Clinical Data Engineer II/III

ClearNote Health•San Mateo or San Diego, CA

2d•Onsite

About The Position

ClearNote Health is an early cancer detection company focused on the development and commercialization of non-invasive epigenomic tests to detect cancer through a standard blood draw, earlier than existing methods and when the disease is still treatable. Leveraging its novel liquid biopsy technology, ClearNote Health is initially focused on high-mortality cancers with the greatest need for early detection, starting with pancreatic and ovarian cancers. The Clinical Data Engineer II/III owns clinical Data Operations: the data pipelines, data warehouse, and reporting infrastructure that transform clinical data, laboratory data, and sequencing results into validated, audit-ready clinical and business data. This position operates in a regulated environment in which accuracy and traceability are as important as well-architected code. The role combines hands-on pipeline and data-modeling work with ongoing production data support for our clinical study operations and is central to the integrity of the data that informs our research and clinical decisions.

Requirements

5+ years of hands-on data engineering experience with production data-transformation frameworks (dbt preferred) and a cloud data warehouse
Software-engineering fundamentals and an expert understanding of database and data-warehouse concepts
Deep SQL expertise, including the ability to identify subtle logic errors in complex queries
Experience with ELT and data-integration tools
Experience with designing, building and using containers
Proficiency in Python or a comparable scripting language
Familiarity with cloud identity and access-management concepts (key-pair authentication, OAuth/OIDC, workload identity federation)
Proven ability to work in a regulated environment, including precise documentation, change-control processes, and audit trails
Enjoys a role that balances building new data systems with keeping production systems reliable and trusted
Strong written and verbal communication skills, with a track record of documenting your work

Nice To Haves

Working knowledge of clinical or laboratory data systems is a plus
Familiarity with clinical data standards (CDASH/CDISC) preferred
Working knowledge of Good Clinical Practice (GCP) and the clinical trial process preferred
Familiarity with cancer-related medical classifications and ontologies (e.g., ICD-10) a plus

Responsibilities

Build and maintain ELT pipelines from clinical source systems — and non-standard sources such as ad hoc spreadsheets — into our data warehouse, and design ingestion frameworks that adapt to evolving report formats
Support bulk data transfer initiatives to external partners and client-facing destinations, including the definition of the data contracts those partners depend on
Develop, test, and refactor data transformation models across core clinical schemas, implementing precise, well-specified business logic, and integrate clinical data with other corporate data
Define methods and metrics for assessing data quality, and monitor and maintain data quality across clinical datasets
Own the reliability of clinical result data end to end, tracing issues to their root cause and strengthening controls through documented change management
Strengthen the resilience of data contracts and design reconciliation logic that unifies data from multiple sources into a single, authoritative record
Serve as a trusted partner to clinical and laboratory operations and external stakeholders, resolving data questions and improving accuracy at the source
Build and maintain dashboards and monitoring, including those subject to formal system validation, and support the data needs of adjacent business systems
Partner with the Regulatory/QA team to ensure clinical data flow and the data warehouse remain compliant with procedural and regulatory requirements
Serve as a subject-matter expert on warehouse clinical data, providing technical guidance and training to research and development teams
Provide project status updates to cross-functional stakeholders