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Genotyping and Statistical Analysis

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Genome-Wide Association Studies

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Abstract

Development of technologies for high-throughput profiling of DNA variation has led to rapid discovery of causal genetic mutations underlying complex phenotypic traits and diseases. These exciting advances were originally enabled by the results from the Human Genome project (1990–2003) that allowed the completion of the first genome-wide association study in 2002 and led to the development of haplotype maps of the human genome. Technological advances in microarray genotyping and next-generation sequencing have since made possible the wide-spread and cost-effective application of this approach and, in combination, have powered the new age of biomedical discovery. This chapter introduces the history and fundamental principles of genetic association analysis, and explains key concepts and current statistical methods for processing these data. In particular, discussed topics include experimental design of association studies, quality control procedures, approaches for dealing with the population stratification, statistical testing for genetic associations and more recent developments in detection of effects of rare variants and genetic interactions.

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Notes

  1. 1.

    https://www.ahc.umn.edu/img/assets/19726/Multiplexing_hME_App_Note.pdf.

  2. 2.

    https://www.illumina.com/science/technology/beadarray-technology.html.

  3. 3.

    http://barleyworld.org/sites/barleyworld.org/files/illuminasnpgenotyping.pdf.

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Author information

Authors and Affiliations

  1. Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

    Artem Lysenko, Keith A. Boroevich & Tatsuhiko Tsunoda

  2. Tsunoda Laboratory (Medical Science Mathematics), Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Tatsuhiko Tsunoda

  3. Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan

    Tatsuhiko Tsunoda

Authors
  1. Artem Lysenko
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  2. Keith A. Boroevich
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  3. Tatsuhiko Tsunoda
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Corresponding author

Correspondence to Tatsuhiko Tsunoda .

Editor information

Editors and Affiliations

  1. Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Tatsuhiko Tsunoda

  2. BioResource Research Center, Tokyo Medical and Dental University, Tokyo, Japan

    Toshihiro Tanaka

  3. Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan

    Yusuke Nakamura

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© 2019 Springer Nature Singapore Pte Ltd.

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Lysenko, A., Boroevich, K.A., Tsunoda, T. (2019). Genotyping and Statistical Analysis. In: Tsunoda, T., Tanaka, T., Nakamura, Y. (eds) Genome-Wide Association Studies. Springer, Singapore. https://doi.org/10.1007/978-981-13-8177-5_1

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