CandrisDB


33876217	CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model. [PMID: 33876217] Wenyi Zhao, Jingwen Yang, Jingcheng Wu, Guoxing Cai, Yao Zhang, Jeffrey Haltom, Weijia Su, Michael J Dong, Shuqing Chen, Jian Wu, Zhan Zhou, Xun Gu Abstract Current cancer genomics databases have accumulated millions of somatic mutations that remain to be further explored. Due to the over-excess mutations unrelated to cancer, the great challenge is to identify somatic mutations that are cancer-driven. Under the notion that carcinogenesis is a form of somatic-cell evolution, we developed a two-component mixture model: while the ground component corresponds to passenger mutations, the rapidly evolving component corresponds to driver mutations. Then, we implemented an empirical Bayesian procedure to calculate the posterior probability of a site being cancer-driven. Based on these, we developed a software CanDriS (Cancer Driver Sites) to profile the potential cancer-driving sites for thousands of tumor samples from the Cancer Genome Atlas and International Cancer Genome Consortium across tumor types and pan-cancer level. As a result, we identified that approximately 1% of the sites have posterior probabilities larger than 0.90 and listed potential cancer-wide and cancer-specific driver mutations. By comprehensively profiling all potential cancer-driving sites, CanDriS greatly enhances our ability to refine our knowledge of the genetic basis of cancer and might guide clinical medication in the upcoming era of precision medicine. The results were displayed in a database CandrisDB (http://biopharm.zju.edu.cn/candrisdb/). Brief Bioinform. 2021:22(5) \| 3 Citations (from Europe PMC, 2025-04-12)
28938601	Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. [PMID: 28938601] Zhou Z, Zou Y, Liu G, Zhou J, Wu J, Zhao S, Su Z, Gu X. Abstract Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels. Both the relaxation of purifying selection on passenger mutations and the positive selection of driver mutations may contribute to the increased CN /CS values of human genes in cancer genomes compared with the pN /pS values in human populations. The CN /CS values also contribute to the improved classification of cancer genes and a better understanding of the onco-functionalization of cancer genes during oncogenesis. The use of our computational pipeline to identify cancer-specific positively and negatively selected genes may provide useful information for understanding the evolution of cancers and identifying possible targets for therapeutic intervention. Oncotarget. 2017:8(35) \| 6 Citations (from Europe PMC, 2025-04-12)

CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model. [PMID: 33876217]

Wenyi Zhao, Jingwen Yang, Jingcheng Wu, Guoxing Cai, Yao Zhang, Jeffrey Haltom, Weijia Su, Michael J Dong, Shuqing Chen, Jian Wu, Zhan Zhou, Xun Gu

Abstract

Current cancer genomics databases have accumulated millions of somatic mutations that remain to be further explored. Due to the over-excess mutations unrelated to cancer, the great challenge is to identify somatic mutations that are cancer-driven. Under the notion that carcinogenesis is a form of somatic-cell evolution, we developed a two-component mixture model: while the ground component corresponds to passenger mutations, the rapidly evolving component corresponds to driver mutations. Then, we implemented an empirical Bayesian procedure to calculate the posterior probability of a site being cancer-driven. Based on these, we developed a software CanDriS (Cancer Driver Sites) to profile the potential cancer-driving sites for thousands of tumor samples from the Cancer Genome Atlas and International Cancer Genome Consortium across tumor types and pan-cancer level. As a result, we identified that approximately 1% of the sites have posterior probabilities larger than 0.90 and listed potential cancer-wide and cancer-specific driver mutations. By comprehensively profiling all potential cancer-driving sites, CanDriS greatly enhances our ability to refine our knowledge of the genetic basis of cancer and might guide clinical medication in the upcoming era of precision medicine. The results were displayed in a database CandrisDB (http://biopharm.zju.edu.cn/candrisdb/).

Brief Bioinform. 2021:22(5) | 3 Citations (from Europe PMC, 2025-04-12)

Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. [PMID: 28938601]

Zhou Z, Zou Y, Liu G, Zhou J, Wu J, Zhao S, Su Z, Gu X.

Abstract

Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels. Both the relaxation of purifying selection on passenger mutations and the positive selection of driver mutations may contribute to the increased CN /CS values of human genes in cancer genomes compared with the pN /pS values in human populations. The CN /CS values also contribute to the improved classification of cancer genes and a better understanding of the onco-functionalization of cancer genes during oncogenesis. The use of our computational pipeline to identify cancer-specific positively and negatively selected genes may provide useful information for understanding the evolution of cancers and identifying possible targets for therapeutic intervention.

Oncotarget. 2017:8(35) | 6 Citations (from Europe PMC, 2025-04-12)

URL:	http://biopharm.zju.edu.cn/candrisdb/
Full name:	Cancer Driver Site Profiling DataBase
Description:	CandrisDB collects somatic mutation data from TCGA PanCanAtlas project, and provides Pan-cancer dirver gene and driver mutation site profiling by using two in-house methods(CNCS calculator, CanDriS) and ten other driver gene prediction methods. CandrisDB also collects data from other public databases on functional and pharmacogenomics annotation for the driver mutation sites, and provides guidance on clinical medication in the upcoming era of Precision Medicine.
Year founded:	2017
Last update:
Version:	V1.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA Protein
Data object:	Animal
Database category:	Genotype phenotype and variation Health and medicine
Major species:	Homo sapiens
Keywords:	somatic mutations cancer drivers

University/Institution:	Zhejiang University
Address:
City:	Hangzhou
Province/State:	Zhejiang
Country/Region:	China
Contact name (PI/Team):	Zhan Zhou
Contact email (PI/Helpdesk):	zhanzhou@zju.edu.cn

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Database Commons a catalog of worldwide biological databases