Exomes vs Genomes (re-visited)

The paper by Lupski et al in Genome Medicine provides fuel to the perpetual debate of Whole Exome Sequencing (WES) vs Whole Genome Sequencing (WGS). It takes me down the memory lane to my own presentation "Genomes or Exomes: evaluation of cost, time and coverage" at Beyond the Genome 2011 conference. (If you would like [...]

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Mitochondrial Gold Rush

Mitochondrial genomes can be extracted from Whole Exome Sequencing (WES) data as outlined by this paper in Nature methods by Ernesto Picardi & Graziano Pesole. Tools like Mito Seek are now available that gather mitochondrial read sequences from NGS data and perform high throughput sequence analysis. Availability of mitochondrial genomes is important as genomic variation in mitochondria has [...]

ExomeSEQ: bringing reads on-target

It is surprising to look at some of the numbers from exome capture followed by sequencing projects.  The nature paper on exome-seq to identify cause of mendelian disorder has as low as 47% of uniquely mapping reads actually mapping on-target. Another study of 12 exome sequences also has a capture specificity of as low as [...]