Bioinformatics Analyst II

Overview

NOTICE OF FILING OF APPLICATION UNDER THE U.S. DEPARTMENT OF LABOR’S

PERMANENT LABOR CERTIFICATION PROGRAM

This Notice is being provided as a result of the filing of an application for permanent alien labor certification for the job opportunity listed below. Any person may provide documentary evidence bearing on the application to: Certifying Officer of the Department of Labor, U.S. Department of Labor, Employment and Training Administration, Office of Foreign Labor Certification, 200 Constitution Avenue NW, Room N-5311, Washington, DC 20210.

JOB TITLE : Bioinformatics Analyst II

DUTIES:

- Design, build, and maintain production-grade NGS pipelines for whole exome sequencing cancer panels, covering somatic variant calling, SCNA profiling, TMB quantification, MSI classification, and tumor purity deconvolution to clinical-grade accuracy and reproducibility standards.

- Develop novel clinical sequencing assays by architecting computational workflows bridging wet-lab protocols to variant calling and allele frequency–based filtering strategies.

- Benchmark and analytically validate pipeline configurations using reference standards; conduct sensitivity, specificity, and limit-of-detection analyses prior to clinical deployment.

- Architect automated report generation systems compiling somatic variants, QC metrics, copy number profiles, and oncological annotations into pathology-ready outputs integrated with LIMS infrastructure.

- Build and maintain containerized bioinformatics workflows (Docker/Singularity) ensuring computational reproducibility across HPC platforms; govern version-controlled pipeline repositories with structured release management.

- Conduct pan-cancer genomic studies characterizing large-scale somatic alterations, clonal dynamics, and therapeutic response signatures across cohorts; apply Cox regression, Kaplan–Meier estimation, and multivariate statistical frameworks to interrogate clinicopathological and molecular determinants of patient outcomes.

- Perform comprehensive genomic profiling of tumor model systems, including mutational landscape characterization, SCNA assessment, and multi-omic DNA-seq integration to support translational oncology research.

- Evaluate sequencing QC parameters — coverage uniformity, duplication rates, insert size distributions — and provide data-driven recommendations to optimize library preparation and maximize diagnostic yield.

- Maintain clinical research data integrity across LIMS and cBioPortal; develop automated cohort curation workflows ensuring data provenance and regulatory compliance.

- Conduct systematic literature surveillance to identify and adopt emerging bioinformatic methodologies, expanding institutional analytical capabilities.

- Collaborate with clinicians, pathologists, and scientists to interpret genomic findings and contribute methods, figures, and results to peer-reviewed publications, grant proposals, and clinical reports.

Must live within normal commuting distance of Seattle, Washington, with up to 1 day per week working from home permitted.

REQUIREMENTS :

- Bachelor’s degree in bioinformatics, computational biology, genetics, or a related field, or foreign degree equivalent; and,

- Five (5) years’ direct experience in computational analysis of large sequence-based molecular datasets, including five (5) years of each of the following:

- End-to-end bioinformatics pipeline development using Nextflow, Snakemake, Docker, and Git.

- Multi-omics data analysis encompassing genomic, transcriptomic, and epigenomic datasets.

- Somatic and germline variant calling, somatic copy number alteration (SCNA) detection, TMB/MSI quantification, and tumor purity/ploidy estimation across sequencing data types.

- Cancer genomics and clinically actionable variants.

- Bulk RNA-seq analysis with multiple contrasts and gene set enrichment.

- Integration of data across multiple modalities including epigenetic profiling and RNA-seq.

- Computational tools and scripting languages including R and Python, used to analyze, represent, and visualize complex biological data.

- End-to-end analysis and biological interpretation of whole-exome (WES), whole-genome (WGS), and targeted sequencing data.

- Linux/Unix proficiency and high-performance computing (HPC) cluster operations.

- Interpretation of genomic results and presentation to clinical and research collaborators.

Experience may be gained concurrently.

SALARY : The annual base salary range for this position is from $80,475.20 to $120,681.60 and the pay offered will be based on experience and qualifications.

Fred Hutchinson Cancer Center offers employees a comprehensive benefits package designed to enhance health, well-being, and financial security. Benefits include medical/vision, dental, flexible spending accounts, life, disability, retirement, family life support, employee assistance program, onsite health clinic, tuition reimbursement, paid vacation (12-22 days per year), paid sick leave (12-25 days per year), paid holidays (13 days per year), paid parental leave (up to 4 weeks), and partially paid sabbatical leave (up to 6 months).

LOCATION : 40 hours/week at Fred Hutchinson Cancer Center in Seattle, Washington.

Must live within normal commuting distance of Seattle, Washington, with up to 1 day per week working from home permitted.

APPLY : [email protected]

## Additional Information
We are proud to be an Equal Employment Opportunity (EEO) and Vietnam Era Veterans Readjustment Assistance Act (VEVRAA) Employer. We do not discriminate on the basis of race, color, religion, creed, ancestry, national origin, sex, age, disability (physical or mental), marital or veteran status, genetic information, sexual orientation, gender identity, political ideology, or membership in any other legally protected class. We desire priority referrals of protected veterans. If due to a disability you need assistance/and or a reasonable accommodation during the application or recruiting process, please send a request to Human Resources at [email protected] or by calling 206-667-4700.