Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Research › peer-review
Consideration of pathogenicity of nsSNVs in CDKN2A gene, as a new tumor marker for leukemia, using bioinformatics methods. / Ghasemi, Farzaneh; Heidari, Mohammad Mehdi; Orlov, Yuriy L. et al.
Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020. Institute of Electrical and Electronics Engineers Inc., 2020. p. 85-87 9214605 (Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Research › peer-review
}
TY - GEN
T1 - Consideration of pathogenicity of nsSNVs in CDKN2A gene, as a new tumor marker for leukemia, using bioinformatics methods
AU - Ghasemi, Farzaneh
AU - Heidari, Mohammad Mehdi
AU - Orlov, Yuriy L.
AU - Khatami, Mehri
AU - Tabikhanova, Ludmila E.
PY - 2020/7
Y1 - 2020/7
N2 - CDKN2A as a tumor suppressor gene (TSG) encodes p14 and p16 that they are tumor suppressor proteins and cell cycle regulators. Downregulation of these proteins causes various cancers. Sequence deletions or promoter hypermethylation lead to downregulation of these proteins. Also, point mutations can be caused malfunction or dysfunction of proteins. The aim of this study is definition of pathogenicity of non-synonymous single nucleotide variants (nsSNVs). We study three nsSNVs including rs104894095, rs786204195 and rs104894098 from NCBI/dbSNP databank. Then, these nsSNVs are considered by bioinformatics tools such as SIFT, PolyPhen-2, I-Mutant2.0, PANTHER, P-Mut, ExPASy/ProtScale, PEPTIDE 2.0 web server and PyMOL software. Plot of hydrophobicity of rs104894098 (V126D) is significantly changed. Also, we study hydrogen bonds length and atom distances in Aspartic acid substituted Valine in position 126 by PyMOL software. These parameters are compared with wild type protein. Finally, we find that rs786204195 and rs104894095 have destructive effects. But, rs104894098 (V126D) is deleterious because polar contacts, protein stability and hydrophobicity are changed in mutant form. This theory should be proved with experimental studies.
AB - CDKN2A as a tumor suppressor gene (TSG) encodes p14 and p16 that they are tumor suppressor proteins and cell cycle regulators. Downregulation of these proteins causes various cancers. Sequence deletions or promoter hypermethylation lead to downregulation of these proteins. Also, point mutations can be caused malfunction or dysfunction of proteins. The aim of this study is definition of pathogenicity of non-synonymous single nucleotide variants (nsSNVs). We study three nsSNVs including rs104894095, rs786204195 and rs104894098 from NCBI/dbSNP databank. Then, these nsSNVs are considered by bioinformatics tools such as SIFT, PolyPhen-2, I-Mutant2.0, PANTHER, P-Mut, ExPASy/ProtScale, PEPTIDE 2.0 web server and PyMOL software. Plot of hydrophobicity of rs104894098 (V126D) is significantly changed. Also, we study hydrogen bonds length and atom distances in Aspartic acid substituted Valine in position 126 by PyMOL software. These parameters are compared with wild type protein. Finally, we find that rs786204195 and rs104894095 have destructive effects. But, rs104894098 (V126D) is deleterious because polar contacts, protein stability and hydrophobicity are changed in mutant form. This theory should be proved with experimental studies.
KW - bioinformatics
KW - cancer
KW - CDKN2A
KW - genes
KW - PyMOL
KW - structural bioinformatics tools
UR - http://www.scopus.com/inward/record.url?scp=85094809918&partnerID=8YFLogxK
UR - https://elibrary.ru/item.asp?id=45182266
U2 - 10.1109/CSGB51356.2020.9214605
DO - 10.1109/CSGB51356.2020.9214605
M3 - Conference contribution
AN - SCOPUS:85094809918
T3 - Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
SP - 85
EP - 87
BT - Proceedings - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 2020 Cognitive Sciences, Genomics and Bioinformatics, CSGB 2020
Y2 - 6 July 2020 through 10 July 2020
ER -
ID: 25841199