Clinical Bioinformatics Scientist — Oncology & Somatic Genomics

Summary

10 years in clinical and translational oncology bioinformatics. Built and validated CAP/CLIA-compliant somatic variant calling pipelines at Foundation Medicine and Memorial Sloan Kettering. Deep expertise in tumour heterogeneity, WGS/WES/ctDNA analysis, and clinical variant interpretation under ACMG/AMP guidelines. Has served as expert contributor on NGS pipeline validation for two FDA submissions.

Experience

Principal Bioinformatics Scientist — Memorial Sloan Kettering (2020–Present)

• Owns MSK-IMPACT WGS clinical pipeline (Mutect2 + CNVkit + LINX ensemble); 12,000+ patient samples/year, CAP/CLIA validated.
• Led bioinformatics validation study for FDA 510(k) submission of liquid biopsy ctDNA assay; submission approved 2023.
• Built tumour heterogeneity analysis platform (PURPLE + PyClone-VI) used across 4 active clinical trials.

Bioinformatics Scientist — Foundation Medicine (2016–2020)

• Contributed to FoundationOne CDx analytical pipeline; participated in PMA approval process.
• Developed automated ACMG/AMP variant classification system reducing curator time by 60%.
• Authored SOPs for somatic SNV, indel, CNV, and fusion calling reviewed by CAP inspectors.

Selected Publications

• Okafor K. et al. “Clonal dynamics of ctDNA predict immunotherapy response in advanced NSCLC.” Nature Medicine, 2023.
• Okafor K. et al. “Automated ACMG/AMP somatic variant classification at scale.” Genetics in Medicine, 2020.

Code Quality Notes

Clinical pipelines maintain change-controlled versioning with release notes auditable by CAP inspectors. All WDL tasks pinned to SHA-digested Docker images. Validation datasets and expected outputs stored in GCS with immutable object versioning; regression tests run on every PR. PostgreSQL schema migrations managed by Flyway with rollback scripts.