Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer

Wang, Yue; Mark, Kenneth M. K.; Ung, Matthew; Kettenbach, Arminja N.; Miller, Todd W.; Xu, Wei; Cheng, Wenqing; Xia, Tian; Cheng, Chao

doi:10.1186/s13073-016-0363-3

Cited by 3 publications

(4 citation statements)

References 55 publications

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“…A similar statistical framework has been applied to integrate cancer gene expression data with gene knockdown profiles with detailed description available from Wang et al . 30 . The calculated BRCA scores were highly consistent with each other using BRCA1 -, BRCA 2- and BRCA1 / 2 -based BRCAness profiles in all datasets we applied in our analyses (Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

“…The Mann-Whitney-Wilcoxon Test was applied to calculate the difference. The calculations of CVN burden and mutation burden were same with our previously study 30 .…”

Section: Methodsmentioning

confidence: 99%

“…BRCA1 , RAD51 and BRIT1 ) 29 . However, our previous study using this approach showed that the resulting gene expression profiles from these knockdown cell line were more likely to reflect the reduced proliferation of cells rather than HR deficiency 30 .…”

Section: Introductionmentioning

confidence: 98%

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Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer

Wang

Ung

Cantor

et al. 2017

Sci Rep

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BRCAness has important implications in the management and treatment of patients with breast and ovarian cancer. In this study, we propose a computational framework to measure the BRCAness of breast and ovarian tumor samples based on their gene expression profiles. We define a characteristic profile for BRCAness by comparing gene expression differences between BRCA1/2 mutant familial tumors and sporadic breast cancer tumors while adjusting for relevant clinical factors. With this BRCAness profile, our framework calculates sample-specific BRCA scores, which indicates homologous recombination (HR)-mediated DNA repair pathway activity of samples. We found that in sporadic breast cancer high BRCAness score is associated with aberrant copy number of HR genes rather than somatic mutation and other genomic features. Moreover, we observed significant correlations of BRCA score with genome instability and neoadjuvant chemotherapy. More importantly, BRCA score provides significant prognostic value in both breast and ovarian cancers after considering established clinical variables. In summary, the inferred BRCAness from our framework can be used as a robust biomarker for the prediction of prognosis and treatment response in breast and ovarian cancers.

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Section: Methodsmentioning

confidence: 99%

“…The Mann-Whitney-Wilcoxon Test was applied to calculate the difference. The calculations of CVN burden and mutation burden were same with our previously study 30 .…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer

Wang

Ung

Cantor

et al. 2017

Sci Rep

Self Cite

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“…A common scenario that demonstrates the need for robust authentication and authorization to cloud-based genomics data is joint analysis of public and private datasets. For instance, an active area of research in precision oncology is using omics data to statistically learn biomarker signatures to guide selection of therapies [11], [12], [13], [14] most likely to be effective for a particular tumor. In these studies, both private as well as public datasets such as The Cancer Genome Atlas (TCGA) require authorized access.…”

Section: A Motivating Applicationmentioning

confidence: 99%

Cloud Bursting Galaxy: Federated Identity and Access Management

Jalili

Afgan

Taylor

et al. 2018

Preprint

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Motivation: Large biomedical datasets, such as those from genomics and imaging, are increasingly being stored on commercial and institutional cloud computing platforms. This is because cloud-scale computing resources, from robust backup to high-speed data transfer to scalable compute and storage, are needed to make these large datasets usable. However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms. While there are open Web protocols for secure authentication and authorization, these protocols are not in wide use in bioinformatics and are difficult to use for even technologically sophisticated users. Results: We have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms. Our approach combines OpenID Connect and OAuth2, best-practice Web protocols for authentication and authorization, together with Galaxy (https://galaxyproject.org), a web-based computational workbench used by thousands of scientists across the world. With our enhanced version of Galaxy, users can access and analyze data distributed across multiple cloud computing providers without any special knowledge of access/authorization protocols. Our approach does not require users to share permanent credentials (e.g., username, password, API key), instead relying on automatically-generated temporary tokens that refresh as needed. Our approach is generalizable to most identity providers and cloud computing platforms. To the best of our knowledge, Galaxy is the only computational workbench where users can access biomedical datasets across multiple cloud computing platforms using best-practice Web security approaches and thereby minimize risks of unauthorized data access and credential use. Availability and Implementation: Freely available for academic and commercial use under the open-source Academic Free License

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Cloud bursting galaxy: federated identity and access management

et al. 2019

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Motivation Large biomedical datasets, such as those from genomics and imaging, are increasingly being stored on commercial and institutional cloud computing platforms. This is because cloud-scale computing resources, from robust backup to high-speed data transfer to scalable compute and storage, are needed to make these large datasets usable. However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms. While there are open Web protocols for secure authentication and authorization, these protocols are not in wide use in bioinformatics and are difficult to use for even technologically sophisticated users. Results We have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms. Our approach combines OpenID Connect and OAuth2, best-practice Web protocols for authentication and authorization, together with Galaxy (https://galaxyproject.org), a web-based computational workbench used by thousands of scientists across the world. With our enhanced version of Galaxy, users can access and analyze data distributed across multiple cloud computing providers without any special knowledge of access/authorization protocols. Our approach does not require users to share permanent credentials (e.g. username, password, API key), instead relying on automatically generated temporary tokens that refresh as needed. Our approach is generalizable to most identity providers and cloud computing platforms. To the best of our knowledge, Galaxy is the only computational workbench where users can access biomedical datasets across multiple cloud computing platforms using best-practice Web security approaches and thereby minimize risks of unauthorized data access and credential use. Availability and implementation Freely available for academic and commercial use under the open-source Academic Free License (https://opensource.org/licenses/AFL-3.0) from the following Github repositories: https://github.com/galaxyproject/galaxy and https://github.com/galaxyproject/cloudauthz.

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Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer

Cited by 3 publications

References 55 publications

Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer

Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer

Cloud Bursting Galaxy: Federated Identity and Access Management

Cloud bursting galaxy: federated identity and access management

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