HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Next generation sequencing (NGS) of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels) that constitute a large part of known human mutations. W...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Lőrinc S Pongor, Ferenc Pintér, István Peták
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4254b9985fbd4005a6b0db7fce1d59ee
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:4254b9985fbd4005a6b0db7fce1d59ee
record_format	dspace
spelling	oai:doaj.org-article:4254b9985fbd4005a6b0db7fce1d59ee2021-11-18T08:00:52ZHeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.1932-620310.1371/journal.pone.0054294https://doaj.org/article/4254b9985fbd4005a6b0db7fce1d59ee2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23349847/?tool=EBIhttps://doaj.org/toc/1932-6203Next generation sequencing (NGS) of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels) that constitute a large part of known human mutations. We have developed HeurAA, an open source, heuristic amplicon aligner program. We tested the program on simulated datasets as well as experimental data from multiplex sequencing of 40 amplicons in 12 oncogenes collected on a 454 Genome Sequencer from lung cancer cell lines. We found that HeurAA can accurately detect all indels, and is more than an order of magnitude faster than previous programs. HeurAA can compare reads and reference sequences up to several thousand base pairs in length, and it can evaluate data from complex mixtures containing reads of different gene-segments from different samples. HeurAA is written in C and Perl for Linux operating systems, the code and the documentation are available for research applications at http://sourceforge.net/projects/heuraa/Lőrinc S PongorFerenc PintérIstván PetákPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e54294 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lőrinc S Pongor Ferenc Pintér István Peták HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
description	Next generation sequencing (NGS) of PCR amplicons is a standard approach to detect genetic variations in personalized medicine such as cancer diagnostics. Computer programs used in the NGS community often miss insertions and deletions (indels) that constitute a large part of known human mutations. We have developed HeurAA, an open source, heuristic amplicon aligner program. We tested the program on simulated datasets as well as experimental data from multiplex sequencing of 40 amplicons in 12 oncogenes collected on a 454 Genome Sequencer from lung cancer cell lines. We found that HeurAA can accurately detect all indels, and is more than an order of magnitude faster than previous programs. HeurAA can compare reads and reference sequences up to several thousand base pairs in length, and it can evaluate data from complex mixtures containing reads of different gene-segments from different samples. HeurAA is written in C and Perl for Linux operating systems, the code and the documentation are available for research applications at http://sourceforge.net/projects/heuraa/
format	article
author	Lőrinc S Pongor Ferenc Pintér István Peták
author_facet	Lőrinc S Pongor Ferenc Pintér István Peták
author_sort	Lőrinc S Pongor
title	HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
title_short	HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
title_full	HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
title_fullStr	HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
title_full_unstemmed	HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
title_sort	heuraa: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/4254b9985fbd4005a6b0db7fce1d59ee
work_keys_str_mv	AT lorincspongor heuraaaccurateandfastdetectionofgeneticvariationswithanovelheuristicampliconalignerprogramfornextgenerationsequencing AT ferencpinter heuraaaccurateandfastdetectionofgeneticvariationswithanovelheuristicampliconalignerprogramfornextgenerationsequencing AT istvanpetak heuraaaccurateandfastdetectionofgeneticvariationswithanovelheuristicampliconalignerprogramfornextgenerationsequencing
_version_	1718422659519217664

HeurAA: accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Ejemplares similares