Bioinformatics
Effortless Genomic Analysis
The OhmX platform is powered by an advanced informatics pipeline that supports both human whole genome variant discovery and variant verification analysis. Using onboard, real-time processing and powerful cloud computing, sample data is acquired and analyzed with just a few clicks and results are available the next day.
Detection & Signal Processing
The OhmX platform creates whole genome maps by detecting sequence-specific tags, incorporated onto long DNA molecules. Electronic detection of tagged DNA molecules occurs as single DNA molecules pass through each of the nanochannels within the OhmX detector. Real-time signal processing tabulates the location of tags on each molecule and generates molecule records that include molecule length in milliseconds, location of tags in milliseconds, and other molecule and tag attributes that are used to assess the quality of reads.
Secondary Analysis
Whole genome variant discovery analysis is performed by Human Chromosome Explorer™ (HCE). HCE is an advanced, cloud-based, whole-genome map assembly and structural variation (SV) analysis software for the OhmX platform. Developed by Hitachi High-Tech in collaboration with Nabsys, HCE uses Google Cloud Platform™. This High-Performance Computing infrastructure creates haplotype-aware, human whole-genome map assemblies and performs SV analysis with results visualized and reported through a web browser.
OhmX signal processed, calibrated, and filtered single molecule reads are de novo assembled by HCE into map contigs containing all labeled locations within the sample and are then aligned against a reference genome map. Shifts in the loci of the labels are indicative of shifts in the genome that serve as the basis for SV analysis.
HCE has several visualization and reporting tools to navigate through SV analysis results.
Security
Along with data encryption, Google Cloud Platform provides a cloud infrastructure with robust built-in compliance and security features applied to the physical datacenter, and the network. Hitachi has further built upon this infrastructure to create a secure platform for genomic data called the HCE Security Framework. Click here to learn more about HCE security.
Variant Verification
Directed variant verification analysis is a hypothesis-based method to test for known SV types. This workflow is based on trained support vector machine (SVM) models to estimate the posterior probability of putative SVs.
First, a set of constructs representing the putative SVs is created. The constructs are assessed for uniqueness to ensure that any construct does not align to a region of the reference or another construct and are appended to the base reference so that molecules may either map to the source or to constructs. OhmX signal processed, calibrated, and filtered single molecule reads are directly aligned to either the reference or to constructs. Post-alignment analysis makes the SV calls for reads that align to a construct.
Explore the EGM Pipeline
