Methods and Applications of Statistics in Clinical Trials, Volume 2: Planning, Analysis, and Inferential Methods

Chapter 47

Software for Genetics/Genomics

Qing Lu, Yeunjoo Song and Courtney Gray-McGuire

47.1 Introduction

As the fields of molecular genetics, genetic epidemiology, and pharmacogenetics continue to expand, so does the availability of bioinformatics tools, particularly software, for the analysis of data from many areas of genetics and genomics research. These software tools can typically be classified into three categories: (1) software for data storage and management, which includes quality control mechanisms; (2) software for investigating patterns of inheritance (genetics), which includes familial aggregation, linkage, allelic association, and linkage disequilibrium; and (3) software for systematic examination of a given genome (genomics), which includes gene expression, microarray data, and sequence analysis. The term genetic data is often used to refer to both classic genetics (the science of inheritance), which emphasize the study of family data and heritability, and molecular genetics, which focuses on the structure and function of genes. Genomic data, on the other hand, usually implies the study of large-scale genetic patterns across the genome. The breadth of these two areas alone gives an indication of the complexity of the software involved. The text of this article therefore serves only as an introduction to and review of the areas of analyses possible currently, and it gives program descriptions and references for many commonly used software packages. Furthermore, ...