Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures

Joanna Zyla; Christophe Badie; Ghazi Alsbeih; Joanna Polanska

doi:10.1007/978-3-319-31744-1_12

Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures

Joanna Zyla^*
, Christophe Badie
, Ghazi Alsbeih
, Joanna Polanska

^*Corresponding author for this work

Radiation Effects

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Dysregulation of apoptosis is a key attribute of cancer, especially the one induced by p53 expression disruption. Radiotherapy, sometimes supported by chemotherapy and/or pre-surgery, is recommended in majority of cases, but despite of the very well defined treatment protocols and high quality irradiation procedure, the huge dispersion in response to the radiotherapy is observed among cancer patients. Patient radiosensitivity, according to up-to-date knowledge, is at least partially responsible for different reactions to ionising radiation. Here we concentrate on investigation of single nucleotide polymorphisms (SNP) which can possibly explain the radiation response phenomena. To reach this goal dependent and independent methods of p-value integrations are presented and compared. Both statistical and molecular function domains are used in comparison study. We propose a novel method of p-value integration which includes the control of gene expression trend and introduces the adaptive significance level. What is more the multigene approach is proposed in contrary to classical single gene investigation. As a result, set of statistically significant polymorphisms was obtained, among which some were identified as possible deleterious for KRAS signalling pathway.

Original language	English
Title of host publication	Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings
Editors	Francisco Ortuno, Ignacio Rojas
Publisher	Springer Verlag
Pages	125-134
Number of pages	10
ISBN (Print)	9783319317434
DOIs	https://doi.org/10.1007/978-3-319-31744-1_12
Publication status	Published - 2016
Event	4th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 - Granada, Spain Duration: 20 Apr 2016 → 22 Apr 2016

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	9656
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	4th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016
Country/Territory	Spain
City	Granada
Period	20/04/16 → 22/04/16

Bibliographical note

Publisher Copyright:
© Springer International Publishing Switzerland 2016.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

P-value integration
Radiosensitivity
Single nucleotide polymorphism

Access to Document

10.1007/978-3-319-31744-1_12

Cite this

Zyla, J., Badie, C., Alsbeih, G., & Polanska, J. (2016). Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures. In F. Ortuno, & I. Rojas (Eds.), Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings (pp. 125-134). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9656). Springer Verlag. https://doi.org/10.1007/978-3-319-31744-1_12

Zyla, Joanna ; Badie, Christophe ; Alsbeih, Ghazi et al. / Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures. Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings. editor / Francisco Ortuno ; Ignacio Rojas. Springer Verlag, 2016. pp. 125-134 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "Dysregulation of apoptosis is a key attribute of cancer, especially the one induced by p53 expression disruption. Radiotherapy, sometimes supported by chemotherapy and/or pre-surgery, is recommended in majority of cases, but despite of the very well defined treatment protocols and high quality irradiation procedure, the huge dispersion in response to the radiotherapy is observed among cancer patients. Patient radiosensitivity, according to up-to-date knowledge, is at least partially responsible for different reactions to ionising radiation. Here we concentrate on investigation of single nucleotide polymorphisms (SNP) which can possibly explain the radiation response phenomena. To reach this goal dependent and independent methods of p-value integrations are presented and compared. Both statistical and molecular function domains are used in comparison study. We propose a novel method of p-value integration which includes the control of gene expression trend and introduces the adaptive significance level. What is more the multigene approach is proposed in contrary to classical single gene investigation. As a result, set of statistically significant polymorphisms was obtained, among which some were identified as possible deleterious for KRAS signalling pathway.",

keywords = "P-value integration, Radiosensitivity, Single nucleotide polymorphism",

author = "Joanna Zyla and Christophe Badie and Ghazi Alsbeih and Joanna Polanska",

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year = "2016",

doi = "10.1007/978-3-319-31744-1\_12",

language = "English",

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Zyla, J, Badie, C, Alsbeih, G & Polanska, J 2016, Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures. in F Ortuno & I Rojas (eds), Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9656, Springer Verlag, pp. 125-134, 4th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016, Granada, Spain, 20/04/16. https://doi.org/10.1007/978-3-319-31744-1_12

Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures. / Zyla, Joanna; Badie, Christophe; Alsbeih, Ghazi et al.
Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings. ed. / Francisco Ortuno; Ignacio Rojas. Springer Verlag, 2016. p. 125-134 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9656).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures

AU - Zyla, Joanna

AU - Badie, Christophe

AU - Alsbeih, Ghazi

AU - Polanska, Joanna

N1 - Publisher Copyright: © Springer International Publishing Switzerland 2016.

PY - 2016

Y1 - 2016

N2 - Dysregulation of apoptosis is a key attribute of cancer, especially the one induced by p53 expression disruption. Radiotherapy, sometimes supported by chemotherapy and/or pre-surgery, is recommended in majority of cases, but despite of the very well defined treatment protocols and high quality irradiation procedure, the huge dispersion in response to the radiotherapy is observed among cancer patients. Patient radiosensitivity, according to up-to-date knowledge, is at least partially responsible for different reactions to ionising radiation. Here we concentrate on investigation of single nucleotide polymorphisms (SNP) which can possibly explain the radiation response phenomena. To reach this goal dependent and independent methods of p-value integrations are presented and compared. Both statistical and molecular function domains are used in comparison study. We propose a novel method of p-value integration which includes the control of gene expression trend and introduces the adaptive significance level. What is more the multigene approach is proposed in contrary to classical single gene investigation. As a result, set of statistically significant polymorphisms was obtained, among which some were identified as possible deleterious for KRAS signalling pathway.

AB - Dysregulation of apoptosis is a key attribute of cancer, especially the one induced by p53 expression disruption. Radiotherapy, sometimes supported by chemotherapy and/or pre-surgery, is recommended in majority of cases, but despite of the very well defined treatment protocols and high quality irradiation procedure, the huge dispersion in response to the radiotherapy is observed among cancer patients. Patient radiosensitivity, according to up-to-date knowledge, is at least partially responsible for different reactions to ionising radiation. Here we concentrate on investigation of single nucleotide polymorphisms (SNP) which can possibly explain the radiation response phenomena. To reach this goal dependent and independent methods of p-value integrations are presented and compared. Both statistical and molecular function domains are used in comparison study. We propose a novel method of p-value integration which includes the control of gene expression trend and introduces the adaptive significance level. What is more the multigene approach is proposed in contrary to classical single gene investigation. As a result, set of statistically significant polymorphisms was obtained, among which some were identified as possible deleterious for KRAS signalling pathway.

KW - P-value integration

KW - Radiosensitivity

KW - Single nucleotide polymorphism

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DO - 10.1007/978-3-319-31744-1_12

M3 - Conference contribution

AN - SCOPUS:84973904663

SN - 9783319317434

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 125

EP - 134

BT - Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings

A2 - Ortuno, Francisco

A2 - Rojas, Ignacio

PB - Springer Verlag

T2 - 4th International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016

Y2 - 20 April 2016 through 22 April 2016

ER -

Zyla J, Badie C, Alsbeih G, Polanska J. Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures. In Ortuno F, Rojas I, editors, Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings. Springer Verlag. 2016. p. 125-134. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-319-31744-1_12

Multigene p-value integration based on SNPs investigation for seeking radiosensitivity signatures

Abstract

Publication series

Conference

Bibliographical note

UN SDGs

Keywords

Access to Document

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