As the pace of discovery in genomics and translational research accelerates, scientists continue to seek tools that bring together genetic and transcriptional insights simultaneously with single-cell resolution. To better understand how researchers are approaching multiomic analysis, and what they value most in a targeted DNA + RNA assay, we surveyed our community of scientists working across oncology, hematology, and cell and gene therapy (CGT).
Respondents shared their perspectives, revealing clear enthusiasm for using targeted single-cell DNA + RNA assays and highlighted the key priorities shaping their experimental design.
Single-Cell DNA + RNA: A Clear Need Among Researchers
Nearly all respondents indicated they would find value in a targeted single-cell DNA + RNA assay, with 82% describing it as “extremely” or “moderately valuable” to their research, underscoring their growing interest in connecting genetic variation to transcript-level function.
When asked to identify how they would apply such a tool, respondents pointed to several key use cases:
- Mutation-to-expression correlation (36%)
- Cell and gene therapy development (26%)
- Resistance mechanism analysis (22%)
- Clonal evolution studies (11%)
These applications highlight the need to bridge genotypic data with downstream biological effects, particularly in areas such as hematologic malignancies, CGT, and solid tumors, which were the top research focuses among respondents.
Understanding the Functional Impact of Mutations Tops the List
When asked to rank the top three potential benefits of targeted single-cell DNA + RNA analysis, the community’s priorities were clear:
- Improved insights into the functional impact of mutations
(e.g., endogenous mutations or on-/off-target edits) - Better understanding of clonal heterogeneity
- Enhanced biomarker and target discovery
Together, these responses emphasize a desire to move beyond genotyping alone and toward understanding how genetic alterations translate into cell state and phenotype.
Current Methods and Gaps in DNA + RNA Analysis
Today, most respondents rely on whole-transcriptome RNA sequencing, targeted DNA or RNA panels, or whole-genome DNA sequencing to interrogate cellular profiles. However, many noted limitations in these approaches, including:
- High cost of current solutions
- Insufficient sensitivity for rare variant detection
- Limited ability to directly link genotype to phenotype
- Data complexity and bioinformatic burden
- Sample constraints and throughput challenges
These challenges suggest an unmet need for cost-effective, high-sensitivity, and workflow-compatible single-cell multiomic solutions, which were features respondents consistently ranked as top priorities.
What Researchers Want in a Targeted DNA + RNA Assay
When asked to rank assay features by importance, the community prioritized the following:
- Cost effectiveness
- High sensitivity
- Compatibility with existing workflows
- User-friendly analysis tools
- Customizable panels
- Speed of results
Taken together, these preferences reveal that practical and economic considerations remain just as important as scientific capabilities in driving adoption of new technologies.
User Perspectives: The Case for Integrated Multiomics
Several responses underscored a desire for greater integration not only of DNA and RNA, but also protein-level data:
“RNA+Protein, or DNA+RNA+Protein would also be useful for cell and cene therapy to look at vector DNA, RNA transcriptome, and presence of transgene protein.”
Another respondent shared:
“The multiomics approach would be ideal for my analysis, where I am looking at low-frequency mutations within rare cell populations in small patient samples. Being able to couple phenotype with mutation detection in the same cell at scale without prior sorting would be ideal for my work. However, cost is also a consideration.”
And perhaps most tellingly:
“Having targeted DNA + RNA in the same single cell would be amazing. Currently, other providers enable this, but in a low-throughput or non-targeted manner.”
These comments highlight the need for a scalable, targeted, and cost-conscious single-cell multiomic platform – one capable of directly linking mutations to their functional and phenotypic outcomes.
One Cell, Many Insights
The results of this survey reinforce a clear message: researchers across oncology, hematology, and CGT need tools that link genotype and transcriptomic information within individual cells without sacrificing sensitivity or throughput. A targeted single-cell DNA + RNA assay enables scientists to better understand clonal dynamics, functional mutations, and treatment resistance mechanisms, ultimately accelerating discoveries that can improve drug development and cell & gene therapies.
Stay tuned as we continue to explore the future of targeted single-cell multiomics.
Want more information about when Mission Bio’s targeted single-cell DNA + RNA assays are available? Fill out this form here to reserve your access.
Thank you to all who participated in this survey. Your responses are helping us set a new standard for single-cell multiomics for research and clinical applications.
