Posts Tagged ‘sv’

Characterizing the Major Structural Variant Alleles of the Human Genome: Cell

November 10, 2019

https://www.cell.com/cell/fulltext/S0092-8674(18)31633-7

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

April 1, 2017

Mechanisms underlying #SV formation in…disorders
http://www.Nature.com/nrg/journal/v17/n4/abs/nrg.2015.25.html 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

Characterization of structural variants with single molecule and hybrid sequencing approaches

May 16, 2015

Characterization of #SVs w. single molecule & hybrid sequencing http://bioinformatics.oxfordjournals.org/content/30/24/3458.abstract Probabilistic read mapping, re-evaluating adjacencies

QT:{{"
We present MultiBreak-SV, an algorithm to detect structural variants
(SVs) from single molecule sequencing data, paired read sequencing
data, or a combination of sequencing data from different platforms.
"}}

remills / SVelter — Bitbucket

May 4, 2015

https://bitbucket.org/remills/svelter

predict bkpts & assess

Genome Biology | Full text | An integrative probabilistic model for identification of structural variation in sequencing data

May 4, 2015

QT:{{”
We introduce GASVPro, an algorithm combining both paired read and read depth signals into a probabilistic model that can analyze multiple alignments of reads.
“}}

http://genomebiology.com/2012/13/3/R22

Characterization of structural variants with single molecule and hybrid sequencing approaches

May 4, 2015

QT:{{”
We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. “}}

uses pacbio

http://bioinformatics.oxfordjournals.org/content/30/24/3458.long

Criteria for Inference of Chromothripsis in Cancer Genomes — ScienceDirect

October 13, 2014

@markgerstein: Korbel mentions: Criteria for Inference of
Chromothripsis in Cancer Genome
http://t.co/TslcrZsmNv #BTGCG14

http://www.sciencedirect.com/science/article/pii/S0092867413002122

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

August 11, 2014

Transduction of nonrepetitive DNA mediated by L1 retrotransposition in #cancer #genomes
http://www.sciencemag.org/content/345/6196/1251343.abs associated w/ hypomethylation

Jose M. C. Tubio1,
Yilong Li1,*,
Young Seok Ju1,*,
Inigo Martincorena1,
Susanna L. Cooke1,

Adrienne M. Flanagan30,31,
P. Andrew Futreal1,32,
Sam M. Janes3,
G. Steven Bova12,
Michael R. Stratton1,
Ultan McDermott1,
Peter J. Campbell1,10,33,‡

QT:{{”
Retrotransposons are DNA repeat sequences that are constantly on the move. By poaching certain cellular enzymes, they copy and insert themselves at new sites in the genome. Sometimes they carry along adjacent DNA sequences, a process called 3′ transduction. Tubio et al. found that 3′ transduction is a common event in human tumors. Because this process can scatter genes and regulatory sequences across the genome, it may represent yet another mechanism by which tumor cells acquire new mutations that help them survive and grow.
“}}

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.

May 20, 2014

Hypomethylation in the human germline associates w/ structural mutability: Many #SVs in #genomic #methylation deserts
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002692

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002692

Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A.

PLoS Genet. 2012;8(5):e1002692. doi: 10.1371/journal.pgen.1002692. Epub 2012 May 17.
PMID: 22615578 [PubMed – indexed for MEDLINE] Free PMC Article

Mutability as a measure of methylation, viz:
QT:{{
The MI model is based on the fact that in mammals DNA methylation predominantly occurs in CpG dinucleotides, increasing the probability of transitions to TpG or CpA dinucleotides. The MI calculation by Sigurdsson et al. [48] implicitly uses mutability of CpGs in the human genome as an indicator of methylation in the germline. We apply this method of by integrating four million non-redundant SNPs from the HapMap project. Methylation index values were calculated for the same set of 100 Kbp windows used for sperm methylome construction to facilitate comparison.
}}

Also :

Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003333

Harris RA, Shaw C, Li J, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A.

PLoS Genet. 2013;9(2):e1003333. doi: 10.1371/journal.pgen.1003333. Epub 2013 Feb 28. No abstract available.
PMID: 23468659 [PubMed – indexed for MEDLINE] Free PMC Article

A Polymerase Theta-dependent repair pathway suppresses extensive genomic instability at endogenous G4 DNA sites : Nature Communications : Nature Publishing Group

May 11, 2014

http://www.nature.com/ncomms/2014/140205/ncomms4216/full/ncomms4216.html Mentioned as a mechanism for “occasional presence of templated insertions.”