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 [...]

How recent are rare variants?

The Department of Genome Sciences at the University of Washington in Seattle, in a multi-institutional effort sequenced 15,336 genes for the NHLBI sponsored ESP project from a total of 6515 individuals of European American and African American descent.To identify approaches for disease-gene discovery, its important to understand evolutionary history of homosapiens and identify the age [...]

Clinical Findings from Sequencing keep flowing…

Just a glance at GenomeWeb's "In Print: Clinical Sequencing Papers of Note of the Last Two Weeks" is enough to show how hard it is to keep up with the sequencing revolution. Of the 37 publications mentioned here, 15 talk about whole-exome sequencing (WES) (and two amplicon sequencing and three whole-genome seq) identifying the causal [...]

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 [...]

Resources for Exome sequencing annotation

With the recent tsunami of sequencing data, and the reduced cost of whole exome capture technologies like Raindance, Agilent SureSelect and Nimblegen, a lot of data is bound to end up with Bioinformaticians. Annotating that data with information like coding variants, synonymous or not, etc is the first thing that needs to be done after [...]