linkstream2 microblog

The biggest threat to the genomic revolution? Spying scandals — pro #sharing with few #privacy worries editorial http://fw.to/aLba6TX

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http://www.theglobeandmail.com/report-on-business/the-biggest-threat-to-the-genomic-revolution-spying-scandals/article13531705

http://bioinformatics.oxfordjournals.org/content/29/17/2199.short?rss=1

this should partially explain the high insertion rate in worm: http://mbe.oxfordjournals.org/content/26/6/1199.full

QT:”
Of the new mutations observed in MA lines, more than half were short indel mutations, with fewer deletions than insertions (Denver, Morris, Lynch, and Thomas 2004). This finding on indels contrasts with previous work with C. elegans pseudogenes in which deletions are more common than insertions (Robertson 2000; Witherspoon and Robertson 2003) but is consistent with findings in C. elegansmicrosatellite mutation data (Frisse 1999; Denver, Morris, Kewalramani, et al. 2004; Seyfert et al. 2008).
“

http://preview.reuters.com/2013/8/7/for-henrietta-lacks-famous-cells-new-and-unique-1

http://www.reuters.com/article/2013/08/07/us-science-hela-idUSBRE9760YD20130807

QT:"

The decision applies only to researchers funded by NIH, which said it
"encourages" other scientists to abide by the agreement. Because
DNA-sequencing technology is cheap and ubiquitous in genetics labs,
the HeLa genome has been partly sequenced many times, and can easily
be fully sequenced again.

"Sequencing" refers to determining the precise order of the chemical
letters on a person’s genome, which is the full library of his or her
genetic information. Bits and pieces of that sequence spell out, for
instance, whether someone is at risk of diabetes or Alzheimer’s or
other genetic traits, as well as personal traits like the consistency
of ear wax.

These loopholes in the access agreement significantly weaken the NIH
move, said Mark Gerstein, a computational biologist at Yale University
who has raised concerns about threats to genetic privacy. "I doubt NIH
will get blanket agreement from scientists in every country" to follow
its protocol, "so it’s not clear what the agreement will be able to
accomplish."

"

http://preview.reuters.com/2013/8/7/for-henrietta-lacks-famous-cells-new-and-unique-1

QT:”

The decision applies only to researchers funded by NIH, which said it “encourages” other scientists to abide by the agreement. Because DNA-sequencing technology is cheap and ubiquitous in genetics labs, the HeLa genome has been partly sequenced many times, and can easily be fully sequenced again.

“Sequencing” refers to determining the precise order of the chemical letters on a person’s genome, which is the full library of his or her genetic information. Bits and pieces of that sequence spell out, for instance, whether someone is at risk of diabetes or Alzheimer’s or other genetic traits, as well as personal traits like the consistency of ear wax.

These loopholes in the access agreement significantly weaken the NIH move, said Mark Gerstein, a computational biologist at Yale University who has raised concerns about threats to genetic privacy. “I doubt NIH will get blanket agreement from scientists in every country” to follow its protocol, “so it’s not clear what the agreement will be able to accomplish.”

“

Two foci for Genomics England are cancer and rare, inherited diseases – not neuro, cardio, &c.

https://twitter.com/timjph/status/353047985808084993
http://www.ft.com/intl/cms/s/0/6a1f001e-e48a-11e2-a74d-00144feabdc0.html#axzz2Y840CSnr

Lister… Ecker

MT @BiomedRevon: Global #epigenomic reconfiguration during mammalian #brain development http://bit.ly/16lbboa cortex methylation over time

A “map showing how methylation changes in the frontal cortex over time. During the first two years of life… a wave of methylation alters the DNA in genes ”

http://www.sciencemag.org/content/early/2013/07/05/science.1237905

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology
Cancer Res July 15, 2013 73:4372-4382; Published OnlineFirst July 15, 2013; http://cancerres.aacrjournals.org/content/73/14/4372.long

Accounting for mutational heterogeneity in identifying cancer genes… MutSigCV by @broadinstitute via @notSoJunkDNA: http://bit.ly/14EPvVx http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12213.html doi:10.1038/nature12213

http://www.1000genomes.org/faq/there-any-gene-expression-data-available-1000-genomes-project-samples