http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html
Genome seq–independent Identification of #RNAediting http://www.Nature.com/nmeth/journal/v12/n4/full/nmeth.3314.html Accurate sites from uncorrelated SNV pair, spanned by reads
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.
“}}
Set of 5.4M phased…variants…from seq. a 3-gen. 17-member [CEPH] pedigree, centered on #NA12878
http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116 $ILMN Pt genomes
A reference data set of 5.4 million phased human
variants validated by genetic inheritance from
sequencing a three-generation 17-member pedigree
Michael A. Eberle,1 Epameinondas Fritzilas,2 Peter Krusche,2 Morten Källberg,2 Benjamin L. Moore,2 Mitchell A. Bekritsky,2 Zamin Iqbal,3 Han-Yu Chuang,1 Sean J. Humphray,2 Aaron L. Halpern,1 Semyon Kruglyak,1 Elliott H. Margulies,1 Gil McVean,3,4 and David R. Bentley2
http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116
Assembling a new picture of humanity by @CarlZimmer
https://www.statnews.com/2016/10/07/dna-genome-sequencing-new-maps/ 1 graph to represent everyone, counterpoint to #personalgenomes
#IHECpapers rollout http://www.Cell.com/consortium/ihec Gr8 work! incl. #privacy, normal breast epigenetics, ETG links, deconvolution, #allelic activity
Allele-specific TF binding in liver & cervix cells [HepG2 & HeLa] unveils many likely drivers of GWAS [SNP] signals
http://www.sciencedirect.com/science/article/pii/S0888754316300271
GERV: stats method for generative evaluation of regulatory variants
for TF binding http://bioinformatics.oxfordjournals.org/content/early/2015/11/05/bioinformatics.btv565 Predicts effect of #allelic SNPs
GERV: a statistical method for generative evaluation of regulatory ariants for transcription factor binding
> Haoyang Zeng
> Tatsunori Hashimoto
> Daniel D. Kang
> David K. Gifford
Splicing is a prim. link betw…variation & disease by @JKPritch, @Y_Gilad &co http://science.sciencemag.org/content/352/6285/600.long many chrom-QTLs effect protein levels
http://science.sciencemag.org/content/352/6285/600.long
Yang I. Li1,
Bryce van de Geijn2,
Anil Raj1,
David A. Knowles3,4,
Allegra A. Petti5,
David Golan1,
Yoav Gilad2,*,
Jonathan K. Pritchard1,6,7,*
http://bioinformatics.oxfordjournals.org/content/early/2015/11/05/bioinformatics.btv565
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding
Haoyang Zeng
Tatsunori Hashimoto
Daniel D. Kang
David K. Gifford