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Recommendations from the international stroke genetics consortium, part 1: standardized phenotypic data collection.

ABSTRACT:

SUBMITTER: Majersik JJ

PROVIDER: S-EPMC4465378 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Recommendations from the international stroke genetics consortium, part 1: standardized phenotypic data collection.

Majersik Jennifer J JJ Cole John W JW Golledge Jonathan J Rost Natalia S NS Chan Yu-Feng Yvonne YF Gurol M Edip ME Lindgren Arne G AG Woo Daniel D Fernandez-Cadenas Israel I Chen Donna T DT Thijs Vincent V Worrall Bradford B BB Kamal Ayeesha A Bentley Paul P Wardlaw Joanna M JM Ruigrok Ynte M YM Battey Thomas W K TW Schmidt Reinhold R Montaner Joan J Giese Anne-Katrin AK Roquer Jaume J Jiménez-Conde Jordi J Lee Chaeyoung C Ay Hakan H Martin Juan Jose JJ Rosand Jonathan J Maguire Jane J

Stroke 20141209 1

PMID: 25492903

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Project description:ObjectiveTo develop a research priority list for the International Stroke Genetics Consortium (ISGC).BackgroundPreviously, stroke progress review groups and other activities provided an opportunity for members within the field to develop priorities for research. These filtered into larger categories which then published the top research priorities of their given field. However, these review groups are no longer forming and thus there has been no clear direction on what the research priorities and needs for stroke genetics research.Design/methodsWe polled members of the stroke genetics community from around the world including collaborations of the major stroke genetics research efforts currently under way asking each respondent to provide their top 3 research priorities. Each priority was then sorted by the authors into major categories based upon the type of suggestion made. The results were presented for commentary and feedback during the presentation.ResultsDeeper Phenotyping related topics were presented in 84% of respondent top research priorities. These included topics related to ethnic/racial variation, third world countries, deeper evaluation of subtypes of stroke. Translational science related topics were present in 40% of respondent top research priorities and consisted of translating our current findings into a greater understanding of their relationship to stroke and clinical pathophysiology. Pooling of our resources through data banking and sample banking was a topic in 36% of respondents. Recovery/outcome related topics were suggested in 32% of respondents and utilizing novel techniques such as epigenetics, whole genome sequencing, proteomics and metabolomics were present in 28% of respondents. Other topics were not present in more than 25% of the responses for top research priorities.ConclusionsTo summarize, greater sample size and research within subtypes and endophenotypes of stroke was the top research priority of the ISGC. In addition, translating our existing findings, pooling our resources, recovery/outcomes research and utilization of novel techniques were among the top research priorities of the ISGC. A working group will be assembled to draft the ISGC Research Priorities paper.

Project description:BackgroundAlthough human leukocyte antigen (HLA) DQ and DR loci appear to confer the strongest genetic risk for type 1 diabetes, more detailed information is required for other loci within the HLA region to understand causality and stratify additional risk factors. The Type 1 Diabetes Genetics Consortium (T1DGC) study design included high-resolution genotyping of HLA-A, B, C, DRB1, DQ, and DP loci in all affected sibling pair and trio families, and cases and controls, recruited from four networks worldwide, for analysis with clinical phenotypes and immunological markers.PurposeIn this article, we present the operational strategy of training, classification, reporting, and quality control of HLA genotyping in four laboratories on three continents over nearly 5 years.MethodsMethods to standardize HLA genotyping at eight loci included: central training and initial certification testing; the use of uniform reagents, protocols, instrumentation, and software versions; an automated data transfer; and the use of standardized nomenclature and allele databases. We implemented a rigorous and consistent quality control process, reinforced by repeated workshops, yearly meetings, and telephone conferences.ResultsA total of 15,246 samples have been HLA genotyped at eight loci to four-digit resolution; an additional 6797 samples have been HLA genotyped at two loci. The genotyping repeat rate decreased significantly over time, with an estimated unresolved Mendelian inconsistency rate of 0.21%. Annual quality control exercises tested 2192 genotypes (4384 alleles) and achieved 99.82% intra-laboratory and 99.68% inter-laboratory concordances.LimitationsThe chosen genotyping platform was unable to distinguish many allele combinations, which would require further multiple stepwise testing to resolve. For these combinations, a standard allele assignment was agreed upon, allowing further analysis if required.ConclusionsHigh-resolution HLA genotyping can be performed in multiple laboratories using standard equipment, reagents, protocols, software, and communication to produce consistent and reproducible data with minimal systematic error. Many of the strategies used in this study are generally applicable to other large multi-center studies.

Dataset Information

Recommendations from the international stroke genetics consortium, part 1: standardized phenotypic data collection.

Publications

Recommendations from the international stroke genetics consortium, part 1: standardized phenotypic data collection.

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