Derisking the Product Roadmap: How Nexco Analytics Delivered Proof-of-Concept Analyses for NGS-Based Tumor Profiling Company
Derisking the Product Roadmap: How Nexco Analytics Delivered Proof-of-Concept Analyses for NGS-Based Tumor Profiling Company
Developing algorithms to detect microsatellite instability (MSI) biomarkers in cell-free DNA (cfDNA)
"Nexco Analytics delivered high-impact, customized bioinformatics solutions with precision, speed, and scientific rigor."
Hedera DX, a leading Swiss NGS-based cancer diagnostics company, provides accurate and streamlined tumor profiling and cancer treatment monitoring for patients. Their technology and advanced algorithms enable hospital laboratories to run CE-IVDR-compliant and clinically actionable liquid biopsies in-house.
Hedera DX achieves this with their cell-free DNA (cfDNA) sequencing kits and advanced bioinformatic pipelines for measuring disease-relevant biomarkers, including copy number variants (CNVs), single-nucleotide variants (SNVs), insertions and deletions (indels), and fusions. These cfDNA biomarkers form the basis of their tumor profiling products and analysis pipelines. Hedera DX also generates data to create initial datasets for downstream patient stratification and longitudinal monitoring of disease progression.
The Aim & Challenges
Nexco Analytics collaborated with Thomas Vetterli, Director of Machine Learning and Bioinformatics at Hedera Dx, to develop an algorithm for detecting the status of the microsatellite instability (MSI) biomarker in circulating free DNA (cfDNA). MSI detection in cfDNA represents a minimally invasive approach to assess genomic instability, with implications for immunotherapy response and cancer prognosis.
Here are the challenges that Hedera Dx faced before they collaborated with Nexco Analytics:
Hedera Dx lacked the in-house bandwidth to perform a feasibility and proof-of-concept study assessing whether it would be possible or beneficial to include MSI biomarker analyses in their product.
The Hedera Dx team faced too many competing priorities but wanted to expand the number of projects they could work on in parallel.
They didn’t know how long it would take to develop a robust MSI analysis pipeline internally, which impacted their product roadmap.
While open-source tools evaluate MSI biomarkers in other contexts, none were suitable for MSI in cfDNA data. Hedera Dx required novel algorithms that they didn’t have time to develop.
"We mostly face a bandwidth problem. Our internal team has all the necessary skills to handle omics data, but we face too many competing priorities and need external assistance to expand the number of projects we can work on in parallel."
The Solution with Nexco Analytics
- Nexco Analytics first evaluated existing public datasets and approaches for MSI detection in the literature to understand the challenges faced in MSI analysis using cfDNA.
- This initial exploration allowed Nexco’s analysts to understand how best to develop algorithms to extract MSI signals from NGS data.
- Nexco’s analysts utilized these insights, combined with existing bioinformatic packages, such as pysam, to develop custom scripts for analyzing cfDNA data in the context of MSI biomarkers.
- The team rigorously evaluated the algorithms they developed to ensure they were as robust, reliable, and streamlined as possible.
The Outcome
This proof of concept confirmed that MSI detection in cfDNA was a viable approach. It helped Hedera Dx advance internal development of a novel diagnostic feature, derisking their product roadmap and accelerating time-to-market.
Nexco Analytics delivered rapid, reliable results that brought clarity to Hedera Dx’s internal R&D timelines and drove their product forward.
Hedera Dx now has the confidence to include MSI detection as one of the biomarkers that their products can measure in cfDNA.
"Nexco Analytics delivered high-impact, customized bioinformatics solutions with precision, speed, and scientific rigor."
"Nexco Analytics’ extensive background in NGS analysis gives us high confidence that their findings are valid and usable."
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