Structural Variant Breakpoint Detection with novoBreak

2018 ◽  
pp. 129-141 ◽  
Author(s):  
Zechen Chong ◽  
Ken Chen
Keyword(s):  
Structural Variant ◽  
Breakpoint Detection

Abstract 4285: Structural variant breakpoint detection in advanced colorectal cancer

2014 ◽  
Author(s):  
E van den Broek ◽  
O Krijgsman ◽  
D Sie ◽  
JC Haan ◽  
M Komor ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Advanced Colorectal Cancer ◽  
Structural Variant ◽  
Breakpoint Detection

Diversity of Glycoprotein Deficiencies in Glanzmann’s Thrombasthenia

1985 ◽  
Vol 54 (03) ◽  
pp. 626-629 ◽  
Author(s):  
M Meyer ◽  
F H Herrmann
Keyword(s):  
High Resolution ◽  
Gel Electrophoresis ◽  
Type Ii ◽  
Two Dimensional ◽  
Two Dimensional Gel Electrophoresis ◽  
Structural Variant ◽  
Glanzmann’S Thrombasthenia ◽  
Crossed Immunoelectrophoresis ◽  
Glanzmann's Thrombasthenia ◽  
Platelet Proteins

SummaryThe platelet proteins of 9 thrombasthenic patients from 7 families were analysed by high resolution two-dimensional gel electrophoresis (HR-2DE) and crossed immunoelectrophoresis (CIE). In 7 patients both glycoproteins (GPs) IIb and Ilia were absent or reduced to roughly the same extent. In two related patients only a trace of GP Ilb-IIIa complex was detected in CIE, but HR-2DE revealed a glycopeptide in the position of GP Ilia in an amount comparable to type II thrombasthenia. This GP Ilia-like component was neither recognized normally by anti-GP Ilb-IIIa antibodies nor labeled by surface iodination. In unreduced-reduced two-dimensional gel electrophoresis two components were observed in the region of GP Ilia. The assumption of a structural variant of GP Ilia in the two related patients is discussed.

scholarly journals A naturally occurring structural variant of human growth hormone.

1978 ◽  
Vol 253 (8) ◽  
pp. 2679-2687 ◽  
Author(s):  
U.J. Lewis ◽  
J.T. Dunn ◽  
L.F. Bonewald ◽  
B.K. Seavey ◽  
W.P. Vanderlaan
Keyword(s):  
Growth Hormone ◽  
Human Growth Hormone ◽  
Human Growth ◽  
Structural Variant ◽  
Naturally Occurring

scholarly journals A spontaneous mutation produced a novel elongated beta-globin chain structural variant (Hb Agnana) with a thalassemia-like phenotype [letter]

Blood ◽  
1990 ◽  
Vol 75 (6) ◽  
pp. 1378-1379 ◽  
Author(s):  
MS Ristaldi ◽  
M Pirastu ◽  
S Murru ◽  
L Casula ◽  
G Loudianos ◽  
...  
Keyword(s):  
Spontaneous Mutation ◽  
Beta Globin ◽  
Globin Chain ◽  
Structural Variant

Breakpoints and breakpoint detection in source-level emulation

1998 ◽  
Vol 3 (2) ◽  
pp. 209-230 ◽  
Author(s):  
Gernot H. Koch ◽  
W. Rosenstiel ◽  
U. Kebschull
Keyword(s):  
Breakpoint Detection ◽  
Source Level

scholarly journals Mutation of a single residue in the ba3 oxidase specifically impairs protonation of the pump site

2015 ◽  
Vol 112 (11) ◽  
pp. 3397-3402 ◽  
Author(s):  
Christoph von Ballmoos ◽  
Nathalie Gonska ◽  
Peter Lachmann ◽  
Robert B. Gennis ◽  
Pia Ädelroth ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Time Constant ◽  
Thermus Thermophilus ◽  
Proton Translocation ◽  
Proton Pumping ◽  
Wild Type ◽  
Structural Variant ◽  
In The Wild ◽  
Membrane Bound ◽  
Proton Uptake

The ba3-type cytochrome c oxidase from Thermus thermophilus is a membrane-bound protein complex that couples electron transfer to O2 to proton translocation across the membrane. To elucidate the mechanism of the redox-driven proton pumping, we investigated the kinetics of electron and proton transfer in a structural variant of the ba3 oxidase where a putative “pump site” was modified by replacement of Asp372 by Ile. In this structural variant, proton pumping was uncoupled from internal electron transfer and O2 reduction. The results from our studies show that proton uptake to the pump site (time constant ∼65 μs in the wild-type cytochrome c oxidase) was impaired in the Asp372Ile variant. Furthermore, a reaction step that in the wild-type cytochrome c oxidase is linked to simultaneous proton uptake and release with a time constant of ∼1.2 ms was slowed to ∼8.4 ms, and in Asp372Ile was only associated with proton uptake to the catalytic site. These data identify reaction steps that are associated with protonation and deprotonation of the pump site, and point to the area around Asp372 as the location of this site in the ba3 cytochrome c oxidase.

A Comparison of Whole Genome Mate Pair Sequencing (MPseq) with Karyotype and FISH for Breakpoint Detection in Hematologic Cancers

2016 ◽  
Vol 209 (6) ◽  
pp. 290
Author(s):  
Sarah H. Johnson ◽  
Stephanie A. Smoley ◽  
Hutton M. Kearney ◽  
William R. Sukov ◽  
Robert B. Jenkins ◽  
...  
Keyword(s):  
Whole Genome ◽  
Mate Pair ◽  
Breakpoint Detection

scholarly journals Viola: a structural variant signature extractor with user-defined classifications

2021 ◽  
Author(s):  
Itsuki Sugita ◽  
Shohei Matsuyama ◽  
Hiroki Dobashi ◽  
Daisuke Komura ◽  
Shumpei Ishikawa
Keyword(s):  
Large Scale ◽  
Computational Time ◽  
Structural Variant ◽  
Analytical Functions ◽  
Dna Variations ◽  
Python Package

Here, we present Viola, a Python package that provides structural variant (SV; large scale genome DNA variations that can result in disease, e.g., cancer) signature analytical functions and utilities for custom SV classification, merging multi-SV-caller output files, and SV annotation. We demonstrate that Viola can extract biologically meaningful SV signatures from publicly available SV data for cancer and we evaluate the computational time necessary for annotation of the data.

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