Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database
Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Mohammad Uzzal Hossain [verfasserIn] Ishtiaque Ahammad [verfasserIn] Md. Moniruzzaman [verfasserIn] Mahbuba Akter Lubna [verfasserIn] Arittra Bhattacharjee [verfasserIn] Zeshan Mahmud Chowdhury [verfasserIn] Istiak Ahmed [verfasserIn] Md. Billal Hosen [verfasserIn] Shourov Biswas [verfasserIn] Keshob Chandra Das [verfasserIn] Chaman Ara Keya [verfasserIn] Md. Salimullah [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2023 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
In: Cancer Reports - Wiley, 2021, 6(2023), 12, Seite n/a-n/a |
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| Übergeordnetes Werk: |
volume:6 ; year:2023 ; number:12 ; pages:n/a-n/a |
| Links: |
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| DOI / URN: |
10.1002/cnr2.1906 |
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| Katalog-ID: |
DOAJ096395249 |
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| 100 | 0 | |a Mohammad Uzzal Hossain |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database |
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| 520 | |a Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. | ||
| 650 | 4 | |a bioinformatics | |
| 650 | 4 | |a database | |
| 650 | 4 | |a GasCanBase | |
| 650 | 4 | |a gastric cancer | |
| 650 | 4 | |a polymorphism | |
| 650 | 4 | |a SNP | |
| 653 | 0 | |a Neoplasms. Tumors. Oncology. Including cancer and carcinogens | |
| 700 | 0 | |a Ishtiaque Ahammad |e verfasserin |4 aut | |
| 700 | 0 | |a Md. Moniruzzaman |e verfasserin |4 aut | |
| 700 | 0 | |a Mahbuba Akter Lubna |e verfasserin |4 aut | |
| 700 | 0 | |a Arittra Bhattacharjee |e verfasserin |4 aut | |
| 700 | 0 | |a Zeshan Mahmud Chowdhury |e verfasserin |4 aut | |
| 700 | 0 | |a Istiak Ahmed |e verfasserin |4 aut | |
| 700 | 0 | |a Md. Billal Hosen |e verfasserin |4 aut | |
| 700 | 0 | |a Shourov Biswas |e verfasserin |4 aut | |
| 700 | 0 | |a Keshob Chandra Das |e verfasserin |4 aut | |
| 700 | 0 | |a Chaman Ara Keya |e verfasserin |4 aut | |
| 700 | 0 | |a Md. Salimullah |e verfasserin |4 aut | |
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| 773 | 1 | 8 | |g volume:6 |g year:2023 |g number:12 |g pages:n/a-n/a |
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10.1002/cnr2.1906 doi (DE-627)DOAJ096395249 (DE-599)DOAJ71b510e2b7c540b1af7e0c69582aee48 DE-627 ger DE-627 rakwb eng RC254-282 Mohammad Uzzal Hossain verfasserin aut Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. bioinformatics database GasCanBase gastric cancer polymorphism SNP Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ishtiaque Ahammad verfasserin aut Md. Moniruzzaman verfasserin aut Mahbuba Akter Lubna verfasserin aut Arittra Bhattacharjee verfasserin aut Zeshan Mahmud Chowdhury verfasserin aut Istiak Ahmed verfasserin aut Md. Billal Hosen verfasserin aut Shourov Biswas verfasserin aut Keshob Chandra Das verfasserin aut Chaman Ara Keya verfasserin aut Md. Salimullah verfasserin aut In Cancer Reports Wiley, 2021 6(2023), 12, Seite n/a-n/a (DE-627)1014116775 (DE-600)2920367-3 25738348 nnns volume:6 year:2023 number:12 pages:n/a-n/a https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/article/71b510e2b7c540b1af7e0c69582aee48 kostenfrei https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/toc/2573-8348 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_266 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2023 12 n/a-n/a |
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10.1002/cnr2.1906 doi (DE-627)DOAJ096395249 (DE-599)DOAJ71b510e2b7c540b1af7e0c69582aee48 DE-627 ger DE-627 rakwb eng RC254-282 Mohammad Uzzal Hossain verfasserin aut Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. bioinformatics database GasCanBase gastric cancer polymorphism SNP Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ishtiaque Ahammad verfasserin aut Md. Moniruzzaman verfasserin aut Mahbuba Akter Lubna verfasserin aut Arittra Bhattacharjee verfasserin aut Zeshan Mahmud Chowdhury verfasserin aut Istiak Ahmed verfasserin aut Md. Billal Hosen verfasserin aut Shourov Biswas verfasserin aut Keshob Chandra Das verfasserin aut Chaman Ara Keya verfasserin aut Md. Salimullah verfasserin aut In Cancer Reports Wiley, 2021 6(2023), 12, Seite n/a-n/a (DE-627)1014116775 (DE-600)2920367-3 25738348 nnns volume:6 year:2023 number:12 pages:n/a-n/a https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/article/71b510e2b7c540b1af7e0c69582aee48 kostenfrei https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/toc/2573-8348 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_266 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2023 12 n/a-n/a |
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10.1002/cnr2.1906 doi (DE-627)DOAJ096395249 (DE-599)DOAJ71b510e2b7c540b1af7e0c69582aee48 DE-627 ger DE-627 rakwb eng RC254-282 Mohammad Uzzal Hossain verfasserin aut Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. bioinformatics database GasCanBase gastric cancer polymorphism SNP Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ishtiaque Ahammad verfasserin aut Md. Moniruzzaman verfasserin aut Mahbuba Akter Lubna verfasserin aut Arittra Bhattacharjee verfasserin aut Zeshan Mahmud Chowdhury verfasserin aut Istiak Ahmed verfasserin aut Md. Billal Hosen verfasserin aut Shourov Biswas verfasserin aut Keshob Chandra Das verfasserin aut Chaman Ara Keya verfasserin aut Md. Salimullah verfasserin aut In Cancer Reports Wiley, 2021 6(2023), 12, Seite n/a-n/a (DE-627)1014116775 (DE-600)2920367-3 25738348 nnns volume:6 year:2023 number:12 pages:n/a-n/a https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/article/71b510e2b7c540b1af7e0c69582aee48 kostenfrei https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/toc/2573-8348 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_266 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2023 12 n/a-n/a |
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10.1002/cnr2.1906 doi (DE-627)DOAJ096395249 (DE-599)DOAJ71b510e2b7c540b1af7e0c69582aee48 DE-627 ger DE-627 rakwb eng RC254-282 Mohammad Uzzal Hossain verfasserin aut Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. bioinformatics database GasCanBase gastric cancer polymorphism SNP Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ishtiaque Ahammad verfasserin aut Md. Moniruzzaman verfasserin aut Mahbuba Akter Lubna verfasserin aut Arittra Bhattacharjee verfasserin aut Zeshan Mahmud Chowdhury verfasserin aut Istiak Ahmed verfasserin aut Md. Billal Hosen verfasserin aut Shourov Biswas verfasserin aut Keshob Chandra Das verfasserin aut Chaman Ara Keya verfasserin aut Md. Salimullah verfasserin aut In Cancer Reports Wiley, 2021 6(2023), 12, Seite n/a-n/a (DE-627)1014116775 (DE-600)2920367-3 25738348 nnns volume:6 year:2023 number:12 pages:n/a-n/a https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/article/71b510e2b7c540b1af7e0c69582aee48 kostenfrei https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/toc/2573-8348 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_266 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2023 12 n/a-n/a |
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10.1002/cnr2.1906 doi (DE-627)DOAJ096395249 (DE-599)DOAJ71b510e2b7c540b1af7e0c69582aee48 DE-627 ger DE-627 rakwb eng RC254-282 Mohammad Uzzal Hossain verfasserin aut Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. bioinformatics database GasCanBase gastric cancer polymorphism SNP Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ishtiaque Ahammad verfasserin aut Md. Moniruzzaman verfasserin aut Mahbuba Akter Lubna verfasserin aut Arittra Bhattacharjee verfasserin aut Zeshan Mahmud Chowdhury verfasserin aut Istiak Ahmed verfasserin aut Md. Billal Hosen verfasserin aut Shourov Biswas verfasserin aut Keshob Chandra Das verfasserin aut Chaman Ara Keya verfasserin aut Md. Salimullah verfasserin aut In Cancer Reports Wiley, 2021 6(2023), 12, Seite n/a-n/a (DE-627)1014116775 (DE-600)2920367-3 25738348 nnns volume:6 year:2023 number:12 pages:n/a-n/a https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/article/71b510e2b7c540b1af7e0c69582aee48 kostenfrei https://doi.org/10.1002/cnr2.1906 kostenfrei https://doaj.org/toc/2573-8348 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_32 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_90 GBV_ILN_95 GBV_ILN_100 GBV_ILN_101 GBV_ILN_105 GBV_ILN_110 GBV_ILN_120 GBV_ILN_138 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_266 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2031 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2039 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2112 GBV_ILN_2113 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 6 2023 12 n/a-n/a |
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Mohammad Uzzal Hossain @@aut@@ Ishtiaque Ahammad @@aut@@ Md. Moniruzzaman @@aut@@ Mahbuba Akter Lubna @@aut@@ Arittra Bhattacharjee @@aut@@ Zeshan Mahmud Chowdhury @@aut@@ Istiak Ahmed @@aut@@ Md. Billal Hosen @@aut@@ Shourov Biswas @@aut@@ Keshob Chandra Das @@aut@@ Chaman Ara Keya @@aut@@ Md. Salimullah @@aut@@ |
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Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. 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Mohammad Uzzal Hossain |
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Mohammad Uzzal Hossain misc RC254-282 misc bioinformatics misc database misc GasCanBase misc gastric cancer misc polymorphism misc SNP misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database |
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RC254-282 Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database bioinformatics database GasCanBase gastric cancer polymorphism SNP |
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misc RC254-282 misc bioinformatics misc database misc GasCanBase misc gastric cancer misc polymorphism misc SNP misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens |
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misc RC254-282 misc bioinformatics misc database misc GasCanBase misc gastric cancer misc polymorphism misc SNP misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens |
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Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database |
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Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database |
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Mohammad Uzzal Hossain |
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Mohammad Uzzal Hossain Ishtiaque Ahammad Md. Moniruzzaman Mahbuba Akter Lubna Arittra Bhattacharjee Zeshan Mahmud Chowdhury Istiak Ahmed Md. Billal Hosen Shourov Biswas Keshob Chandra Das Chaman Ara Keya Md. Salimullah |
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investigation of pathogenic germline variants in gastric cancer and development of “gascanbase” database |
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Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database |
| abstract |
Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. |
| abstractGer |
Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. |
| abstract_unstemmed |
Abstract Background Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non‐synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression. Aim The aim of this study is to examine the nsSNP in GC‐associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC‐associated genes and their impacts. Methods and Results A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named “GasCanBase” was developed to make data available to researchers. Conclusion The findings of this study and the “GasCanBase” database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/. |
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| title_short |
Investigation of pathogenic germline variants in gastric cancer and development of “GasCanBase” database |
| url |
https://doi.org/10.1002/cnr2.1906 https://doaj.org/article/71b510e2b7c540b1af7e0c69582aee48 https://doaj.org/toc/2573-8348 |
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Ishtiaque Ahammad Md. Moniruzzaman Mahbuba Akter Lubna Arittra Bhattacharjee Zeshan Mahmud Chowdhury Istiak Ahmed Md. Billal Hosen Shourov Biswas Keshob Chandra Das Chaman Ara Keya Md. Salimullah |
| author2Str |
Ishtiaque Ahammad Md. Moniruzzaman Mahbuba Akter Lubna Arittra Bhattacharjee Zeshan Mahmud Chowdhury Istiak Ahmed Md. Billal Hosen Shourov Biswas Keshob Chandra Das Chaman Ara Keya Md. Salimullah |
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10.1002/cnr2.1906 |
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2024-07-03T19:56:35.096Z |
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| score |
7.3979836 |