Introduction to Sentieon

Sentieon Vision

01.Sentieon Vision

Sentieon is dedicated to solving the bottleneck of speed and accuracy in bioinformatics data analysis, through the deep optimization of algorithms and enterprise-level software engineering, to significantly improve the efficiency, accuracy and reliability of NGS data processing.

Sentieon provides software solutions to partners and research institutions in the fields of molecular diagnostics, drug discovery and development, clinical medicine, animal and plant genomics, etc. Sentieon is committed to advancing the development of genetic technology and realizing the vision of “Achieving Precision Data, Serving Precision Medicine”.

02.Bioinformatics Industry Pain Points

Currently, for secondary analysis of second-generation sequencing data (SNP/Indel variant detection), BWA + GATK, as a best-practice process, has been widely recognized by the industry after more than a decade of repeated validation with a large number of samples, and is widely acknowledged as the gold standard.

However, the BWA + GATK process has several significant problems:

Long runtime, low resource utilization, and high computational cost;
GATK's random downsampling in high sequencing depth regions significantly affects the sensitivity and accuracy of variant detection, especially in the case of low abundance (VAF) variants in tumors, and GATK causes inconsistency in the results when repeated runs are performed.

03.Sentieon Solutions

Sentieon introduces a complete software-only secondary analysis solution that covers the entire process from gene matching to mutation detection for both germline mutation detection and somatic mutation detection.

Sentieon software is faithful to the mathematical models of gold standards such as BWA, GATK, MuTect, MuTect2, Minimap2, etc., and improves the analysis efficiency by more than 10 times under the premise of ensuring that the results exactly match the gold standards.

04.Awards

Since Sentieon officially launched its software product in 2015, it has won first place or tied for first place in several international raw letter competitions:

• Bio-IT Innovative Practices Award.
• PrecisionFDA Truth Challenge.
• PrecisionFDA Consistency Challenge
• ICGC-TCGA Dream Mutation Calling Challenge.
• PrecisionFDA Hidden Treasures Warm-up.
• PrecisionFDA NCI-CPTAC Crowdsourced Multi-omics Sample Mislabeling Big Data Challenge.

software functionality

01.Highlights

Pure soft solution: can be efficiently and flexibly deployed on different computing environments. No special hardware is required, reducing operation and maintenance costs. Can support X86\ARM architecture processor at the same time.

Highlights

1.Accelerated analysis: 10x faster than original BWA/GATK process

2.No downsampling: no differences between batches, better for high depth and low abundance detection.

3.Accurate results: 99.7% consistency compared to BWA/GATK/Mutect2/Minimap2 process.

4.Cost Savings: Cost savings of up to 90%, dramatically improving the accuracy of shallow sequencing results.

5.Joint Calling: One-time joint call operation for 100,000 WGS samples, no need for large memory and no intermediate steps.

6.Enterprise-level service: Provide comprehensive customer support from trial to use and establish long-term partnership with customers.

02.functional module

Sentieon software is very flexible, you can use the complete process directly, or according to the specific needs of the relevant modules to replace the original module. Users can directly use the complete process, but also according to the specific needs of the relevant modules to replace the original process modules, Sentieon software input and output files in strict accordance with industry norms for the operation, the user can easily get started to reduce the learning time. Currently Sentieon software can provide customers with the use of the module and the specific functions please refer to the following table:

03.application scenario

As an alternative acceleration solution to the industry gold-standard BWA/GATK/Mutect2/STAR processes, Sentieon software is also suitable for basic research, translational medicine, clinical and other fields. Some of the applicable scenarios are listed below:

Industry Recognition

Sentieon software is widely certified and used by nearly 1,000 commercial companies and research organizations, including:

• Several large multinational pharmaceutical companies sequencing service providers and molecular diagnostic companies worldwide.
• Hospitals and medical research institutions: including the O'Brien Project led by 15 large hospitals and pharmaceutical companies in the U.S., Fudan University Pediatrics Hospital, Shanghai Jiaotong University Children's Hospital, Xiangya Hospital, and CUHK Cancer Medical Center.
• Governmental organizations: including the U.S. Food and Drug Administration (FDA), the China Food and Drug Administration (CFDA), the U.S. National Institutes of Health (NIH), and the U.S. National Cancer Institute (NCI).
• Universities and research institutes: including Harvard, Yale, Stanford, Cornell, Chinese Academy of Sciences, Union Medical College, Fudan University, Shanghai Jiaotong University, Sun Yat-sen University, Yunnan University, Chinese Academy of Agricultural Sciences, State Key Laboratory of Crop Genetic Improvement and so on.

So far, Sentieon software has run and processed more than 1430 PB of data, with millions of samples and more than 360 million kernel hours, and has been cited many times in journals with world-class impact factors, including NEJM, Cell, and Nature.