Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumoursReportar como inadecuado




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Genome Biology

, 18:125

First Online: 27 June 2017Received: 09 December 2016Accepted: 08 June 2017

Abstract

Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches.

KeywordsHi-C Chromosome conformation capture Cancer Tumour Glioblastoma Anaplastic astrocytoma Chromosome rearrangement Copy number variation Abbreviations3CChromosome conformation capture

AAAnaplastic astrocytoma

bpBasepair

CGHComparative genomic hybridisation

CNVCopy number variation

DSBDouble strand breaks

FISHFluorescence in-situ hybridisation

GBGlioblastomas

kbKilobases

MbMegabase

mgMilligrams

NGSNext generation sequencing

sWGSShallow whole-genome sequencing

WGSWhole-genome sequencing

Electronic supplementary materialThe online version of this article doi:10.1186-s13059-017-1253-8 contains supplementary material, which is available to authorized users.

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Autor: Louise Harewood - Kamal Kishore - Matthew D. Eldridge - Steven Wingett - Danita Pearson - Stefan Schoenfelder - V. Peter 

Fuente: https://link.springer.com/



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