Patent
Identifying rearrangements in a sequenced genome
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TLDR
In this article, the authors present methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence.Abstract:
Methods, apparatuses, and systems for identification of junctions (e.g., resulting from large-scale rearrangements) of a sequenced genome with respect to a human genome reference sequence is provided. For example, false positives can be distinguished from actual junctions. Such false positives can result from many sources, including mismapping, chimeric reactions among the DNA of a sample, and problems with the reference genome. As part of the filtering processes, a base pair resolution (or near base pair resolution) of a junction can be provided. In various implementations, junctions can be identified using discordant mate pairs and/or using a statistical analysis of the length distributions of fragments for local regions of the sample genome. Clinically significant junctions can also be identified so that further analysis can be focused on genomic regions that may have more of an impact on the health of a patient.read more
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References
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Journal ArticleDOI
Paired-end mapping reveals extensive structural variation in the human genome.
Jan O. Korbel,Alexander E. Urban,Jason P. Affourtit,Brian C. Godwin,Fabian Grubert,Jan Fredrik Simons,Philip M. Kim,Dean Palejev,Nicholas Carriero,Lei Du,Bruce E. Taillon,Zhoutao Chen,Andrea Tanzer,A. C. Eugenia Saunders,Jianxiang Chi,Fengtang Yang,Nigel P. Carter,Matthew E. Hurles,Sherman M. Weissman,Timothy T. Harkins,Mark Gerstein,Michael Egholm,Michael Snyder +22 more
TL;DR: High-throughput and massive paired-end mapping (PEM) was used to map SVs in an African and in a putatively European individual and identified shared and divergent SVs relative to the reference genome, documenting that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function.
Journal ArticleDOI
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
Peter J. Campbell,Philip J. Stephens,Erin Pleasance,Sarah O’Meara,Heng Li,Thomas Santarius,Thomas Santarius,Lucy Stebbings,Catherine Leroy,Sarah Edkins,Claire Hardy,Jon W. Teague,Andrew Menzies,Ian Goodhead,Daniel J. Turner,C M Clee,Michael A. Quail,Antony V. Cox,Clive Gavin Brown,Richard Durbin,Matthew E. Hurles,Paul A.W. Edwards,Graham R. Bignell,Michael R. Stratton,P. Andrew Futreal +24 more
TL;DR: The results demonstrate the feasibility of systematic, genome-wide characterization of rearrangements in complex human cancer genomes, raising the prospect of a new harvest of genes associated with cancer using this strategy.
Journal ArticleDOI
Computational methods for discovering structural variation with next-generation sequencing
TL;DR: A new generation of methods are being developed to tackle the challenges of short reads, while taking advantage of the high coverage the new sequencing technologies provide.
Journal ArticleDOI
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
TL;DR: Paired-end tag (PET) sequencing for various applications, collectively called the PET sequencing strategy, in which short and paired tags are extracted from the ends of long DNA fragments for ultra-high-throughput sequencing, has a bright future ahead.
Journal ArticleDOI
Chimeric transcript discovery by paired-end transcriptome sequencing
Christopher G. Maher,Nallasivam Palanisamy,J.C. Brenner,Xuhong Cao,Shanker Kalyana-Sundaram,Shujun Luo,Irina Khrebtukova,Terrence R. Barrette,Catherine S. Grasso,Jindan Yu,Robert J. Lonigro,Gary P. Schroth,Chandan Kumar-Sinha,Arul M. Chinnaiyan +13 more
TL;DR: A sensitive, high-throughput methodology to comprehensively catalog functional gene fusions in cancer by evaluating a paired-end transcriptome sequencing strategy is established and is successfully used to detect previously undescribed ETS gene fusion in prostate tumors.