Fast, scalable prediction of deleterious #noncoding variants from functional & population genomic data
https://www.Nature.com/articles/ng.3810 LINSIGHT, by @ASiepel et al., combines DNAse & conservation information
Yi-Fei Huang, Brad Gulko & Adam Siepel
Nature Genetics 49, 618–624 (2017)
doi:10.1038/ng.3810
Published online:
13 March 2017
.@Genome_Gov Extramural Grant Portfolio
https://www.Genome.Gov/27569006/july-6-2017-the-nhgri-extramural-grant-portfolio-using-different-approaches-to-fund-genomics-research Nice grid divides programs into PI-initiated/consortia & RFA-solicited v not
Zhou, J. and Troyanskaya, O.G. (2015). Predicting effects of noncoding variants with deep learning–based sequence model. Nature Methods, 12, 931–934.
Predicting (& prioritizing) effects of noncoding variants w. [DeepSEA] #DeepLearning…model
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data
FissionNet: Proteome-wide [pombe] Interactome Reveals #Network Evolution Principles
http://www.Cell.com/cell/abstract/S0092-8674(15)01556-1 Involving ~1300 soluble proteins
Identification of…expr.-Modulating Variants using #MPRA, by @sabeti_lab http://www.cell.com/cell/fulltext/S0092-8674(16)30421-4 Some w. allelic skew related to PWM change
Massively parallel quantification of…regulatory effects of #noncoding…variation in a…cohort
http://genome.cshlp.org/content/25/8/1206.long new popstarr assay
http://www.ncbi.nlm.nih.gov/pubmed/26084464
Genome Res. 2015 Aug;25(8):1206-14. doi: 10.1101/gr.190090.115. Epub 2015 Jun 17.
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.
Vockley CM1, Guo C2, Majoros WH3, Nodzenski M4, Scholtens DM4, Hayes MG5, Lowe WL Jr5, Reddy TE6.
The Race to Clone #BRCA1 http://www.sciencemag.org/content/343/6178/1462.abstract
Lessons on #LOF mutations, synthetic lethality, silly gene names & the 2-hit hypothesis
synthetic lethality (PARP inhibitors), gene names (RING fingers)
From noncoding variant to phenotype…at…#cholesterol locus http://www.nature.com/nature/journal/v466/n7307/full/nature09266.html
Gold standard ex of #SNP functional effect: LDL changes
Kiran Musunuru,
Alanna Strong,
Maria Frank-Kamenetsky,
et al.
Nature 466, 714–719 (05 August 2010) doi:10.1038/nature09266
Changes LDL level
linkstream2 microblog 