Posts Tagged ‘SVs’

whole genome assembly from Hi-C data

April 2, 2017

De novo assembly of the A aegypti genome using #HiC, by @erezaterez et al Works on human too, w. promise for #SVs

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

Olga Dudchenko1,2,3,4,
Sanjit S. Batra1,2,3,*,
Arina D. Omer1,2,3,*,
Sarah K. Nyquist1,3,
Marie Hoeger1,3,
Neva C. Durand1,2,3,
Muhammad S. Shamim1,2,3,
Ido Machol1,2,3,
Eric S. Lander5,6,7,
Aviva Presser Aiden1,2,8,9,
Erez Lieberman Aiden1,2,3,4,5,†

Science 23 Mar 2017:
DOI: 10.1126/science.aal3327

on whole genome assembly from Hi-C reads. There is also some info on chromosomal rearrangement from Hi-C.

Mechanisms underlying structural variant formation in genomic disorders : Nature Reviews Genetics : Nature Publishing Group

April 1, 2017

Mechanisms underlying #SV formation in…disorders Highlights importance of repeats in creating genomic plasticity

Nat Rev Genet. 2016 Apr;17(4):224-38. doi: 10.1038/nrg.2015.25. Epub 2016 Feb 29.
Mechanisms underlying structural variant formation in genomic disorders. Carvalho CM, Lupski JR

Jclub paper

January 16, 2017

The impact of #SVs on…gene expression 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

BMC Genomics | Full text | PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

June 25, 2015

PacBio-LITS: a…targeted sequencing method for characterization of…disease-associated SVs Capture reagent+@PacBio