MH Guide CAS
Variant annotation and
reporting solution

MH Guide Case Annotation Solution (CAS) is a software as a service (SaaS) for research labs to annotate next-generation sequencing (NGS) data or genetic and molecular alteration data from a tumor specimen with published therapy associations, biomarkers, and recruiting clinical trials. MH Guide CAS is designed to be easy to use and intuitive for rapid onboarding. As a hosted SaaS software product, accessible from anywhere through your web browser and equipped with the latest IT security standards, you can quickly start using MH Guide CAS without the burden of purchasing server hardware or other IT resources.

MH Guide CAS requires data in Variant Call Format (VCF) from analysis pipelines. MH Guide CAS is NGS panel and secondary analysis pipeline agnostic. MH provides adaptation tools to generate compatible VCF input from popular secondary analysis products such as Archer Analysis, Illumina Dragen, and Thermo Fisher Ion Reporter. Automatically generated reports can be extended and refined to include results from non-NGS methods (e.g. FISH, IHC, (q)PCR). The software generates well-designed, customizable report templates in PDF and JSON formats.

You can upload cases via:

• MH Order Portal CAS (GUI) for low case volumes,
• MH VCF Adapter Suite (GUI or command line) for medium case volumes, or
• MH Connector (GUI or command line + APIs) for medium-to-high case volumes. MH Connector is the option designed for full automation, enabling automated data submission and results retrieval with well-documented APIs. Find the MH Connector Flyer here.

Yes. MH Connector supports multi-modal biomarkers, e.g., gene/protein expression, methylation, and gene wild-type status, in one unified workflow.

Based on data derived from our exclusive, up-to-date, and quality-controlled MH Guide CAS knowledge base, information for interpreting clinically relevant variants is compiled in the context of each tumor specimen and presented to you in standardized Curated Variant Information (CVI) narratives (concept of MH CVI scores published in M. Winter et al. 2026, Biomedicines 14(1):157).

The comprehensive presentation of all information in the CVIs dramatically reduces and streamlines the time required to interpret identified variants. The CVIs include details on the identified variants and their unique descriptions, specifying the type of biomarker (predictive, diagnostic, prognostic), source citations, a clinical evaluation of the biomarkers based on internationally accepted actionability tiering systems, and the approval status of the associated treatment options. An undisputed strength of MH Guide CAS is its ability to provide region-specific content matching based on the institute’s location, e.g., drug approvals according to FDA, or EMA, as well as location-based clinical trial matching, including distance calculations to help minimize inconveniences. MH Guide CAS users will also benefit from automated pre-classification of variant pathogenicity (ACMG/AMP) and variant oncogenicity (ClinGen/CGC/VICC) according to current recommendations.

All content coming from external databases (public and commercial) is transparently labeled and traceable. Typical external databases used for annotation in MH Guide are various gene and protein models (e.g. Ensemble, RefSeq, UniProt), variant frequency databases (gnomAD, cancerhotspots.org, COSMIC, FLOSSIES, ToMMo), DNA variation databases (ClinVar, dbSNP, BRCA Exchange), selected computational prediction scores such as MaxEntScan, dbNSFP (REVEL, MetaLR, MetaSVM, and many more), and dbscSNV, as well as selected scores for computational prediction of phylogenetic conservation (GERP, PhastCons, PhyloP), and a variety of drug approval and drug information sources, medical ontologies, and practice guidelines.

The MH knowledge base is updated on a monthly basis to ensure that professionals have access to up-to-date information.

Security and privacy are highly prioritized and embedded throughout the MH Guide CAS system design process. MH uses data centers and hosting providers that are certified to international security standards, including Trusted Site Infrastructure (TSI) and/or ISO 27001. Molecular Health is committed to complying with regional and global security guidelines to ensure seamless implementation of software services for MH Guide CAS customers. In addition, MH Guide CAS complies with data residency and privacy requirements to meet local data privacy and data security requirements. The product also meets all data sovereignty requirements, allowing customers to maintain control over their confidential data, which is transmitted using advanced encryption standards (SSL/TLS, AES-256).

MH Guide CAS supports customers operating in regulated environments and complies with current data protection laws, including GDPR (General Data Protection Regulation), HIPAA (Health Insurance Portability and Accountability Act), and the German Genetic Diagnostics Act (GenDG). MH Guide CAS supports full pseudonymization of data. Molecular Health processes sensitive data in accordance with applicable regulations and employs industry best practices.

MH Guide CAS, our advanced NGS tertiary analysis software, is designed to meet the highest standards for data residency, cybersecurity, and health data hosting, both at the national and regional levels.

Your data will be securely processed and hosted in region-specific data centers operated by certified providers. All data centers and hosting providers meet international security standards, such as Trusted Site Infrastructure (TSI) and/or ISO 27001 certification.

For customers in the United States, MH Guide CAS – our Research Use Only (RUO) version of MH Guide (CE-IVD) – is hosted on AWS, an ISO 27001-certified provider that complies with modern security and healthcare data requirements: aws.amazon.com/security.

Both MH Guide CAS and AWS are certified under the Texas Risk and Authorization Management Program (TX-RAMP), ensuring full compliance with Texas state-level cybersecurity and data handling requirements.

Service Providers

Source Code Genomics, LLC

Source Code Genomics is an experienced partner with extensive expertise in integrating genomic and genetic analysis tools and data into IT infrastructures. The company offers:

• Over 10 years of experience integrating MH Guide into various IT environments
• Over 5 years of in-depth experience with IDT/Archer NGS assays and their bioinformatics platform
• Customized genomic data integration and workflow management for NGS, microarrays, cytogenetics, mass spectrometry, and more
• Development and management of automated workflows
• Over 30 years of comprehensive bioinformatics support in genomics and genetics
• Consulting and assistance with CAP inspections, assay validations, Z-code submissions, and more

Rely on Source Code Genomics expertise to ensure secure, efficient, and compliant implementation of your genetic analysis solutions!

Get in contact with Anthony Caruso (apcaruso@sourcecodegenomics.com)

Other integration providers: ELLKAY, Zifo RnD Solutions

Request a free demo here.