How Biodesix Development Services, Biodesix Biopharma Services, Help with Biomarker Programs; Frequently Asked Questions about Biodesix Biopharma Services

Frequently Asked Questions | July 27, 2026

How Biodesix Development Services, Biodesix Biopharma Services, Help with Biomarker Programs; Frequently Asked Questions about Biodesix Biopharma Services

What is Biodesix Biopharma Services? What is Biodesix Development Services?

Biodesix supports pharmaceutical and biotechnology companies with biomarker assay development, biomarker testing, and biomarker strategy execution.

Biodesix works with clients, partners, and sponsors across the drug development continuum, including discovery, translational research, IND-enabling studies, clinical trials, and regulatory submission support.

Biodesix helps biopharma teams generate genomic, proteomic, and other molecular insights that can inform therapeutic development decisions.

What types of biopharma, biotech, and life sciences organizations does Biodesix partner with? What are the medical specialty areas of focus for Biodesix?

Biodesix serves or partners with pharmaceutical, biotechnology, and life sciences organizations that are developing therapeutic programs which require biomarker testing, and molecular and proteomic insights.

Biodesix supports companies working in oncology, rare diseases, and neurodegenerative drug development.

At what stages of clinical development can Biodesix support a therapeutic program?

Biodesix can support therapeutic programs from discovery and translational research through clinical trial testing. Biodesix works with pharmaceutical and biotechnology teams to generate biomarker data that may inform early discovery, patient enrollment and stratification, mechanism-of-action research, pharmacodynamic assessment, therapeutic response monitoring, and clinical development decision-making.

How experienced is Biodesix in supporting pharmaceutical clinical trials?

Biodesix has experience supporting clinical trial programs across early and later-stage development, including Phase 1, Phase 2, and Phase 3 studies.

How does Biodesix use ddPCR™ assays, NGS, and LC-MS/MS in its biopharma services portfolio?

Biodesix uses ddPCR, NGS, and LC-MS/MS as complementary technologies across genomic and proteomic biomarker testing. Each platform supports different study needs, from broad molecular profiling to targeted longitudinal monitoring, and protein-level analysis.

What is Biodesix multi-omic approach to supporting drug development?

The Biodesix multi-omic approach combines genomic and proteomic testing to help biopharma clients and sponsors evaluate drug development programs from multiple biological perspectives.

  • Genomic data can identify molecular alterations and track known biomarkers, but it may not fully reflect protein-level biology or pathway activity.
  • Proteomic analysis can help evaluate pharmacodynamic response, pathway modulation, target engagement, and changes in protein expression over time.
  • Together, genomic and proteomic data can support biomarker strategy, longitudinal monitoring, patient subgroup analysis, and clinical development decision-making.

Genomic Testing Services

What is a Droplet Digital™ PCR (ddPCR) assay and how does Biodesix use it in biopharma projects?

The Droplet Digital PCR (ddPCR) assay is a highly sensitive molecular testing method used to detect and quantify specific nucleic acid targets, such as known mutations or circulating biomarkers. In biopharma projects, Biodesix uses ddPCR to support targeted biomarker testing, including longitudinal monitoring across multiple study timepoints. The ddPCR assay can be especially useful when a client has already identified the biomarkers of interest and needs a precise, efficient method for measuring those targets in clinical or translational research samples.

How does Biodesix use next-generation sequencing (NGS) for biopharma clients?

Biodesix offers next-generation sequencing (NGS) solutions to meet diverse clinical and research needs:

  • The GeneStrat NGS® panel analyzes 52 clinically relevant genes, detecting actionable alterations linked to approved therapies and established medical guidelines while also enabling the discovery of novel mutations.
  • Biodesix also supports applications in myeloid malignancies, helping to identify key genomic alterations that inform diagnosis, prognosis, and monitoring in hematologic cancers.
  • In addition to pre-validated panels, Biodesix provides customizable assay development, including copy number variation (CNV) analysis and whole-gene sequencing tailored to unique project requirements and validated to the highest quality standards.
  • All testing services are supported by rapid turnaround times and adaptable reporting formats, ensuring timely, precise, and meaningful insights that integrate seamlessly into the client’s biomarker strategy.

Which pre-validated genomic assays does Biodesix currently offer?

As of July 2026, Biodesix offers the following pre-validated genomic assays that are NYS-CLEP approved:

  • KRAS: G12C, G12D, G12V
  • EGFR: L858R, del19, del19 multiplex*, Uncommon Variants (G719A, G719C, G719S, S758I and L861Q) multiplex*, T790M, C797S multiplex (discriminating)
  • ALK fusions
  • ROS1
  • RET
  • BRAF: V600E
  • ESR1 multiplex
  • AKT1: E17K

For genomic targets not listed above, Biodesix can discuss assay feasibility and support validation of additional target assays based on the sponsor’s program needs.

*Multiplexed assays screen for the presence or absence of multiple mutations in a single sample. They can be discriminating or non-discriminating

Can Biodesix develop and validate a custom genomic assay for a specific target?

Yes. Biodesix can develop and validate custom genomic assays for a specific target. Examples of assays that have been functionally tested in our CLIA-certified laboratory:

  • Microsatellite instability (MSI)
  • KRAS multiplex
  • YAP/TAZ fusions
  • EGFR exon 20 INDELs
  • HER2 exon 20 INDELs
  • GNAQ/GNA11

When should a company, client, partner, sponsor choose ddPCR assays versus NGS for a circulating biomarker?

Clients and Sponsors often use next-generation sequencing (NGS) when broader biomarker profiling is needed, such as at baseline or endpoint timepoints where a more comprehensive molecular view may be useful.

Droplet Digital PCR (ddPCR) assays are often better suited for longitudinal monitoring when target biomarkers are already known, and multiple samples will be tested across defined timepoints. For known targets, ddPCR assays can provide a faster, more cost-efficient approach than NGS, depending on the study design, assay requirements, and sample volume.

Proteomic Testing Services

What proteomic services does Biodesix offer to biopharma customers, sponsors, clients, partners, companies?

Proteomic profiling at Biodesix supports discovery and targeted workflows to assess drug mechanism of action, therapeutic response, and protein-based biomarkers. Use cases include MRD, PKPD, targeted protein degradation, and antibody drug conjugates.

Discovery Proteomics gathers comprehensive proteomic insights from biological samples through discovery proteomics. Characterize protein-protein interactions, post-translational modifications, and differential protein expression. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) provides a window into the plasma proteome for biomarker discovery, facilitates the development of protein-based classifiers and enables next-generation spatial omics.

Targeted Proteomics evaluates the abundance of proteins associated with a drug’s mechanism of action or the patient’s therapeutic response over time. Biodesix can provide absolute quantification of proteins of interest by targeted LC-MS/MS for biomarker validation, minimal residual disease (MRD), monitoring drug response, targeted protein degradation (TPD), disease mechanism, pharmacokinetic/pharmacodynamic (PK/PD) and cell signaling studies.

What is the difference between discovery proteomics and targeted protein monitoring at Biodesix?

Untargeted liquid chromatography tandem MS (LC-MS/MS) allows for the unbiased identification and relative quantification of thousands of protein targets in a single liquid biopsy, tissue or cell culture sample.

Targeted protein monitoring allows for the absolute quantification of a defined set of proteins in a sample.

When should a program use MALDI-TOF MS versus LC-MS/MS proteomics?

MALDI-TOF MS is ideal for rapid liquid biopsy profiling when a snapshot of the proteome is desired. Spectral signatures identified using MALDI-TOF can be used to stratify patients, predict therapy response, profile host-immune biology, and build patient classifiers.

When a deeper understanding of the proteome is desired, LC-MS/MS-based proteomics is a preferrable technology. LC-MS/MS can be used to specifically identify and measure thousands of proteins in a sample.

Put simply, MALDI-TOF allows for a “first look” into the proteome while LC-MS/MS provides a more thorough investigation.

How does Biodesix use untargeted LC-MS/MS to measure thousands of proteins from a single sample?

Untargeted LC-MS/MS provides an unbiased measurement of the proteome, meaning that the instrument does not preselect a list of proteins to measure. Instead, the protein content of a sample is extracted and digested into peptides. These peptides are then separated using liquid chromatography then their masses are recorded inside the mass spectrometer. Using the characteristics measured for each peptide, the peptides are identified and used as surrogates to confirm the presence of the corresponding protein in the sample.

How does Biodesix support targeted protein degradation, TPD, programs?

Biodesix supports Targeted Protein Degradation, TPD, programs with mass spectrometry approaches. During early development and lead optimization, untargeted mass spectrometry can be used to observe target degradation and detect off-target interactions. Later in the pipeline, targeted mass spectrometry can be used to measure treatment-induced target degradation, and therefore therapeutic efficacy, in the tissue or peripheral blood mononuclear cells (PBMCs) of clinical trial patients.

Can Biodesix provide absolute quantification of specific proteins of interest?

Yes, Biodesix can provide absolute quantification of proteins of interest through the development of a targeted mass spectrometry assay. Targeted mass spectrometry uses spiked-in heavy labeled peptide standards to provide absolute quantification of corresponding endogenous peptides down to single attomolar sensitivity.

How does Biodesix support pharmacokinetic / pharmacodynamic (PK/PD), biomarker validation, and cell signaling studies?

Biodesix can support pharmacokinetic / pharmacodynamic  (PK/PD) studies using targeted proteomics. By measuring the treatment-affected protein, temporal changes in abundance can show pharmacodynamic degradation in TPD programs. For biomarker validation and cell signaling, untargeted discovery proteomics can be used to observe protein biomarkers associated with a certain condition or treatment and validate protein signaling networks.

Can a Biodesix targeted LC-MS/MS assay be transferred to an ELISA format for scale?

Targeted LC-MS/MS assays are easily transferrable to an enzyme-linked immunosorbent assay (ELISA) format for scalability and cost-effectiveness.

Bio Sample Types and Logistics

What sample types does Biodesix accept for biopharma testing?

Biodesix accepts these sample types: plasma, serum, whole blood, cerebrospinal fluid (CSF), urine, bone marrow aspirates (BMA), tissue (fresh and FFPE), and cell cultures.

For rare sample types, please contact the Biodesix Development Services team.

Does Biodesix provide custom prospective sample collection kits for clinical trials?

Biodesix has an FDA-registered manufacturing facility that can provide custom sample collection kits for your clinical trials.

Regulatory, Quality, and Companion Diagnostics

What lab accreditations and certifications does Biodesix hold?

Biodesix is CAP-accredited, CLIA-certified, NYS-CLEP approved, and ISO 13485 certified. Our certifications can be found here.

What off-the-shelf assays does Biodesix have?

Biodesix has the following pre-validated genomic assays that are NYS-CLEP approved:

  • KRAS: G12C, G12D, G12V
  • EGFR: L858R, del19, del19 multiplex*, Uncommon Variants (G719A, G719C, G719S, S758I and L861Q) multiplex*, T790M, C797S multiplex (discriminating)
  • ALK fusions
  • ROS1
  • RET
  • BRAF: V600E

*Multiplexed assays screen for the presence or absence of multiple mutations in a single sample. They can be discriminating or non-discriminating.

Does Biodesix do custom assay development?

Yes, Biodesix can design and develop custom assays for novel mutation targets.

Consulting and Project Engagement

How does a biopharma company start a project with Biodesix?

A biopharma company can start a project with Biodesix Biopharma Services by scheduling an introductory discussion. During this initial conversation, Biodesix learns about the client’s therapeutic program, biomarker strategy, sample types, testing needs, timelines, and project goals. If Biodesix capabilities align with the program requirements, the next step is typically to put a confidentiality agreement in place so that both teams can more fully discuss technical details, study design, and project scope.

Who do I contact to discuss a collaboration with Biodesix Biopharma Services?

To discuss a biopharma services collaboration with Biodesix, contact the Biodesix Business Development team. The team can help determine whether Biodesix biomarker testing, genomic testing, proteomic testing, and clinical trial laboratory services align with your therapeutic program, study design, sample requirements, and development goals.

ddPCR and Droplet Digital are trademarks of Bio-Rad Laboratories, Inc.

Editor’s Comment: Biodesix Development Services is a business line within Biodesix, Inc. Biodesix Development Services enables the world’s leading biopharmaceutical, life sciences, and research institutions with scientific, technological, and operational capabilities that fuel the development of diagnostic tests, tools, and therapeutics.