AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal

Jérôme Ambroise; Anne Sophie Piette; Cathy Delcorps; Leen Rigouts; Bouke C. De Jong; Leonid Irenge; Annie Robert; Jean Luc Gala

doi:10.1093/bioinformatics/btt339

AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal

Jérôme Ambroise, Anne Sophie Piette, Cathy Delcorps, Leen Rigouts, Bouke C. De Jong, Leonid Irenge, Annie Robert, Jean Luc Gala

DLD Bio

Research output: Contribution to journal › Article › peer-review

Abstract

Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).Availability: AdvISER-PYRO is implemented in an R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.Contact: or [email protected]

Original language	English
Pages (from-to)	1963-1969
Number of pages	7
Journal	Bioinformatics
Volume	29
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/btt339
Publication status	Published - 15 Aug 2013

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@article{96dfae44e2704ae3b2d80369ca0f42c6,

title = "AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal",

abstract = "Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2\% versus 56.5\%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5\%).Availability: AdvISER-PYRO is implemented in an R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.Contact: or [email protected]",

author = "J{\'e}r{\^o}me Ambroise and Piette, \{Anne Sophie\} and Cathy Delcorps and Leen Rigouts and \{De Jong\}, \{Bouke C.\} and Leonid Irenge and Annie Robert and Gala, \{Jean Luc\}",

note = "Funding Information: Funding: This work was supported by the Defence Laboratories Department of the Belgian Armed Forces.",

year = "2013",

month = aug,

day = "15",

doi = "10.1093/bioinformatics/btt339",

language = "English",

volume = "29",

pages = "1963--1969",

journal = "Bioinformatics",

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TY - JOUR

T1 - AdvISER-PYRO

T2 - Amplicon Identification using SparsE Representation of PYROsequencing signal

AU - Ambroise, Jérôme

AU - Piette, Anne Sophie

AU - Delcorps, Cathy

AU - Rigouts, Leen

AU - De Jong, Bouke C.

AU - Irenge, Leonid

AU - Robert, Annie

AU - Gala, Jean Luc

N1 - Funding Information: Funding: This work was supported by the Defence Laboratories Department of the Belgian Armed Forces.

PY - 2013/8/15

Y1 - 2013/8/15

N2 - Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).Availability: AdvISER-PYRO is implemented in an R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.Contact: or [email protected]

AB - Motivation: Converting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.Results: In the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%).Availability: AdvISER-PYRO is implemented in an R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.Contact: or [email protected]

UR - https://www.scopus.com/pages/publications/84880981589

U2 - 10.1093/bioinformatics/btt339

DO - 10.1093/bioinformatics/btt339

M3 - Article

C2 - 23772051

AN - SCOPUS:84880981589

SN - 1367-4803

VL - 29

SP - 1963

EP - 1969

JO - Bioinformatics

JF - Bioinformatics

IS - 16

ER -

AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal

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