2010年统计遗传学暑期培训班(北京)
随着基因测序技术的飞速发展，基因组数据不断快速增长，如何正确、快速地对这些数据进行各种统计学分析已成为研究的瓶颈，“2010年统计遗传学暑期培训班”将邀请美国华盛顿大学生物统计学系的“Summer Institute in Statistical Genetics”(http://www.biostat.washington.edu/suminst/sisg/general)中的部分老师到北京进行相关课程的讲授，同时具体指导相关数据的分析。
“2010年统计遗传学暑期培训班(北京)”中的课程将于8月23-27日在北京大学举办，培训班共有七个短期课程，每个课程持续两天半，具体课程如下：
第一部分：8月23至8月25日上午第一讲课程：种群遗传数据分析(Population Genetic Data Analysis)Kent Holsinger (Professor of Ecology and Evolutionary, Biology, University of Connecticut )
Bruce S. Weir (Professor and Chair of Biostatistics, University of Washington, Director, Summer Institute in Statistical Genetics)
第二讲课程：基因表达谱分析(Gene Expression Profiling)Gregory C. Gibson (Professor, School of Biology Georgia Institute of Technology)
John Storey (Associate Professor, Lewis-Sigler Institute Department of Molecular Biology, Princeton University)
第三讲课程：数量遗传学(Quantitative Genetics)J. Bruce Walsh (Professor of Ecology and Evolutionary, Biology, University of Arizona)
Dahlia M. Nielsen (Research Assistant Professor of Genetics North Carolina State University)
第二部分：8月25下午至8月27日第四讲课程：人类群体基因定位关联统计方法(Human Association Mapping)Alison Motsinger-Reif (Assistant Professor of Statistics, North Carolina State University)
Dahlia M. Nielsen (Research Assistant Professor of Genetics, North Carolina State University)
第五讲课程：动植物群体基因定位关联统计方法(Plant and Animal Association Mapping)Bruce S. Weir (Professor and Chair of Biostatistics, University of Washington, Director, Summer Institute in Statistical Genetics)
Michel Georges (Professor of Molecular Genetics, Université de Liège)
第六讲程：数量性状基因定位的统计方法(QTL Mapping)Rebecca W. Doerge (Professor of Statistics, Purdue University)
Zhao-Bang Zeng (Reynolds Distinguished Professor of Statistics and Genetics, North Carolina State University)
第七讲课程：用R语言对遗传数据进行分析(Genetic Data Analysis with R)Thomas Lumley (Professor of Biostatistics, University of Washington)
Kenneth M. Rice (Associate Professor of Biostatistics, University of Washington)
8月23至8月25日上午有三个同时进行的课程；8月25下午至8月27日有四个同时进行的课程。每个学员每个时段只能选择其中一个课程。
对选课学生的要求：
具有遗传学基础和生物统计学基础，自带手提电脑(以MS Windows操作系统为宜)
培训班收费：
学生及博士后收费：单选一个课程收费1200元，两个课程收费1600元
其他学员收费：单选一个课程收费1600元，两个课程收费2000元
每一课程学员人数：
30-40人，报满为止。
食宿安排：
提供午餐，住宿及早晚餐自理。培训班组织者在中关新园预定了一部分住房，学员可自行与中关新园联系(http://www.pkugv.com/index.asp)，联系时请说明是“2010年统计遗传学暑期培训班”的学员。
报名方式：
请将报名表通过电子邮件传给张湘波老师：xiangbozhang@pku.edu.cn
报名截止日期：2010年8月15日
培训班详细内容及参考资料：
第一讲课程：群体遗传数据分析
主讲人：
Kent Holsinger (Professor of Ecology and Evolutionary, Biology, University of Connecticut )
Bruce S. Weir (Professor and Chair of Biostatistics, University of Washington, Director, Summer Institute in Statistical Genetics)
本课程讲述群体遗传数据分析的基本原理和方法。讲述内容包括等位基因频率估计和样本方差；哈代-温伯格和连锁不平衡；群体结构F-统计量分析法；群体亲缘关系分析法。讲解使用公共领域的软件，包括GDA和Hickory。
阅读材料：
Weir, B.S. (1996). Genetic Data Analysis II. Sinauer Associates.
Holsinger, K., Weir, B. (2009). Genetics in geographically structured populations: defining, estimating, and interpreting Fst. Nature Reviews Genetics 10:639-50.
Module 1: Population Genetic Data Analysis
Instructors: K. Holsinger, and B. Weir
Estimates and sample variances of allele frequencies; Hardy-Weinberg and linkage disequilibrium; characterization of population structure with F-statistics; relationship estimation. Use of public domain software, including GDA and Hickory.
Background reading: Weir, B.S. (1996). Genetic Data Analysis II. Sinauer Associates.
Holsinger, K., Weir, B. (2009). Genetics in geographically structured populations: defining, estimating, and interpreting Fst. Nature Reviews Genetics 10:639-50.
第二讲课程：基因表达数据分析
主讲人：
Gregory C. Gibson (Professor, School of Biology Georgia Institute of Technology)
John Storey (Associate Professor, Lewis-Sigler Institute Department of Molecular Biology, Princeton University)
本课程涵盖基因表达数据统计分析的各个方面. 其方法也适用与蛋白质组和代谢物组数据的统计分析。通过理论与实例相结合的方式，讲解资料质量控制和规范化，方差分析和假设检验，时间序列，替代变量分析和优化分析方法。并讨论其方法在基因芯片和下一代DNA序列资料分析中的应用。讲解将和相关的统计软件示范应用相结合。
Module 2: Gene Expression Profiling
Instructors: G. Gibson and J. Storey
This course covers all aspects of the statistical analysis of gene expression profiling; the methods are also relevant to analysis of proteomic and metabolomic data. Theory will be integrated with case studies demonstrating the principles of quality control, normalization, analysis of variance and hypothesis testing, time series, surrogate variable analysis, and optimal discovery procedures. Discussion will include microarray and nextgen sequencing applications, and relevant statistical software will be demonstrated.
第三讲课程：数量遗传学
主讲人：
J. Bruce Walsh (Professor of Ecology and Evolutionary, Biology, University of Arizona)
Dahlia M. Nielsen (Research Assistant Professor of Genetics North Carolina State University)
数量遗传学研究复杂数量性状的遗传规律。数量性状同时受遗传和环境因素的影响。由于它包括大多数生物性状，例如疾病的易感性，作物产量以及基因芯片的数据，对数量遗传学的了解可以为植物和动物育种，人类遗传学，基因组学，生态学和进化生物学等多学科的研究起到很大的帮助。本课程将涵盖数量遗传学基础：包括Fisher方差分解，亲缘之间的相关及协方差，遗传力，近亲繁殖，杂交育种和选择反应。同时也适当介绍其它复杂问题，比如混合统计模式，BLUP方法，QTL定位，相关形状以及多元选择反应。
阅读材料：Lynch, M., Walsh, B. (1998). Genetics and analysis of quantitative traits. Sinauer.
Module 3: Quantitative Genetics
Instructors: B. Walsh and D. Nielsen
Quantitative Genetics is the analysis of complex characters where both genetic and environment factors contribute to trait variation. Since this includes most traits of interest, such as disease susceptibility, crop yield, and all microarray data, a working knowledge of quantitative genetics is critical in diverse fields from plant and animal breeding, human genetics, genomics, to ecology and evolutionary biology. The course will cover the basics of quantitative genetics including: Fisher’s variance decomposition, covariance between relatives, heritability, inbreeding and crossbreeding, and response to selection. Also an introduction to advanced topics such as: Mixed Models, BLUP, QTL mapping; correlated characters; and the multivariate response to selection.
Background reading: Lynch, M., Walsh, B. (1998). Genetics and analysis of quantitative traits, Sinauer.
第四讲课程：人类群体基因定位的关联统计方法
主讲人：
Alison Motsinger-Reif (Assistant Professor of Statistics, North Carolina State University)
Dahlia M. Nielsen (Research Assistant Professor of Genetics North Carolina State University)
本课程将介绍针对人类群体基因定位的关联统计方法。讨论题目包括：利用连锁不平衡进行基因定位的理论; 基因定位实验设计；基于群体和家系的基因关联定位统计方法；离散和连续分布性状统计分析方法；处理群体结构的统计方法; 多测试问题；复杂的遗传模型的分析方法。
Module 4: Human Association Mapping
Instructors: A. Motsinger-Reif, and D. Nielsen
This module is an introduction to association mapping, focusing on human populations. Topics include: theory of linkage disequilibrium and mapping; basics of gene mapping study design; population and family-based association techniques for discrete and continuous traits; methods for detecting and accounting for population structure; and multiple testing issues. New data-mining methods for detecting complex genetics models are also discussed.
第五讲课程：动植物群体基因定位的关联统计方法
主讲人：
Bruce S. Weir (Professor and Chair of Biostatistics, University of Washington, Director, Summer Institute in Statistical Genetics)
Michel Georges (Professor of Molecular Genetics, Université de Liège)
本课程将介绍针对动植物群体基因定位的关联统计方法。讨论题目包括：连锁不平衡基因定位的理论，对离散和连续性状进行群体和家系的关联分析方法，检测群体结构，多倍体植物分析问题，多测试问题，以及基因型的测定方法。授课使用真实数据并和统计软件实际操作相结合。
Module 5: Plant and Animal Association Mapping
Instructors: B. Weir and M. Georges
This module is an introduction to association mapping, focusing on plant and animal populations. Topics include theory of linkage disequilibrium and mapping, population and family-based association techniques for discrete and continuous traits, methods for detecting and accounting for population structure, issues in polyploid organisms, multiple testing issues, and genotyping strategies. Use real data and hands-on experience with publicly available software packages for instruction.
第六讲课程：数量性状基因定位的统计方法
主讲人：
Rebecca W. Doerge (Professor of Statistics, Purdue University)
Zhao-Bang Zeng (Reynolds Distinguished Professor of Statistics and Genetics, North Carolina State University)
本课程将系统地介绍适于杂交群体的数量性状基因定位(QTL)的统计方法。讨论题目包括：实验设计; 连锁图谱构建; 单标记分析; 区间作图法; 复合区间作图法；多区间作图法。同时也讨论对全基因组扫描模型统计量阈值的确定。本课程将利用公共领域的软件Windows QTL Cartographer作演讲示范及练习。
Module 6: QTL Mapping
Instructors: R. Doerge and Z-B. Zeng
This module will systematically introduce statistical methods for mapping quantitative trait loci (QTL) in experimental cross populations. Topics include experimental designs, linkage map construction, single-marker analyses, interval mapping, composite interval mapping, and multiple interval mapping. Significance thresholds for genome scan and model selection will also be discussed. Uses public domain software Windows QTL-Cartographer for computer lab exercises.
第七讲课程：用R语言对遗传数据进行分析
主讲人：
Thomas Lumley (Professor of Biostatistics, University of Washington)
Kenneth M. Rice (Associate Professor of Biostatistics, University of Washington)
本课程将介绍用R语言作遗传资料分析的方法。讨论题目包括：面向对象程序设计；SQL数据库的使用；一些Bioconductor数据基础设施；从R语言里调用C代码。本课程适用与对R语言或其他语言编程具有足够经验的学生。
阅读材料：Gentleman. R. (2008). R Programming in Bioinformatics. Taylor and Francis.
Module 7: Genetic Data Analysis with R
Instructors: T. Lumley and K. Rice
This module covers object-oriented programming, SQL database use, some of the Bioconductor data infrastructure, and calling C code from R. The module is aimed at people who have either substantial R experience or programming experience in other languages.
Back-ground reading: Gentleman. R. (2008). R Programming in Bioinformatics. Taylor and Francis.
