Recommended reading
Textbooks
| Year | Category | Reference |
|---|---|---|
| 2020 | Statistical Genetics | An Introduction to Statistical Genetic Data Analysis By Melinda C. Mills, Nicola Barban and Felix C. Tropf https://mitpress.mit.edu/books/introduction-statistical-genetic-data-analysis |
| 2019 | Statistical Genetics | Handbook of Statistical Genomics: Fourth Edition https://onlinelibrary.wiley.com/doi/book/10.1002/9781119487845 |
| 2009 | Statistical Analysis and Machine Learning | The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition (Springer Series in Statistics)introduction-statistical-genetic-data-analysis. Trevor Hastie, Robert Tibshirani, Jerome Friedman. https://hastie.su.domains/ElemStatLearn/ (PDF book is available) |
Overview Reviews
| Year | Reference | Link |
|---|---|---|
| 2021 | Uffelmann, E., Huang, Q. Q., Munung, N. S., De Vries, J., Okada, Y., Martin, A. R., … & Posthuma, D. (2021). Genome-wide association studies. Nature Reviews Methods Primers, 1(1), 1-21. | Pubmed |
| 2019 | Tam, V., Patel, N., Turcotte, M., Bossé, Y., Paré, G., & Meyre, D. (2019). Benefits and limitations of genome-wide association studies. Nature Reviews Genetics, 20(8), 467-484. | Pubmed |
| 2017 | Pasaniuc, B., & Price, A. L. (2017). Dissecting the genetics of complex traits using summary association statistics. Nature reviews genetics, 18(2), 117-127. | Pubmed |
| 2023 | Abdellaoui, A., Yengo, L., Verweij, K. J., & Visscher, P. M. (2023). 15 years of GWAS discovery: Realizing the promise. The American Journal of Human Genetics. | Pubmed |
| 2017 | Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017). 10 years of GWAS discovery: biology, function, and translation. The American Journal of Human Genetics, 101(1), 5-22. | Pubmed |
| 2005 | Hirschhorn, J. N., & Daly, M. J. (2005). Genome-wide association studies for common diseases and complex traits. Nature reviews genetics, 6(2), 95-108. | Pubmed |
| 2006 | Balding, D. J. (2006). A tutorial on statistical methods for population association studies. Nature reviews genetics, 7(10), 781-791. | Pubmed |
| 2008 | McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J., & Hirschhorn, J. N. (2008). Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature reviews genetics, 9(5), 356-369. | Pubmed |
| 2010 | Price, A. L., Zaitlen, N. A., Reich, D., & Patterson, N. (2010). New approaches to population stratification in genome-wide association studies. Nature reviews genetics, 11(7), 459-463. | Pubmed |
| 2009 | Ioannidis, J., Thomas, G., & Daly, M. J. (2009). Validating, augmenting and refining genome-wide association signals. Nature Reviews Genetics, 10(5), 318-329. | Pubmed |
Topic-specific
LD
| Year | Reference | Link |
|---|---|---|
| 2008 | Slatkin, M. (2008). Linkage disequilibrium—understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics, 9(6), 477-485. | Pubmed |
Imputation
| Year | Reference | Link |
|---|---|---|
| 2010 | Marchini, J., & Howie, B. (2010). Genotype imputation for genome-wide association studies. Nature Reviews Genetics, 11(7), 499-511. | Pubmed |
| 2018 | Das S, Abecasis GR, Browning BL. (2018). Genotype Imputation from Large Reference Panels. Annu. Rev. Genomics Hum. Genet. | link |
Heritability
| Year | Reference | Link |
|---|---|---|
| 2017 | Yang, J., Zeng, J., Goddard, M. E., Wray, N. R., & Visscher, P. M. (2017). Concepts, estimation and interpretation of SNP-based heritability. Nature genetics, 49(9), 1304-1310. | Pubmed |
| 2009 | Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., … & Visscher, P. M. (2009). Finding the missing heritability of complex diseases. Nature, 461 (7265), 747-753. | Pubmed |
Genetic correlation
| Year | Reference | Link |
|---|---|---|
| 2019 | Van Rheenen, W., Peyrot, W. J., Schork, A. J., Lee, S. H., & Wray, N. R. (2019). Genetic correlations of polygenic disease traits: from theory to practice. Nature Reviews Genetics, 20(10), 567-581. | Pubmed |
Fine-mapping
| Year | Reference | Link |
|---|---|---|
| 2019 | Schaid, D. J., Chen, W., & Larson, N. B. (2018). From genome-wide associations to candidate causal variants by statistical fine-mapping. Nature Reviews Genetics, 19(8), 491-504. | Pubmed |
| 2023 | 王 青波, ゲノムワイド関連解析のその先へ：統計的fine-mappingの基礎と発展, JSBi Bioinformatics Review, 2023, 4 巻, 1 号, p. 35-51 | J-STAGE |
| ### Polygenic risk scores |
| Year | Reference | Link |
|---|---|---|
| 2022 | Wang, Y., Tsuo, K., Kanai, M., Neale, B. M., & Martin, A. R. (2022). Challenges and opportunities for developing more generalizable polygenic risk scores. Annual review of biomedical data science. | link |
| 2020 | Choi, S. W., Mak, T. S. H., & O’Reilly, P. F. (2020). Tutorial: a guide to performing polygenic risk score analyses. Nature protocols, 15(9), 2759-2772. | Pubmed |
| 2019 | Martin, A. R., Kanai, M., Kamatani, Y., Okada, Y., Neale, B. M., & Daly, M. J. (2019). Clinical use of current polygenic risk scores may exacerbate health disparities. Nature genetics, 51(4), 584-591. | Pubmed |
Rare variants
| Year | Reference | Link |
|---|---|---|
| 2014 | Lee, S., Abecasis, G. R., Boehnke, M., & Lin, X. (2014). Rare-variant association analysis: study designs and statistical tests. The American Journal of Human Genetics, 95(1), 5-23. | Pubmed |
| 2015 | Auer, P. L., & Lettre, G. (2015). Rare variant association studies: considerations, challenges and opportunities. Genome medicine, 7(1), 1-11. | Pubmed |
Genetic architecture
| Year | Reference | Link |
|---|---|---|
| 2018 | Timpson, N. J., Greenwood, C. M., Soranzo, N., Lawson, D. J., & Richards, J. B. (2018). Genetic architecture: the shape of the genetic contribution to human traits and disease. Nature Reviews Genetics, 19(2), 110-124. | Pubmed |
Useful Websites
| Description | Link |
|---|---|
| A Bioinformatician's UNIX Toolbox | http://lh3lh3.users.sourceforge.net/biounix.shtml |
| Osaka university, Department of Statistical Genetics Homepage | http://www.sg.med.osaka-u.ac.jp/school_2021.html |
| Genome analysis wiki (Abecasis Group Wiki) | https://genome.sph.umich.edu/wiki/Main_Page |
| EPI 511, Advanced Population and Medical Genetics (Alkes Price, Harvard School of Public Health) |
https://alkesgroup.broadinstitute.org/EPI511 |
| fiveMinuteStats (Matthew Stephens, Statistics and Human Genetics at the University of Chicago) |
https://stephens999.github.io/fiveMinuteStats |
| Course homepage and digital textbook for Human Genome Variation with Computational Lab | https://mccoy-lab.github.io/hgv_modules/ |
和文
| Year | Category | Reference |
|---|---|---|
| 2015 | Linux | 新しいLinuxの教科書 単行本 – 2015/6/6 三宅 英明 (著), 大角 祐介 (著) |
| 2012 | 統計解析（と少し機械学習） | はじめてのパターン認識 単行本（ソフトカバー） – 2012/7/31 平井 有三 (著) |
| 1991 | 統計解析（と少し機械学習） | 統計学入門 (基礎統計学Ⅰ) 単行本 – 1991/7/9 東京大学教養学部統計学教室 (編集) |
| 1992 | 統計解析（と少し機械学習） | 自然科学の統計学 (基礎統計学) 単行本 – 1992/8/1 東京大学教養学部統計学教室 (編集) |
| 2012 | 統計解析（と少し機械学習） | データ解析のための統計モデリング入門――一般化線形モデル・階層ベイズモデル・MCMC (確率と情報の科学) 単行本 – 2012/5/19 久保 拓弥 (著) |
| 2015 | 遺伝統計学全般 （基礎から発展まで） | 遺伝統計学入門 (岩波オンデマンドブックス) オンデマンド (ペーパーバック) – 2015/12/10 鎌谷 直之 (著) |
| 2020 | 遺伝統計学全般 （基礎から発展まで） | 実験医学 2020年3月 Vol.38 No.4 GWASで複雑形質を解くぞ! 〜多因子疾患・形質のバイオロジーに挑む次世代のゲノム医科学 単行本 – 2020/2/23 鎌谷 洋一郎 (著) |
| 2020 | 遺伝統計学全般 （基礎から発展まで） | ゼロから実践する 遺伝統計学セミナー〜疾患とゲノムを結びつける 単行本 – 2020/3/13 岡田 随象 (著) |
| ~ | 遺伝統計学全般 （基礎から発展まで） | 遺伝子医学 シリーズ企画 Statistical Genetics 〈遺伝統計学の基礎〉 - 鎌谷 洋一郎 + α |