Stunning advances have been made over the last 5 years in the ability to rapidly and inexpensively detect variation in the human genome. In the mid-2000s massively parallel detection of single-nucleotide polymorphisms (SNPs) on gene chips (genotyping) burst on to the scene, launching the era of genome-wide association studies and high-profile direct-to-consumer marketing of genetic testing of questionable clinical value.1 More recently, substantial credible evidence has been accumulating for the research and clinical value of whole-exome sequencing (WES) for conditions ranging from cancer to developmental delay to mendelian disorders.2- 5 Whole-exome sequencing uses high-throughput sequencing technologies to determine the arrangement of DNA base pairs specifying the protein coding regions of an individual’s genome, also known as the exome. As remarkable as SNP genotyping and WES technologies are, they are both interim methods for detecting DNA variation. Assuming perfect technical accuracy, both are limited in the extent of variation that they can discover in a patient. In the case of SNP genotyping, this is because of the type of known variations the platforms can detect and in WES because the exome comprises about 1% of the entire genome.
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