linkstream2 microblog

Figure 1 in a recent Nature Genetics paper useful for LOF — saturation of LoF, essentially something that describes how many LoF variants we see as we keep adding more samples :

http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html

QT:”
Basically, LoF variants are so enriched for ultra-rare variants that they show no sign of saturation, and the catalogue will continue to grow as more and more exomes are sequenced.
“

http://www.bio-itworld.com/news/09/27/12/Knome-launches-knoSYS100-genome-supercomputer-enhance-interpretation.html

http://www.nature.com/nature/journal/v488/n7409/full/nature11284.html
Appears there’s germline variant calls (from JK) for potentially ~125 matched pairs

http://www.newscientist.com/article/mg21528826.200-a-brief-history-of-the-human-genome.html
mitochondria as the answer to a SA-to-Vol energy production puzzle introns as the remnants of self-splicing transposons from mitochondria

http://www.genomicron.evolverzone.com/2007/04/onion-test/
QT:”
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human? The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. “

http://www.nature.com/news/correction-algorithms-extend-the-reach-of-genome-sequencing-1.10924

combining technologies for better reconstruction

http://www.newscientist.com/special/accidents-human-evolution
Genes with well-known mutations betw. humans & chimps :
MYH16 for bigger skulls, SRGAP2 & HAR1 for bigger brains, foxp2 for language, amylase for diet change

http://www.nytimes.com/2012/08/23/health/fathers-age-is-linked-to-risk-of-autism-and-schizophrenia.html

Paper with the NS/S ratio: (See Fig 2C).
http://www.sciencemag.org/content/337/6090/100.abstract
Presaging what we’ll see in exomes to come….

Here is the link to the 21 Breast Cancer genomes:
http://www.ncbi.nlm.nih.gov/pubmed/22608084
Found hotspots of mutation….

Genome sequence data have been deposited at the European Genome-Phenome Archive (http://www.ebi.ac.uk/ega/ at the EBI) with accession number EGAD00001000138. SNP6 array data have been deposited with ArrayExpress Archive (EBI, accession number E-MTAB-1087).