Genowis Launches iGenomeCloud 2.0: An AI-Powered Enterprise Platform for Tumor Immunogenomic Big Data Analysis

On December 8, 2018, Genome Wisdom Inc., a precision medicine big data company, unveiled its latest-generation big data product—“iGenomeCloud 2.0”: an AI-driven, enterprise-grade big data analytics platform for tumor immunogenomics—at the 2018 Global Precision Medicine Summit.

With the domestic launch of the oncology immune checkpoint inhibitors Keytruda and Opdivo this year, the cancer genetic testing industry is facing challenges in big genomic data analysis and a new round of industry reshuffling. Dr. Ling Shaoping, CEO and Chief Scientist of Genome Wisdom Inc., stated during the afternoon’s roundtable discussion on third-party in vitro diagnostics: “In response to these challenges, genetic testing institutions need to build capabilities for immuno-therapy data analysis and for interpreting medication recommendation reports, specifically requiringQuantitative Analysis of Immunogenomic Metrics, Construction of a Baseline Database for Immunotherapy Benefit, Development of an Immunology Knowledge Base, and Logic for Report Interpretation“By establishing end-to-end capabilities across four key domains, institutions that take the lead in building such competencies will undoubtedly gain a first-mover advantage in the next round of industry reshuffling.”

At the launch event of the “Smart Gene Cloud,” Dr. Ling began by providing an accessible yet comprehensive overview of various genomic biomarkers associated with tumor immunotherapy, such as tumor mutational burden (TMB), microsatellite instability (MSI), neoantigens, and gene mutations related to immunotherapy efficacy. He particularly highlighted that TMB was included in October as a recommended genetic testing indicator for immunotherapy in the NCCN Guidelines. He pointed out that the current quantitative immunogenomic metric, TMB, suffers from methodological diversity and a lack of standardized criteria; therefore, harmonization of this metric is a necessary step toward its integration into clinical decision-making. Major international pharmaceutical companies are collaborating with genetic testing institutions and big data firms on this initiative (Friends of Cancer Research – TMB Harmonization Project).

In China, Genome Wisdom Inc. is actively advancing the “Tumor Mutational Burden GVC Harmonization Project.” Leveraging its proprietary intelligent gene cloud platform, the company has completed TMB standardization for whole-exome sequencing (WES) data across 20 cancer types with immunotherapy applications from the International Cancer Genome Consortium (ICGC). Currently, Genome Wisdom Inc. is collecting relevant clinical trial data to establish a Chinese patient-specific baseline standard for TMB in tumor immunotherapy.

GVC-Normalized Tumor Mutation Burden Project

Unlike international TMB normalization initiatives, Genome Wisdom Inc. focuses not only on investigator-led clinical trial data but also actively promotes real-world studies. To this end, Genome Wisdom is establishing the China Precision Oncology Big Data Platform and Collaborative Network—Anti-Cancer Moonshot (www.0cancer.cn). This platform provides services for project posting and collaboration, patient recruitment, and data management and analysis to support real-world studies of immunotherapy in China.

Dr. Ling introduced that Smart Gene Cloud completed the full standardization process for 6,063 whole-exome sequencing (WES) datasets—from raw sequences (~300 TB) to variant detection, and calculation of tumor mutational burden (TMB) and other immunogenomic metrics—within one month. This achievement primarily relies on GVC, a next-generation AI-based algorithm for tumor variant detection independently developed by Genome Wisdom Inc. The GVC algorithm previously won an award in the ICGC-TCGA International Cancer Analysis Challenge. Currently, it surpasses other open-source algorithms in both sensitivity and specificity, and its actual computational results (TMB-GVC) align more closely with the ICGC-published TMB-MC3 benchmark than any other algorithm. Furthermore, the computational efficiency of the GVC algorithm is 30 to 128 times higher than that of conventional algorithms (http://gvc.0cancer.cn).

Currently, the GVC algorithm is freely available to researchers via the Cancer Moonshot website. By submitting normal and tumor whole-exome sequencing (WES) data (in BAM format) to the platform (http://gvc.0ancer.cn), researchers can use the online version of GVC to calculate tumor mutational burden (TMB) in real time. The resulting TMB values can be compared against TMB-GVC baselines across 20 cancer types from the International Cancer Genome Consortium (ICGC). This addresses a key limitation of current single-software TMB calculations, which cannot be directly compared with the ICGC’s TMB-MC3 baseline.

Dr. Ling stated that, in addition to completing the cross-cancer TMB standardization work for the ICGC, Genome Wisdom Inc. is also leveraging its Intelligent Gene Cloud to analyze genomic data from all publicly published immunotherapy clinical trials, thereby recalculating various immunotherapy-related genomic biomarkers. By integrating efficacy data from these clinical trials, the Intelligent Gene Cloud can establish drug benefit baselines for immune biomarkers such as TMB and normalize different drug baselines, providing auxiliary support for clinical decision-making.

Finally, Dr. Ling provided a detailed introduction to the features of the newly released Intelligent Gene Cloud (iGenome® Cloud Data Center Solutions (DCS)). This system offers a one-stop solution to address key challenges faced by testing institutions, including quantitative analysis of immune markers for Whole Exome Sequencing (WES), construction of baseline databases for immune markers, development of immune knowledge bases, and assisted interpretation logic in reporting.

This system features precision, real-time processing, low investment requirements, and accelerated translation of clinical research into practice. It enables clients to enhance their data quality control systems, upgrade immunoassay products and services, improve data analysis efficiency, and achieve end-to-end automated delivery from data to results—with minimal investment and in the shortest possible time. As Genome Wisdom Inc.’s first big-data production system designed specifically for oncology genetic testing companies, the Intelligent Gene Cloud System will deliver a novel experience in intra-enterprise collaboration, data analysis, and report delivery.

(The above is from Tencent Video, URL: https://v.qq.com/x/page/n0783rrigl1.html)

“Designing products based on Chinese genetic testing companies and aligning with users’ actual usage habits is a crucial prerequisite for our development of the Intelligent Gene Cloud,” mentioned Dr. Ling. “The Intelligent Gene Cloud system has established a comprehensive intelligent production quality control framework, capable of automatically performing a series of analytical tasks on Fastq files generated by sequencers, including sequence alignment, quality control, mutation detection, and annotation. Based on an immunology knowledge base and a standardized baseline database of immune indicators, the system automatically generates preliminary reports on immunotherapy and targeted therapy according to the derived variant list. These drafts are then reviewed by a professional medical team before the final report is issued.”

Meanwhile, to align with the actual backend production workflows and management needs of genetic testing companies, Genome Wisdom Inc. retains the flexibility for customized redevelopment for its clients. According to reports, multiple modules—including IT hardware configuration, initialization of AI models for variant detection, iterative refinement of AI models for variant detection, LIMS interfaces, advanced quality control alerts, task management and scheduling, report generation workflows, and data analysis management systems—can all be customized according to client requirements to expand functionality and computational throughput.

Genome Wisdom Inc. is a precision medicine big data company that masters multimodal artificial intelligence technology, dedicated to providing advanced precision medicine big data solutions to medical institutions by leveraging artificial intelligence and bioinformatics technologies.