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Common SNPs explain a large proportion of the heritability for human height : Nature Genetics : Nature Research

June 2, 2017

Common SNPs explain a large proportion (45%) of heritability for…height (85%)
http://www.Nature.com/ng/journal/v42/n7/abs/ng.608.html Cf 2010 GWASes could only explain 5%

Jian Yang,
Beben Benyamin,
Brian P McEvoy,
Scott Gordon,
Anjali K Henders,
Dale R Nyholt,
Pamela A Madden,
Andrew C Heath,
Nicholas G Martin,
Grant W Montgomery,
Michael E Goddard
& Peter M Visscher

Nature Genetics 42, 565–569 (2010) doi:10.1038/ng.608

QT:{{”
…conveniently implemented with a mathematically equivalent model that uses the SNPs to calculate the genomic relationship between pairs of subjects). Using this approach, we estimated the proportion of phenotypic variance explained by the SNPs as 0.45 (s.e. = 0.08, Table 1), a nearly tenfold increase relative to the 5% explained by published and validated individual SNPs
“}}

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Tags: from_jclub, from_jw, jclub, jw, mynotes0mg, paperE, quote

CATO score

May 28, 2017

Seq. variants influencing…TF occupancy
http://www.Nature.com/ng/journal/v47/n12/full/ng.3432.html Uses allelic analysis to develop the CATO score, how variants alter binding

QT:{{”
This approach resulted in a simple scoring scheme, termed contextual analysis of transcription factor occupancy (CATO), that provides a recalibrated probability of affecting the binding of any transcription factor, as well as a quantitatively ranked list of transcription factor families whose binding might be altered.
“}}

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Tags: alleledb, alleleseq, from, from_jr, i0gpwrite, jr, quote

The structural repertoire of the human V kappa domain. – PubMed – NCBI

May 16, 2017

https://www.ncbi.nlm.nih.gov/pubmed/7556106

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Tags: antibodymodelling, wc0mg, x57l

Standard conformations for the canonical structures of immunoglobulins. – PubMed – NCBI

May 16, 2017

https://www.ncbi.nlm.nih.gov/pubmed/9367782

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Tags: antibodymodelling, wc0mg, x57l

Conformations of the third hypervariable region in the VH domain of immunoglobulins. – PubMed – NCBI

May 16, 2017

https://www.ncbi.nlm.nih.gov/pubmed/9466909

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Tags: antibodymodelling, wc0mg, x57l

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network | Science

May 15, 2017

The #Brain #Somatic Mosaicism Network
http://science.ScienceMag.org/content/356/6336/eaal1641 Long lifespan of neurons accentuates impact of individual somatic mutations

QT:{{”
Neuropsychiatric disorders have a complex genetic architecture. Human genetic population-based studies have identified numerous heritable sequence and structural genomic variants associated with
susceptibility to neuropsychiatric disease. However, these germline variants do not fully account for disease risk. During brain development, progenitor cells undergo billions of cell divisions to generate the ~80 billion neurons in the brain. The failure to accurately repair DNA damage arising during replication,
transcription, and cellular metabolism amid this dramatic cellular expansion can lead to somatic mutations. Somatic mutations that alter subsets of neuronal transcriptomes and proteomes can, in turn, affect cell proliferation and survival and lead to neurodevelopmental disorders. The long life span of individual neurons and the direct relationship between neural circuits and behavior suggest that somatic mutations in small populations of neurons can significantly affect individual neurodevelopment. The Brain Somatic Mosaicism Network has been founded to study somatic mosaicism both in neurotypical human brains and in the context of complex neuropsychiatric disorders.” “}}

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Tags: brain, psychencode, quote, somatic, sombr, texp

Bit by Bit: The Darwinian Basis of Life

May 15, 2017

Bit by Bit: The #Darwinian Basis of Life
http://www.PLoSBiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001323 Overview of the amount of generated information in replicating molecules

QT:{{”
“The number of possible compositions is xn. If these are all equally probable, then each has a prior probability of occurrence of x−n, and the information content (number of bits) associated with a particular realized composition is log2(xn). This can also be expressed as 2#bits = xn. For a binary polymer, #bits = n; for a nucleic acid polymer, #bits = 2n.

If the various compositions do not have the same prior probability of occurrence, then the information content associated with a particular realized composition must be calculated based on its prior probability of occurrence (pk), which ranges from 0 to 1. The information content (number of bits) associated with a particular realized composition is −log2(pk).”
“}}

Gerald F. Joyce
Published: May 8, 2012
https://doi.org/10.1371/journal.pbio.1001323

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Tags: Darwinian, quote