Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase cha...

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Main Authors: Boeva, Valentina, Popova, Tatiana, Lienard, Maxime, Toffoli, Sebastien, Kamal, Maud, Le Tourneau, Christophe, Gentien, David, Servant, Nicolas, Gestraud, Pierre, Rio Frio, Thomas, Hupé, Philippe, Barillot, Emmanuel, Laes, Jean-François
Format: Online
Language:English
Published: Oxford University Press 2014
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253825/
id pubmed-4253825
recordtype oai_dc
spelling pubmed-42538252014-12-04 Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data Boeva, Valentina Popova, Tatiana Lienard, Maxime Toffoli, Sebastien Kamal, Maud Le Tourneau, Christophe Gentien, David Servant, Nicolas Gestraud, Pierre Rio Frio, Thomas Hupé, Philippe Barillot, Emmanuel Laes, Jean-François Hitseq Papers Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing. Oxford University Press 2014-12-15 2014-07-12 /pmc/articles/PMC4253825/ /pubmed/25016581 http://dx.doi.org/10.1093/bioinformatics/btu436 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Boeva, Valentina
Popova, Tatiana
Lienard, Maxime
Toffoli, Sebastien
Kamal, Maud
Le Tourneau, Christophe
Gentien, David
Servant, Nicolas
Gestraud, Pierre
Rio Frio, Thomas
Hupé, Philippe
Barillot, Emmanuel
Laes, Jean-François
spellingShingle Boeva, Valentina
Popova, Tatiana
Lienard, Maxime
Toffoli, Sebastien
Kamal, Maud
Le Tourneau, Christophe
Gentien, David
Servant, Nicolas
Gestraud, Pierre
Rio Frio, Thomas
Hupé, Philippe
Barillot, Emmanuel
Laes, Jean-François
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
author_facet Boeva, Valentina
Popova, Tatiana
Lienard, Maxime
Toffoli, Sebastien
Kamal, Maud
Le Tourneau, Christophe
Gentien, David
Servant, Nicolas
Gestraud, Pierre
Rio Frio, Thomas
Hupé, Philippe
Barillot, Emmanuel
Laes, Jean-François
author_sort Boeva, Valentina
title Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
title_short Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
title_full Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
title_fullStr Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
title_full_unstemmed Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
title_sort multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
description Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing.
publisher Oxford University Press
publishDate 2014
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253825/
_version_ 1613163487854329856

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