Kyoko Watanabe

PhD student
Team Member

Short CV

01/2016 - Current | PhD student at VU University Amsterdam, Complex Trait Genetics
01/2015 - 12/2015 | MSc in Bioinformatics at University of Leicester (UK)
04/2012 - 03/2014 | BSc in Chemistry at Nara Women’s University (Japan)
04/2007 - 03/2012 | Associated degree in Engineering at Nagaoka National College of Technology (Japan)


Development of a new bioinformatics pipeline of post-GWAS analysis for complex traits
Since genome-wide association studies (GWAS) was introduced more than decade ago, a variety of complex traits has been investigated to identify significantly associated loci which hopefully answer the questions of genotype-phenotype associations. However, the multiple hypothesis problems and complexity of the biological network has failed to explain the whole story on how genotype variants cause a specific phenotype. Single nucleotide polymorphisms (SNPs) found from GWAS often have only small effects to phenotype and missing heritability has been the main issue which brings difficulties to occupy a gap between genotype and phenotype. To explore the findings of GWAS, instead of analysing single data type, multiple level of biological data such as functionality of SNPs (non-synonymous, synonymous and non-coding), deleteriousness, copy number variants, gene expression and protein-protein interaction, have to be integrated. Although, a number of tools and statistical methods for biological data integration have been developed, none of them can solely describe the biological mechanisms of complex traits. Therefore, my PhD project is aimed to develop a new pipeline integrating existing databases and scoring methods of the functionality of variants to identify the causative genes and pathways in which those genes are acting. Eventually, we aim to discover more detail mechanisms of psychiatric disorders by applying the new pipeline and contribute to design experiments with iPS cells.

Contact info


Vrije Universiteit Amsterdam
Center for Neurogenomics and Cognitive Research (CNCR)
Department of Complex Trait Genetics
W&N building, Room B-628
De Boelelaan 1085
1081 HV Amsterdam
The Netherlands


+ 31 (0) 20 598 32 66