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Goals and objectives for pipeline enhancements.

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Bibliographic Details
Title: Goals and objectives for pipeline enhancements.
Authors: Cu Nguyen, Trinh Nguyen, Gloria Trivitt, Brian Capaldo, Chunhua Yan, Qingrong Chen, Nicholas Renzette, Umit Topaloglu, Daoud Meerzaman
Publication Year: 2025
Subject Terms: Genetics, Molecular Biology, Evolutionary Biology, Developmental Biology, Cancer, Virology, Biological Sciences not elsewhere classified, national cancer institute, improve cancer immunotherapy, confidence biomarker detection, cancer immune monitoring, evolving bioinformatics standards, google cloud platform, cidc &# 8217, based bioinformatics pipelines, bioinformatics workflows, based technologies, %22">xlink ">, work establishes, variant calling, transcript quantification, source tools, scalable framework, omic analyses, network aims, nci ), leveraging open, gcp ), efficient deployment
Description: Background The Cancer Immune Monitoring and Analysis Centers – Cancer Immunologic Data Center (CIMAC-CIDC) network aims to improve cancer immunotherapy by providing harmonized molecular assays and standardized bioinformatics analysis. Results In response to evolving bioinformatics standards and the migration of the CIDC to the National Cancer Institute (NCI), we undertook the enhancement of the CIDC’s extant whole exome sequencing (WES) and RNA sequencing (RNA-Seq) pipelines. Leveraging open-source tools and cloud-based technologies, we implemented modular workflows using Snakemake and Docker for efficient deployment on the Google Cloud Platform (GCP). Benchmarking analyses demonstrate improved reproducibility, precision, and recall across validated truth sets for variant calling, transcript quantification, and fusion detection. Conclusion This work establishes a scalable framework for harmonized multi-omic analyses, ensuring the continuity and reliability of bioinformatics workflows in multi-site clinical research aimed at advancing cancer biomarker discovery and personalized medicine.
Document Type: dataset
Language: unknown
Relation: https://figshare.com/articles/dataset/Goals_and_objectives_for_pipeline_enhancements_/29990832
DOI: 10.1371/journal.pone.0330827.t001
Availability: https://doi.org/10.1371/journal.pone.0330827.t001
https://figshare.com/articles/dataset/Goals_and_objectives_for_pipeline_enhancements_/29990832
Rights: CC BY 4.0
Accession Number: edsbas.B76B4672
Database: BASE
Description
Abstract:Background The Cancer Immune Monitoring and Analysis Centers – Cancer Immunologic Data Center (CIMAC-CIDC) network aims to improve cancer immunotherapy by providing harmonized molecular assays and standardized bioinformatics analysis. Results In response to evolving bioinformatics standards and the migration of the CIDC to the National Cancer Institute (NCI), we undertook the enhancement of the CIDC’s extant whole exome sequencing (WES) and RNA sequencing (RNA-Seq) pipelines. Leveraging open-source tools and cloud-based technologies, we implemented modular workflows using Snakemake and Docker for efficient deployment on the Google Cloud Platform (GCP). Benchmarking analyses demonstrate improved reproducibility, precision, and recall across validated truth sets for variant calling, transcript quantification, and fusion detection. Conclusion This work establishes a scalable framework for harmonized multi-omic analyses, ensuring the continuity and reliability of bioinformatics workflows in multi-site clinical research aimed at advancing cancer biomarker discovery and personalized medicine.
DOI:10.1371/journal.pone.0330827.t001