Targeted Sequencing Bags a Rare Disease
This looks neato. One of the first papers to use the Agilent Tech to do targeted re-sequencing. I can't wait to get my hands on a PDF.
The impressive economy of this paper is that they targeted (using Agilent chips) less than 30Mb of the human genome, which is less than 1%. They also worked with very few samples; only about 30 cases of Miller Syndrome have been reported in the literature. While I've expressed some reservations about "exome sequencing", this paper does illustrate why it can be very cost effective and my objections (perhaps not made clear enough before) is more a worry about being too restricted to "exomes" and less about targeting.
More @ Omics! Omics!
Sexually Antagonistic Selection, Sexual Dimorphism, and the Resolution of Intralocus Sexual Conflict
Haven't read much on this particular topic, but given direction that my thesis is going I gotta start brushing up on the sexual selection literature. Anyway, this unusual review discusses the importance of sexual selection from an intra-locus perspective the essential idea being that in sexually dimorphic species single locus traits may be under different selective regimes depending upon the sex in which they are expressed (= sexually antagonistic selection). The authors find, with some caveats, that sexually antagonistic selection may be present in as many as 17% of species that exhibit sexual dimorphism.
- Cox R, Calsbeek R. (2009) Sexually Antagonistic Selection, Sexual Dimorphism, and the Resolution of Intralocus Sexual Conflict. American Naturalist, vol. 173 [link]
OOE: Another blog I help write
- From Tophat to Pysam July 21, 2010I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file. This meant I need to convert filetypes. So, I fired up sa […]
- Inferring Heterozygosity from SNP data April 20, 2010This looks straightforward. n = total number of reads aligning to a base y = total number of reads aligning to a base that match the reference p = probability that reads match the reference base Bases with LOD>3 were called SNPs or sites of heterozygosity. From Bloom et al. (2009) Measuring differential gene expression by short read sequencing: quantitat […]
- Why we are "Python Fanboys" April 15, 2010I think I can safely say that we’re all Python evangelists. In fact, I’m pretty sure my first conversation with ‘FixedByDrift’ revolved around just how enamored with Python he is. Likewise my first email with ‘AmbiguousBase’ was a code exchange of microsatellite finding software written in Python. We just love Python. So why should you learn to love Python […]
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- Does England Just Need a Good Shag?Published: June 22, 2010Things are not looking good for England. Two draws against opponents many in the global football community had quickly written off. The passes aren’t coming through, the runs are being cut off, the set pieces...
- Environmental change enhances cognitive abilities in fish.Published: April 26, 2010Source: pubmed: "plos biology"[jour]My Note: Clearly it's important to eat well.Environmental change enhances cognitive abilities in fish. PLoS Biol. 2010;8(4):e1000351 Authors: Kotrschal A, Taborsky B Flexible or innovative behavior is advantageous, espe...
- Version Control FailurePublished: April 8, 2010Source: Omics! Omics!My Note: This is moderately terrifying. Luckily, there is only one anole genome version publicly available at this point in time.Well, it was inevitable. A huge (and expensive) case of confused human genome versions.While the human genome is 10 years old, that was hardly the final word. Lots of mopping up remained on the original proj...
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