Masahiro Kanai

PhD student in the Bioinformatics and Integrative Genomics (BIG) PhD Program, Harvard Medical School.

Education

Aug. 2017 - present
Bioinformatics and Integrative Genomics PhD Program, Division of Medical Sciences, Harvard Medical School
PhD student
Apr. 2013 - Mar. 2017
Department of Biosciences and Informatics, Keio University
B.S. in Bioinformatics
Apr. 2010 - Mar. 2013
Senior High School at Komaba, University of Tsukuba

Research Experience

Jan. 2018 - present
Analytic and Translational Genetics Unit, Massachusetts General Hospital & Broad Institute of MIT and Harvard
Graduate Student
Advisor: Drs. Mark Daly & Hilary Finucane
Apr. 2017 - present
Department of Statistical Genetics, Graduate School of Medicine, Osaka University
Research Student
Advisor: Dr. Yukinori Okada
May. 2015 - Jul. 2019
Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences
Research Assistant
Advisor: Drs. Yoichiro Kamatani & Yukinori Okada
Apr. 2016 - Mar. 2017
Laboratory for Bioinformatics (Sakakibara Lab.), Department of Biosciences and Informatics, Keio University
Undergraduate Researcher
Advisor: Dr. Yasubumi Sakakibara
Apr. 2014 - Mar. 2016
Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University
Technical Assistant
Advisor: Drs. Yukinori Okada & Toshihiro Tanaka

Research Interests

  • Statistical Genetics
  • Bioinformatics

Technical Skills

  • C/C++
  • C#
  • Python
  • R
  • Data Visualization
  • UNIX
  • Photoshop
  • Illustrator
  • After Effects

Awards and Fellowships

2020
Charles J. Epstein Trainee Awards for Excellence in Human Genetics Research, Finalist (Predoctoral), the American Society of Human Genetics 2020 Virtual Meeting Link
2019
Reviewers’ Choice Abstract Award, the American Society of Human Genetics 2019 Annual Meeting
2018-2021+
Masason Foundation Fellowship (Research Grant)
2017-2021+
Nakajima Foundation Fellowship (Predoctoral Fellowship)
2011
Microsoft Imagine Cup 2011 Windows 7 Touch Challenge, Worldwide Finals the 3rd place Video
2010
Microsoft Imagine Cup 2010 Software Design Competition National Finals, the 1st place & Worldwide Finalist Report1 Report2

Membership

2014 - present
The Japan Society of Human Genetics
2015 - present
The Japanese Society of Bioinformatics
2015 - present
Information Processing Society of Japan
2016 - present
The American Society of Human Genetics

Certification

2015
The Certification for Bioinformatics Engineers (certificated by the Japanese Society of Bioinformatics)

Software & Data

Details

Publications

Google ScholarORCIDPubMed

Selected Publications and Preprints

(* = co-first)

  1. *Sakaue, S., *Kanai, M., Karjalainen, J., Akiyama, M., Kurki, M., Matoba, N. et al. Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan. Nature Medicine 26, 542–548 (2020). PubMed PR
  2. Martin, A. R., Kanai, M., Kamatani, Y., Okada, Y., Neale, B. M. & Daly, M. J. Clinical use of current polygenic risk scores may exacerbate health disparities. Nature Genetics 51, 584–591 (2019). PubMed PR
  3. Kanai, M., Akiyama, M., Takahashi, A., Matoba, N., Momozawa, Y., Ikeda, M. et al. Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases. Nature Genetics 50, 390–400 (2018). PubMed PR RIKEN Research Highlight

Other Publications and Preprints

  1. Rämö, J. T., Kiiskinen, T., Karjalainen, J., Krebs, K., Kurki, M., ..., Kanai, M. et al. Genome-wide Screen of Otosclerosis in Population Biobanks: 18 Loci and Shared Heritability with Skeletal Structure. medRxiv (2020). doi:10.1101/2020.11.15.20227868
  2. *Sakaue, S., *Kanai, M., Tanigawa, Y., Karjalainen, J., Kurki, M., Koshiba, S. et al. A global atlas of genetic associations of 220 deep phenotypes. medRxiv (2020). doi:10.1101/2020.10.23.20213652
  3. Wang, Q. S., Kelley, D. R., Ulirsch, J., Kanai, M., Sadhuka, S., Cui, R. et al. Leveraging supervised learning for functionally-informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs. bioRxiv (2020). doi:10.1101/2020.10.20.347294
  4. Weeks, E. M., Ulirsch, J. C., Cheng, N. Y., Trippe, B. L., Fine, R. S., ..., Kanai, M. et al. Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. medRxiv (2020). doi:10.1101/2020.09.08.20190561
  5. Zheng, J., Zhang, Y., Rasheed, H., Walker, V., Sugawara, Y., ..., Kanai, M. et al. Trans-ethnic Mendelian randomization study reveals causal relationships between cardio-metabolic factors and chronic kidney disease. medRxiv (2020). doi:10.1101/2020.09.04.20188284
  6. Chen, M.-H., Raffield, L. M., Mousas, A., Sakaue, S., Huffman, J. E., ..., Kanai, M. et al. Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations. Cell 182, 1198–1213.e14 (2020). PubMed PR
  7. Vuckovic, D., Bao, E. L., Akbari, P., Lareau, C. A., Mousas, A., ..., Kanai, M. et al. The Polygenic and Monogenic Basis of Blood Traits and Diseases. Cell 182, 1214–1231.e11 (2020). PubMed PR
  8. Shirai, Y., Honda, S., Ikari, K., Kanai, M., Takeda, Y., Kamatani, Y. et al. Association of the RPA3-UMAD1 locus with interstitial lung diseases complicated with rheumatoid arthritis in Japanese. Annals of the Rheumatic Diseases 79, 1305–1309 (2020). PubMed PR
  9. Luo, Y., Kanai, M., Choi, W., Li, X., Yamamoto, K., Ogawa, K. et al. A high-resolution HLA reference panel capturing global population diversity enables multi-ethnic fine-mapping in HIV host response. medRxiv (2020). doi:10.1101/2020.07.16.20155606
  10. Ishigaki, K., Akiyama, M., Kanai, M., Takahashi, A., Kawakami, E., Sugishita, H. et al. Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases. Nature Genetics 52, 669–679 (2020). PubMed PR
  11. Atkinson, E. G., Maihofer, A. X., Kanai, M., Martin, A. R., Karczewski, K. J., Santoro, M. L. et al. Tractor: A framework allowing for improved inclusion of admixed individuals in large-scale association studies. bioRxiv (2020). doi:10.1101/2020.05.17.100727
  12. Reilly, S. K., Gosai, S. J., Guiterrez, A., Ulirsch, J. C., Kanai, M., Berenzy, D. et al. HCR-FlowFISH: A flexible CRISPR screening method to identify cis-regulatory elements and their target genes. bioRxiv (2020). doi:10.1101/2020.05.11.078675
  13. Sakaue, S., Hirata, J., Kanai, M., Suzuki, K., Akiyama, M., Lai Too, C. et al. Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction. Nature Communications 11, 1569 (2020). PubMed PR
  14. Pirastu, N., Cordioli, M., Nandakumar, P., Mignogna, G., Abdellaoui, A., ..., Kanai, M. et al. Genetic analyses identify widespread sex-differential participation bias. bioRxiv (2020). doi:10.1101/2020.03.22.001453
  15. Ray, J. P., Boer, C. G. de, Fulco, C. P., Lareau, C. A., Kanai, M., Ulirsch, J. C., Tewhey, R. et al. Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nature Communications 11, 1237 (2020). PubMed
  16. Matoba, N., Akiyama, M., Ishigaki, K., Kanai, M., Takahashi, A., Momozawa, Y. et al. GWAS of 165,084 Japanese individuals identified nine loci associated with dietary habits. Nature Human Behaviour 4, 308–316 (2020). PubMed PR
  17. Clark, D. W., Okada, Y., Moore, K. H. S., Mason, D., Pirastu, N., ..., Kanai, M. et al. Associations of autozygosity with a broad range of human phenotypes. Nature Communications 10, 4957 (2019). PubMed
  18. Shi, H., Gazal, S., Kanai, M., Koch, E. M., Schoech, A. P., Kim, S. S. et al. Population-specific causal disease effect sizes in functionally important regions impacted by selection. bioRxiv (2019). doi:10.1101/803452
  19. Leu, C., Stevelink, R., Smith, A. W., Goleva, S. B., Kanai, M., Ferguson, L. et al. Polygenic burden in focal and generalized epilepsies. Brain 142, 3473–3481 (2019). PubMed
  20. Tin, A., Marten, J., Halperin Kuhns, V. L., Li, Y., Wuttke, M., ..., Kanai, M. et al. Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels. Nature Genetics 51, 1459–1474 (2019). PubMed
  21. Akiyama, M., Ishigaki, K., Sakaue, S., Momozawa, Y., Horikoshi, M., ..., Kanai, M. et al. Characterizing rare and low-frequency height-associated variants in the Japanese population. Nature Communications 10, 4393 (2019). PubMed PR
  22. Wuttke, M., Li, Y., Li, M., Sieber, K. B., Feitosa, M. F., ..., Kanai, M. et al. A catalog of genetic loci associated with kidney function from analyses of a million individuals. Nature Genetics 51, 957–972 (2019). PubMed
  23. *Nakatochi, M., *Kanai, M., *Nakayama, A., *Hishida, A., *Kawamura, Y., Ichihara, S. et al. Genome-wide meta-analysis identifies multiple novel loci associated with serum uric acid levels in Japanese individuals. Communications Biology 2, 115 (2019). PubMed PR
  24. Matoba, N., Akiyama, M., Ishigaki, K., Kanai, M., Takahashi, A., Momozawa, Y. et al. GWAS of smoking behaviour in 165,436 Japanese people reveals seven new loci and shared genetic architecture. Nature Human Behaviour 3, 471–477 (2019). PubMed PR
  25. Suzuki, K., Akiyama, M., Ishigaki, K., Kanai, M., Hosoe, J., Shojima, N. et al. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nature Genetics 51, 379–386 (2019). PubMed PR
  26. Hirata, J., Hosomichi, K., Sakaue, S., Kanai, M., Nakaoka, H., Ishigaki, K. et al. Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population. Nature Genetics 51, 470–480 (2019). PubMed PR
  27. Kanai, M., Maeda, Y. & Okada, Y. Grimon: graphical interface to visualize multi-omics networks. Bioinformatics 34, 3934–3936 (2018). PubMed
  28. Horikoshi, M., Day, F. R., Akiyama, M., Hirata, M., Kamatani, Y., ..., Kanai, M. et al. Elucidating the genetic architecture of reproductive ageing in the Japanese population. Nature Communications 9, 1977 (2018). PubMed
  29. Okada, Y., Momozawa, Y., Sakaue, S., Kanai, M., Ishigaki, K., Akiyama, M. et al. Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese. Nature Communications 9, 1631 (2018). PubMed PR
  30. Malik, R., Chauhan, G., Traylor, M., Sargurupremraj, M., Okada, Y., ..., Kanai, M. et al. Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. Nature Genetics 50, 524–537 (2018). PubMed PR
  31. Hirata, J., Hirota, T., Ozeki, T., Kanai, M., Sudo, T., Tanaka, T. et al. Variants at HLA-A , HLA-C , and HLA-DQB1 confer risk of psoriasis vulgaris in Japanese. Journal of Investigative Dermatology 138, 542–548 (2018). PubMed
  32. Akiyama, M., Okada, Y., Kanai, M., Takahashi, A., Momozawa, Y., Ikeda, M. et al. Genome-wide association study identifies 112 new loci for body mass index in the Japanese population. Nature Genetics 49, 1458–1467 (2017). PubMed PR
  33. Sudo, T., Okada, Y., Ozaki, K., Urayama, K., Kanai, M., Kobayashi, H. et al. Association of NOD2 Mutations with Aggressive Periodontitis. Journal of Dental Research 96, 1100–1105 (2017). PubMed PR
  34. Okada, Y., Suzuki, A., Ikari, K., Terao, C., Kochi, Y., ..., Kanai, M. et al. Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis. The American Journal of Human Genetics 99, 366–374 (2016). PubMed PR
  35. Kanai, M., Tanaka, T. & Okada, Y. Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes Project data set. Journal of Human Genetics 61, 861–866 (2016). PubMed
  36. Okada, Y., Muramatsu, T., Suita, N., Kanai, M., Kawakami, E., Iotchkova, V. et al. Significant impact of miRNA–target gene networks on genetics of human complex traits. Scientific Reports 6, 22223 (2016). PubMed PR
  37. Okada, Y., Momozawa, Y., Ashikawa, K., Kanai, M., Matsuda, K., Kamatani, Y. et al. Construction of a population-specific HLA imputation reference panel and its application to Graves’ disease risk in Japanese. Nature Genetics 47, 798–802 (2015). PubMed PR

Reviews (in Japanese)

  1. Kanai, M. Genetic analysis of quantitative traits with integration of multi-omics data. The Medical Frontline (SAISHIN IGAKU) 74, 220–226 (2019).
  2. Kanai, M., Okada, Y. & Kamatani, Y. Genetics of clinical measurements in the Japanese population: large-scale genome-wide association study of 58 quantitative traits. Clinical Immunology & Allergology 71, 78–85 (2019).
  3. Kanai, M., Okada, Y. & Kamatani, Y. Large-scale genome-wide association study in the Japanese population elucidates genetic backgrounds of 58 quantitative traits. Life Science First Author’s Review (2018). doi:10.7875/first.author.2018.025 Link
  4. Kanai, M. & Okada, Y. Identification of genetic loci associated with chronic kidney disease and applications for drug development. Kidney and Metabolic Bone Diseases 31, 19–26 (2018).
  5. Kanai, M. & Okada, Y. HLA imputation: construction of a population-specific reference panel in Japanese. Journal of Clinical and Experimental Medicine (IGAKU NO AYUMI) 257, 939–940 (2016).

Presentations

International Conference

  1. Kanai, M., Ulirsch, J. C., Karjalainen, J., Kurki, M., Ishigaki, K., Kamatani, Y., Reilly, S., Sabeti, P., Tewhey, R., FinnGen, Okada, Y., Daly, M. J. & Finucane, H. K. Insights into fine-mapping causal variants of complex traits from diverse populations. The 70th Annual Meeting of the American Society of Human Genetics, Plenary Session (2020).
  2. Kanai, M., Ulirsch, J. C., McCaw, Z. R., Albors, C., Fan, Z., Ishigaki, K., Karjalainen, J., Kurki, M., FinnGen, Kamatani, Y., Okada, Y., Daly, M. J. & Finucane, H. K. Cross-population fine-mapping of 50 complex traits and diseases in  675,000 individuals across three global biobanks. The 69th Annual Meeting of the American Society of Human Genetics, Poster Session (2019).
  3. Kanai, M., Akiyama, M., Okada, Y., Ikeda, M., Iwata, N., Kubo, M. & Kamatani, Y. Trans-ethnic comparison of partitioned heritability reveals shared cell-type specific enrichment between East Asian and European genome-wide association studies. The 66th Annual Meeting of the American Society of Human Genetics, Poster Session (2016).
  4. Kanai, M., Tanaka, T. & Okada, Y. Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes Project. The 13th International Congress of Human Genetics, Oral Session (2016).
  5. Kanai, M., Okada, Y., Muramatsu, T., Suita, N., Kawakami, E., Iotchkova, V., Soranzo, N., Inazawa, J. & Tanaka, T. Significant impact of miRNA–target gene networks on genetics of human complex traits. The 13th International Congress of Human Genetics, Oral Session (2016).

Domestic Conference (in Japan)

  1. Kanai, M., Tanaka, T. & Okada, Y. Empirical estimation of a genome-wide significance threshold based on the 1000 Genomes Project. The 60th Annual Meeting of the Japan Society of Human Genetics, Oral Session (2015).
  2. Kanai, M., Yamane, K., Higuchi, C., Tanaka, T. & Okada, Y. Performance evaluation of PLINK v.1.90: a next version of a tool set for genome-wide association study. The 59th Annual Meeting of the Japan Society of Human Genetics, Poster Session (2014). PDF (ja)