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Securing the use of existing sample collections for future human genetic research.

ABSTRACT: Hundreds of thousands of individuals have been genotyped in the past decades using genotyping arrays, representing both a valuable data resource for future biomedical research and a substantial investment in human genetic research. However, novel chip designs and their altered sets of single-nucleotide polymorphisms (SNPs) pose the question of how well established data resources, such as large samples of healthy controls genotyped on legacy arrays, can be combined with newer samples genotyped on those novel arrays using genotype imputation. We exemplarily investigated this question based on genotype data of 30 European and 30 African unrelated samples from the 1000 Genomes project and on markers present on two legacy SNP arrays, namely Affymetrix's Human SNP 6.0 and Illumina's 550k array, and three newer arrays, namely two Axiom arrays from Affymetrix and an OmniExpress array from Illumina. We cross-compared the imputation accuracy as well as efficacy and assessed genotype concordance among these arrays. Although the accuracy of genotype prediction was uniformly high across all arrays, the imputation efficacy, that is, the proportion of successfully imputed markers, differed considerably between array combinations in both sample sets, with legacy arrays showing a trend towards lower efficacy values compared with newer arrays when serving as imputation basis. We conclude that, given the substantial losses of markers covered by the legacy arrays, the re-genotyping of existing samples sets, in particular those of healthy population controls, would be a worthwhile endeavor to secure their continued use in the future.

SUBMITTER: Kanoungi G

PROVIDER: S-EPMC5437900 | biostudies-other | 2017 May

REPOSITORIES: biostudies-other

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Securing the use of existing sample collections for future human genetic research.

Kanoungi George G Nürnberg Peter P Nothnagel Michael M

European journal of human genetics : EJHG 20170201 5

Hundreds of thousands of individuals have been genotyped in the past decades using genotyping arrays, representing both a valuable data resource for future biomedical research and a substantial investment in human genetic research. However, novel chip designs and their altered sets of single-nucleotide polymorphisms (SNPs) pose the question of how well established data resources, such as large samples of healthy controls genotyped on legacy arrays, can be combined with newer samples genotyped on ...[more]

PMID: 28145429

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Project description:BACKGROUND:Connected health (CH) technologies have resulted in a paradigm shift, moving health care steadily toward a more patient-centered delivery approach. CH requires a broad range of disciplinary expertise from across the spectrum to work in a cohesive and productive way. Building this interdisciplinary relationship at an earlier stage of career development may nurture and accelerate the CH developments and innovations required for future health care. OBJECTIVE:This study aimed to explore the perceptions of interdisciplinary CH researchers regarding the design and delivery of an interdisciplinary education (IDE) module for disciplines currently engaged in CH research (engineers, computer scientists, health care practitioners, and policy makers). This study also investigated whether this module should be delivered as a taught component of an undergraduate, master's, or doctoral program to facilitate the development of interdisciplinary learning. METHODS:A qualitative, cross-institutional, multistage research approach was adopted, which involved a background study of fundamental concepts, individual interviews with CH researchers in Greece (n=9), and two structured group feedback sessions with CH researchers in Ireland (n=10/16). Thematic analysis was used to identify the themes emerging from the interviews and structured group feedback sessions. RESULTS:A total of two sets of findings emerged from the data. In the first instance, challenges to interdisciplinary work were identified, including communication challenges, divergent awareness of state-of-the-art CH technologies across disciplines, and cultural resistance to interdisciplinarity. The second set of findings were related to the design for interdisciplinarity. In this regard, the need to link research and education with real-world practice emerged as a key design concern. Positioning within the program context was also considered to be important with a need to balance early intervention to embed integration with later repeat interventions that maximize opportunities to share skills and experiences. CONCLUSIONS:The authors raise and address challenges to interdisciplinary program design for CH based on an abductive approach combining interdisciplinary and interprofessional education literature and the collection of qualitative data. This recipe approach for interdisciplinary design offers guidelines for policy makers, educators, and innovators in the CH space. Gaining insight from CH researchers regarding the development of an IDE module has offered the designers a novel insight regarding the curriculum, timing, delivery, and potential challenges that may be encountered.

Dataset Information

Securing the use of existing sample collections for future human genetic research.

Publications

Securing the use of existing sample collections for future human genetic research.

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