linkstream2 microblog

https://www.nature.com/articles/ncomms4122

Common #schizophrenia alleles are enriched in mutation-intolerant genes & in regions under strong background selection
https://www.nature.com/articles/s41588-018-0059-2 50 novel SCZ loci & 145 loci in total, from #GWAS – associated w/ 33 candidate causal genes

QT:{{”
We report a new genome-wide association study of schizophrenia (11,260 cases and 24,542 controls), and through meta-analysis with existing data we identify 50 novel associated loci and 145 loci in total. Through integrating genomic fine-mapping with brain expression and chromosome conformation data, we identify candidate causal genes within 33 loci.
“}}

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection
Nature Genetics (2018)
doi:10.1038/s41588-018-0059-2

Dynamic Topic Models
https://mimno.infosci.cornell.edu/info6150/readings/dynamic_topic_models.pdf Classic work by @Blei_lab & J Lafferty adapts the #LDA formalism describing documents in terms of latent topics – to allow these to evolve over time

Points of significance – #MachineLearning: supervised methods https://www.Nature.com/articles/nmeth.4551 Nice discussion of the k in k-NN & the slack parm. C, penalizing misclassified points in SVM — both which act somewhat analogously as regularizers. Good for #teaching

Genic Intolerance to Functional Variation & the Interpretation of Personal Genomes
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003709 Nice plot of the number of rare v common variants in each gene to find outliers particularly tolerant to impactful (eg #LOF) mutations

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003709

Petrovski et al ’13

Credit scores, cardiovascular disease risk & human capital
http://www.PNAS.org/content/111/48/17087 Non-obvious correlations creating potential #privacy risks

http://science.sciencemag.org/content/359/6376/693.full
+
perspective
http://science.sciencemag.org/content/359/6376/619.full

Gene Expression Overlaps Among Psychiatric Disorders

Transcriptional profiling of post-mortem human brains reveals commonalities in the genes over- and under-expressed in schizophrenia, bipolar disorder, autism, and major depression.

https://www.nature.com/articles/ng.3861?WT.ec_id=NG-201706&spMailingID=54145295&spUserID=MTc2NTYxNjY4OQS2&spJobID=1164335784&spReportId=MTE2NDMzNTc4NAS2

3D clusters of somatic mutations…reveal numerous rare mutations as functional targets
https://GenomeMedicine.BiomedCentral.com/articles/10.1186/s13073-016-0393-x Introduces 3DHotSpots, which is one of a number of recent approaches (incl. CLUMPS, Hotspot3D, Mutation3D & HotMAPS) for finding groupings of somatic SNVs via structure

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in #eQTL Studies http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000770 Early discussion & development of PEER factors