GWAS Recommended Reading – GWAS相关推荐阅读

  1. 遗传统计学入门书籍 Textbooks
  2. 课件 Slides
  3. GWAS综述或教程 Reviews & Tutorials
  4. 分类综述文章 Reviews on topics
    1. 遗传模型与相关概念 Models and Concepts
    2. 定相与插补 Phasing and imputation
    3. 稀有变异（或基因）的关联检验 Gene-based analysis
    4. 遗传力估计 Heritability
    5. 精细定位 Fine-mapping
    6. 多基因风险分数 Polygenic risk scores
    7. 孟德尔随机化 Mendelian Randomization

最近更新：20220701

遗传统计学入门书籍 Textbooks

Mills, M. C., Barban, N., & Tropf, F. C. (2020). An introduction to statistical genetic data analysis. Mit Press.

Balding, D. J., Moltke, I., & Marioni, J. (Eds.). (2019). Handbook of statistical genomics. John Wiley & Sons.

课件 Slides

1 Association Mapping: GWAS and Sequencing Data
Instructors: Timothy Thornton and Michael Wuhttp://faculty.washington.edu/tathornt/SISG2019.html

2 遺伝統計学・夏の学校＠大阪大学

http://www.sg.med.osaka-u.ac.jp/tools.html

https://www.slideshare.net/YukinoriOkada/presentations

3 Biostatistics 666 : https://genome.sph.umich.edu/wiki/Biostatistics_666:_Main_Page

GWAS综述或教程 Reviews & Tutorials

GWAS入门 – 综述推荐与导读

  • Brandes, N., Weissbrod, O., & Linial, M. (2022). Open problems in human trait genetics. Genome Biology, 23(1), 1-32.
  • Uffelmann, E., Huang, Q.Q., Munung, N.S. et al. Genome-wide association studies. Nat Rev Methods Primers 1, 59 (2021). https://doi.org/10.1038/s43586-021-00056-9
  • 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.
  • 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.
  • Visscher, P. M., Brown, M. A., McCarthy, M. I., & Yang, J. (2012). Five years of GWAS discovery. The American Journal of Human Genetics, 90(1), 7-24.
  • Pearson, T. A., & Manolio, T. A. (2008). How to interpret a genome-wide association study. Jama, 299(11), 1335-1344.
  • 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.
  • Wang, W., Barratt, B. J., Clayton, D. G., & Todd, J. A. (2005). Genome-wide association studies: theoretical and practical concerns. Nature Reviews Genetics, 6(2), 109-118.
  • Hirschhorn, J. N., & Daly, M. J. (2005). Genome-wide association studies for common diseases and complex traits. Nature reviews genetics, 6(2), 95-108.

分类综述文章 Reviews on topics

遗传模型与相关概念 Models and Concepts

  • Timpson, N., Greenwood, C., Soranzo, N. et al. Genetic architecture: the shape of the genetic contribution to human traits and disease. Nat Rev Genet 19, 110–124 (2018). https://doi.org/10.1038/nrg.2017.101

定相与插补 Phasing and imputation

  • Das, S., Abecasis, G. R., & Browning, B. L. (2018). Genotype imputation from large reference panels. Annu Rev Genomics Hum Genet, 19(1), 73-96.
  • Marchini, J., Howie, B. Genotype imputation for genome-wide association studies. Nat Rev Genet 11, 499–511 (2010). https://doi.org/10.1038/nrg2796
  • Li, Y., Willer, C., Sanna, S., & Abecasis, G. (2009). Genotype imputation. Annual review of genomics and human genetics, 10, 387.

稀有变异（或基因）的关联检验 Gene-based analysis

  • Povysil, G., Petrovski, S., Hostyk, J., Aggarwal, V., Allen, A. S., & Goldstein, D. B. (2019). Rare-variant collapsing analyses for complex traits: guidelines and applications. Nature Reviews Genetics, 20(12), 747-759.
  • 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.
  • Gibson, G. (2012). Rare and common variants: twenty arguments. Nature Reviews Genetics, 13(2), 135-145.

遗传力估计 Heritability

  • 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.
  • Zhu, H., & Zhou, X. (2020). Statistical methods for SNP heritability estimation and partition: A review. Computational and Structural Biotechnology Journal, 18, 1557-1568.
  • Visscher, P. M., Hill, W. G., & Wray, N. R. (2008). Heritability in the genomics era—concepts and misconceptions. Nature reviews genetics, 9(4), 255-266.

精细定位 Fine-mapping

  • 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.

多基因风险分数 Polygenic risk scores

  • 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.
  • Wray, N. R., Lin, T., Austin, J., McGrath, J. J., Hickie, I. B., Murray, G. K., & Visscher, P. M. (2021). From basic science to clinical application of polygenic risk scores: a primer. JAMA psychiatry, 78(1), 101-109.
  • Torkamani, A., Wineinger, N. E., & Topol, E. J. (2018). The personal and clinical utility of polygenic risk scores. Nature Reviews Genetics, 19(9), 581-590.
  • Lewis, C. M., & Vassos, E. (2020). Polygenic risk scores: from research tools to clinical instruments. Genome medicine, 12(1), 1-11.

孟德尔随机化 Mendelian Randomization

  • Davies, N. M., Holmes, M. V., & Smith, G. D. (2018). Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians. bmj, 362.
  • Sanderson, E., Glymour, M.M., Holmes, M.V. et al. Mendelian randomization. Nat Rev Methods Primers 2, 6 (2022). https://doi.org/10.1038/s43586-021-00092-5