NGS and PCR Diagnostics Applications

01/ Curation

Dockerized PacBio Workflows

With the advent of long read sequencing solutions, such as Pacific Biosciences’ HiFi and Revio long read systems, many tools with varying dependencies, configurations and setups have been developed. Creating a workflow that harnesses these tools can lead to inconsistent environments, inefficiency in execution and fragmented outputs.

We recently created a unified Docker-based solution which streamlines tool execution, enabling consistent environments, parallel processing and simplified commands for efficient genomic analysis.

02/ Curation

Variant Curation and Reporting

Our Variant Curation and Reporting services are powered by experience gained over tens of thousands of reports and a proven track record of variant curation under ACMG (germline) and AMP (somatic) guidelines. We help major Dx companies create curated variant databases or provide reporting-ready variant content.

02/ Curation

Strand Iris

Strand Iris is an interpretation service to generate clinical reports from VCF or FASTQ files obtained from somatic NGS testing. Our oncology clinical reporting team uses an internal rules engine and associated technology, also named Strand Iris, for somatic reporting to generate reports. Strand Iris has the following features:

Effect prediction for variants in 520 genes
Therapy annotation with AMP tiers for ≈112 FDA-approved drugs and 748 targeted drugs
Identification of clinical trials from ≈68,000 clinical trials.

Strand Iris has been tried and tested in over 5,000 reports, and covers the numerous subtleties that come with the field.

02/ Curation

NGS Assay Validation (CAP/CLIA/CDx)

We have reliable expertise in establishing limits of detection, sensitivity, specificity, and reproducibility for various variant types in somatic, germline, and liquid biopsy settings. Our services include:

Generation of data using appropriately sourced control samples (from commercial sources as well as from our own internal library of samples)
Analysis of data generated by our customers to deliver analytical and clinical validation reports for CLIA, CAP and NY State certification

01/ Curation

Software Service Teams

Our software service teams help our customers streamline and automate their lab processes, including for ex.:

Deployment and scale-up of secondary analysis (fastq to variant calls)
Streamlining of tertiary analysis (variant calls to reports)
Ordering and report delivery (physician portals)
Supporting research infrastructure (e.g., EDC systems for clinical research, aggregate data pools for mining)

03/ Getting curious about our RWD solutions

Frequently Asked Questions

Our nearly automated Strand Iris software takes in VCF files and generates a clinical report with AMP-tiered clinical therapies within 2-3 minutes. See Strand Iris microsite for more information.

Strand’s team of Curation Scientists has manually compiled a comprehensive somatic variant knowledge base (KB) consisting of 520+ genes, 112 FDA-approved targeted drugs, and nearly 70K clinical trials. This KB undergoes regular reviews and updates, along with continuous monitoring of medical abstracts and conference literature. See Strand Iris microsite for more information.

Our nearly automated software, powered by a comprehensive and up-to-date KB and a robust variant/therapy classification rules engine, assists clinicians in generating concise reports without overwhelming them. See Strand Iris microsite for more information.

Our collaboration with Dr. Nishant Agarwal led to the development of a sensitive and cost-effective liquid biopsy panel for OCSCC detection. This also resulted in the spinoff company OrisDx, focused on molecular diagnostics using saliva biomarkers. See A Case Study on the Development of a Saliva-based Oral Cancer Assay for more information.

Strand built a custom NGS panel covering over 85% of OCSCC patients across cohorts, achieving 100% sensitivity and 99.97% specificity. The design focuses on clinically significant genes while keeping costs affordable. See A Case Study on the Development of a Saliva-based Oral Cancer Assay for more information.

The Provider Portal streamlines test ordering and result access by reducing delays and improving data accuracy through mandatory information checks and insurance eligibility verification. See A Case Study on Physician Portal and Electronic Data Capture Software for more information.

03/ CONNECT

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