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BreakDancer: An algorithm for high resolution mapping of genomic structural variation
TLDR
The algorithm BreakDancer predicts a wide variety of structural variants including insertion-deletions (indels), inversions and translocations and sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach.
Recurring mutations found by sequencing an acute myeloid leukemia genome.
TLDR
By comparing the sequences of tumor and skin genomes of a patient with AML-M1, recurring mutations that may be relevant for pathogenesis are identified.
Segmental duplications and copy-number variation in the human genome.
TLDR
This study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements.
DNA sequencing of a cytogenetically normal acute myeloid leukemia genome
TLDR
This study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.
Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome.
TLDR
A combination of BAC-based and high-density customized oligonucleotide arrays were used to resolve the molecular basis of structural rearrangements and underscore the need for complete maps of genetic variation in duplication-rich regions of the genome.
Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content
TLDR
It is suggested that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, ‘genetic hitchhiking’ effects in the absence of meiotic crossing over, frequent ectopic recombination within theMSY, and species differences in mating behaviour.
Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft
TLDR
The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within thePrimary tumour.
Comparative and demographic analysis of orangutan genomes
TLDR
The orang-utan species, Pongo abelii and Pongo pygmaeus, are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution and a primate polymorphic neocentromere, found in both Pongo species are described.
Genome analysis of the platypus reveals unique signatures of evolution
TLDR
This corrects the article to show that the method used to derive the H2O2 “spatially aggregating force” is based on a two-step process, not a single step, like in the previous version of this paper.
Identification of four highly conserved genes between breakpoint hotspots BP1 and BP2 of the Prader-Willi/Angelman syndromes deletion region that have undergone evolutionary transposition mediated by
TLDR
Two known and two novel genes are identified in this region in human and their orthologs in mouse chromosome 7C, supporting a model in which duplications of the HERC2 gene at BP3 in primates first flanked the four-gene cassette, with subsequent transposition of these four unique genes by a Herc2 duplicon-mediated process to form the BP1-BP2 region.
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