Posts Tagged ‘from_jclub’

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
“}}

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

June 1, 2017

http://www.nature.com/ng/journal/v42/n7/abs/ng.608.html

Common SNPs explain a large proportion of the heritability for human height

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
"}}

Common SNPs explain a large proportion (45%) of heritability for…height (80%) http://www.Nature.com/ng/journal/v42/n7/abs/ng.608.html Vs ’10 GWAS SNPs could only expl. 5%

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors : Nature Genetics : Nature Research

May 6, 2017

http://www.nature.com/ng/journal/v49/n5/full/ng.3818.html

Ref component analysis..of transcriptomes, by @Robson_Paul &co http://www.Nature.com/ng/journal/v49/n5/full/ng.3818.html Clustering similarity of samples to tissue references

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression: Cell

April 16, 2017

"Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression"

(http://www.sciencedirect.com/science/article/pii/S0092867417301289)

#Neanderthal-Introgressed Sequences [&]…Gene Expression http://www.Cell.com/cell/abstract/S0092-8674(17)30128-9?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867417301289%3Fshowall%3Dtrue ASE for Hn SNPs shows lower #brain expression vs reference

Phys. Rev. E 92, 032810 (2015) – Thermodynamic characterization of networks using graph polynomials

March 31, 2017

Thermodynamic characterization of #networks using graph polynomials https://journals.APS.org/pre/abstract/10.1103/PhysRevE.92.032810 Application to the stockmarket & biological data

Is American Pet Health Care (Also) Uniquely Inefficient?

March 11, 2017

Is American Pet Health Care (Also) Uniquely Inefficient?
http://www.NBER.org/papers/w22669 High correlation betw. #healthcare costs for people & pets

Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage | Science

March 4, 2017

Transmissible Dog Cancer Genome Reveals…History of an Ancient Cell Lineage http://science.sciencemag.org/content/343/6169/437.full After 11k yrs 2M SNVs & 646 genes KO’ed

Elizabeth P. Murchison1,2,*,†,
David C. Wedge1,*,
Ludmil B. Alexandrov1,
Beiyuan Fu1,
Inigo Martincorena1,
Zemin Ning1,
Jose M. C. Tubio1,
Emma I. Werner1,
Jan Allen3,
Andrigo Barboza De Nardi4,
Edward M. Donelan3,
Gabriele Marino5,
Ariberto Fassati6,
Peter J. Campbell1,
Fengtang Yang1,
Austin Burt7,
Robin A. Weiss6,
Michael R. Stratton1,†

+ See all authors and affiliations

Science 24 Jan 2014:
Vol. 343, Issue 6169, pp. 437-440
DOI: 10.1126/science.1247167

Jclub Paper

January 28, 2017

#RNA Struc. Determinants of Optimal Codons…by MAGESeq
http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4 Probing effect of synonymous changes; towards a better dN/dS

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30368-4

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder : Nature Neuroscience : Nature Research

January 28, 2017

Genome-wide…analysis implicates miRNA dysregulation in #ASD http://www.nature.com/neuro/journal/v19/n11/full/nn.4373.html 58 diff. expr. miRNAs incl 17 strongly down in cases

http://www.nature.com/neuro/journal/v19/n11/full/nn.4373.html

QT:{{”
The miRNA expression profiles were very similar between the frontal and temporal cortex, but were distinct in the cerebellum
(Supplementary Fig. 2a–f), consistent with previous observations for mRNAs11, 12. We therefore combined 95 covariate-matched samples (47 samples from 28 ASD cases and 48 samples from 28 controls;
Supplementary Fig. 1c and Supplementary Table 1) from the FC and TC for differential gene expression (DGE) analysis, comparing ASD and CTL using a linear mixed-effects regression framework to control for potential confounders (Online Methods). We identified 58 miRNAs showing significant (false discovery rate (FDR) < 0.05) expression changes between ASD and CTL: 17 were downregulated and 41 were upregulated in ASD cortex (Fig. 1b and Supplementary Table 2). The fold changes for the differentially expressed miRNAs were highly concordant between the FC and TC (Pearson correlation coefficient R = 0.96, P < 2.2 × 10−16; Fig. 1c).
“}}

Jclub paper

January 16, 2017

The impact of #SVs on…gene expression
http://biorxiv.org/content/early/2016/06/09/055962 24k in 147 people in GTEx pilot act as causal variants in 3-7% of ~25k eQTLs

The impact of structural variation on human gene expression

Colby Chiang, Alexandra J Scott, Joe R Davis, Emily
K Tsang, Xin Li, Yungil Kim, Farhan N Damani, Liron Ganel, GTEx Consortium, Stephen B Montgomery, Alexis Battle, Donald F Conrad, Ira M Hall
doi: https://doi.org/10.1101/055962