Читать книгу Genetic Analysis of Complex Disease - Группа авторов - Страница 21

There are two general, but not mutually exclusive, ways to approach gene discovery for complex traits. The first is to take a genome‐wide screening approach. Genomic screening can aim to identify areas of genetic linkage in family‐based designs (Chapter 6) or areas of association in either family‐ or population‐based designs (Chapters 8 and 9). A good genomic screen will attempt to cover the entire human genome using markers evenly spaced across the genome. Current high‐throughput genotyping technologies enable genotyping of hundreds of thousands to millions of single nucleotide polymorphisms in a rapid, inexpensive manner for use in linkage or association studies. More recently, high‐throughput sequencing technology has been used to screen the entire coding sequence of the genome (WES) or the entire genome (WGS) for trait‐associated variants, without first conducting genome‐wide linkage or association studies. As sequencing costs continue to decline, a shift to “genotyping by sequencing” is likely, in which results from WGS might be used to conduct a genome‐wide screen and follow‐up in a single molecular experiment. These same high‐throughput genotyping and sequencing technologies allow large‐scale examination of gene expression (through gene expression microarrays or RNA‐Seq) and epigenetic changes (through methylation arrays or Methyl‐Seq) in trait‐relevant tissues. The results of such experiments are often used in conjunction with genome‐wide screens to identify high‐priority candidate genes for follow‐up studies. These technologies and their application to genomic studies are discussed in Chapter 10.

In contrast to the genomic screening approach, a directed screening approach may be used. This approach, sometimes termed a “candidate‐gene” approach, focuses on an area of the genome selected for examination based on prior information. The additional information could come from many sources, including results from a previous genome‐wide screen, results from gene expression studies, genes suggested by pathophysiology, or candidate genes identified in model systems. For example, multiple sclerosis is an autoimmune disease in which the myelin sheaths around nerves are attacked and often destroyed. This information suggests that certain genes, such as the human leukocyte antigen genes, T‐cell receptor genes, and the myelin basic protein gene, are prime candidates for analysis. The strength and weakness of this approach arise from the confidence in the role of these genes. If the evidence is strong that a direct role is played, only a few such genes may need to be tested to find a trait‐associated variant. If the evidence is more circumstantial, then many genes may have equal justification for being studied, and not much is gained over conducting a genome‐wide screen. Such studies are now most often conducted as follow‐up of prior genomic screens or other hypothesis‐generating experiments.