Mendelian disease gene identification was a challenging process. Exome sequencing provides a quicker and cheaper solution. When using exome sequencing to identify a causative mutation, a list of... Show moreMendelian disease gene identification was a challenging process. Exome sequencing provides a quicker and cheaper solution. When using exome sequencing to identify a causative mutation, a list of variants needs to be sifted. The standard strategy is to focus on variants that are novel, conform to the inheritance pattern, and have an apparent functional effect. A drawback of this type of rough filtering strategy is that the pathogenic mutation might be lost. For example, the mutation that was predicted to be silent can affect splicing. Though exome sequencing is not designed to detect intronic variants, they are seen in exome sequencing lists. This additional data may yield unexpected findings, like branch point mutations. Next generation sequencing reads are much shorter. For substitutions and small indels, BWA is the most popular tool, but it can sacrifice information and generate false negative results with larger indels. By applying GMAP/GSNAP, larger indels can be identified, suggesting that when one tool does not work well, one should try with another one. Whole genome sequencing will help pinpoint the cause of diseases that cannot be solved by exome sequencing. The use of exome sequencing can be considered as a first step towards this era. Show less
