosis. Goals developed by the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children (ACHDNC) for NBS timeliness were adopted (time-critical results reported by five days of life, and non-time-critical results reported by day seven), and implemented into a multi-year quality improvement initiative (NewSTEPS 360) aimed to decrease the time to result reporting and intervention. METHODS:The NBS system from specimen collection through reporting of results was assessed (bloodspot specimen collection, specimen shipping, sample testing, and result reporting). Annual data from 25 participating NBS programs were analyzed; the medians (and interquartile range, IQR) of state-specific percent of specimens that met the goal are presented. RESULTS:The percent of specimens collected before 48 hours of life increased from 95% (88-97%) in 2016 to 97% (IQR 92-98%) in 2018 for the 25 states, with 20 (80%) of programs collecting more than 90% of the specimens within 48 hours of birth. Approximately 41% (IQR 29-57%) of specimens were transported within one day of collection. Time-critical result reporting in the first five days of life improved from 49% (IQR 26-74%) in 2016 to 64% (42%-71%) in 2018, and for non-time critical results from 64% (IQR 58%-78%) in 2016 to 81% (IQR 68-91%) in 2018. Laboratories open seven days a week in 2018 reported 95% of time-critical results within five days, compared to those open six days (62%), and five days (45%). CONCLUSION:NBS programs that participated in NewSTEPs 360 made great strides in improving timeliness; however, ongoing quality improvement efforts are needed in order to ensure all infants receive a timely diagnosis.

Dataset Information

Meta-analysis of repository data: impact of data regularization on NIMH schizophrenia linkage results.

Publications

Meta-analysis of repository data: impact of data regularization on NIMH schizophrenia linkage results.

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