GWAS學習筆記——imputation的含義 (Truth of Imputation)
Do not imput onther's sin to yourself
scheme of imputation in statistics
GWAS學習筆記——imputation的含義 (Truth of Imputation)
by Baoyu
7月份參加了Fudan主辦的首期GWAS研修班，對國內外GWAS有了系統、深入的感知。學習過程中，需要精准地理解一些重要概念，才能避免一知半解。
GWAS相關重要的名詞有Effect heterogeneity，Pooling，ReplicationJointPooled analysis，Geographic variation，Hierarchical Clustering，imputation，marginal effects，Manhattan Forest，GWAS consortium (如Genetic Association Information Network, GAIN)。這次班上不少老師把Manhattan Forest改稱為Pudong Forest，Pudong樓群的高度和密度都不亞於Manhattan)，呵呵。
GWAS研究中，imputation前承高通量測序，下啟數據分析；對缺失數據的imputation是進行數據分析的前提，重要性不言而喻。
Impute願意是歸罪,歸咎,歸因,非難,詆毀。Merian-Webster辭典的解釋既是此義：
Main Entry: impute
Function: transitive verb
Inflected Form:imputed ; imputing
Etymology: Middle English inputen, from Latin imputare, from in- + putare to consider Date: 14th century
1: to lay the responsibility or blame for often falsely or unjustly
2: to credit to a person or a cause: ATTRIBUTE *our vices as well as our virtues have been imputed to bodily derangement B. N. Cardozo
synonyms see ASCRIBE.
統計遺傳學中意為預測、插補，由已知的基因型預測未知的基因型並對缺失的數據進行補缺，如這句：
This imputation method uses the dense genotype data available from the HapMap CEU samples and the linkage disequilibrium (LD) relationships of the SNPs to impute (predict) genotypes for a large number of SNPs that were not measured experimentally in our Finnish cases and controls.
Statistical genetics中imputation 的三個主要作用：
Allows testing of untyped variation ，
Allows easy combination of data across genotyping platforms ，
Provides complete data for analysis with multiple SNPs.
實現imputation的常用軟件：
1. IMPUTE
Developed by Jonathan Marchini
Nature Genetics, Advance online publication
http://www.stats.ox.ac.uk/~marchini/#software
2. Mach 1.0, Markov Chain Haplotyping
Developed by Goncalo Abecasis
http://www.sph.umich.edu/csg/abecasis/MACH/
附件1是U Michigen 的小牛Scott對imputation等分析方法的一個介紹。
附件2是Eric E Schadt (Rosetta Inpharmatics)實驗室最近在BMC Genetis上一篇題為GWAS中插補（imputation）准確度及對關聯分析統計效力的影響，值得一讀。
附件1 Scott_Handling and analyzing data of GWAS
附件2 09 Accuracy of genome-wide imputation of untyped markers and...