https://www.nature.com/articles/s41586-020-2371-0
think allele frequencies are publicly available
Posts Tagged ‘sv’
Mapping and characterization of structural variation in 17,795 human genomes
May 28, 2020Mechanisms underlying structural variant formation in genomic disorders : Nature Reviews Genetics : Nature Publishing Group
April 1, 2017Mechanisms 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, 2015Characterization 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, 2015https://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, 2015QT:{{”
We introduce GASVPro, an algorithm combining both paired read and read depth signals into a probabilistic model that can analyze multiple alignments of reads.
“}}
Characterization of structural variants with single molecule and hybrid sequencing approaches
May 4, 2015QT:{{”
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, 2014Transduction 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, 2014Hypomethylation 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
linkstream2 microblog 