Bioinformatics Cytogenetics/FISH Technologist

Bioinformatics Cytogenetics/FISH Technologist

Location: New York Schedule: Full-Time

Job Summary

We are seeking a Bioinformatics Cytogenetics/FISH Technologist with experience supporting genomic analysis workflows, particularly within cancer genomics, long-read sequencing, germline and somatic variant analysis, and complex structural variation.

This position will focus heavily on the development, integration, optimization, and troubleshooting of bioinformatics workflows used to analyze complex genomic datasets. The successful candidate will have the ability to identify clinically relevant genomic alterations, including large chromosomal aberrations, structural variants, germline variants, and somatic variants, while working with multiple sequencing and variant-calling platforms.

Experience in Cytogenetics and/or FISH is highly desirable because it provides additional insight into chromosomal abnormalities and complex genomic variation; however, this role is primarily focused on computational genomic analysis and bioinformatics workflow development.

Responsibilities

• Develop, implement, and support bioinformatics workflows for cancer genomics and sequencing-based analysis.
• Analyze data generated through long-read sequencing workflows and other genomic sequencing technologies.
• Perform and support germline and somatic variant calling.
• Analyze complex genomic datasets to identify:
  • Large chromosomal aberrations
  • Structural variants
  • Copy-number alterations
  • Germline variants
  • Somatic variants
  • Complex genomic rearrangements
• Integrate multiple existing long-read variant-calling and genomic analysis workflows into streamlined analytical pipelines.
• Work with relevant open-source, GitHub-based, and internally developed bioinformatics tools and pipelines, including platforms such as Lumos.
• Utilize and integrate somatic variant-calling workflows, Human Variation Caller (HVC), structural variant callers, and other germline and somatic variant analysis tools.
• Evaluate the performance of different variant callers and analytical workflows across complex datasets.
• Perform workflow optimization, validation, troubleshooting, and performance improvement.
• Investigate discrepancies or unexpected results generated by sequencing or variant-calling pipelines.
• Develop methods for analyzing difficult or highly complex genomic datasets.
• Build visual representations and data visualizations to communicate results generated by multiple analytical workflows.
• Compare and correlate genomic findings across different sequencing, bioinformatics, Cytogenetics, and FISH methodologies.
• Support the interpretation of genomic abnormalities within the context of cancer and other clinically relevant conditions.
• Assist with development and validation of new bioinformatics tools, workflows, and sequencing applications.
• Maintain detailed documentation of analytical workflows, pipeline modifications, validation studies, troubleshooting activities, and results.
• Collaborate with bioinformaticians, laboratory scientists, molecular technologists, cytogenetic technologists, pathologists, laboratory directors, and other clinical or scientific personnel.
• Participate in continuous improvement initiatives related to genomic analysis, data quality, workflow efficiency, and analytical accuracy.

Qualifications / Requirements

• Bachelor's degree or higher in Bioinformatics, Computational Biology, Genetics, Genomics, Molecular Biology, Cytogenetics, Computer Science, Medical Laboratory Science, or a related scientific discipline.
• Experience working with bioinformatics or genomic sequencing workflows.
• Experience with long-read sequencing and/or cancer genomics workflows strongly preferred.
• Knowledge of germline and somatic variant calling.
• Experience analyzing structural variants, chromosomal abnormalities, copy-number changes, and complex genomic variation.
• Experience integrating or working with multiple variant-calling pipelines and bioinformatics workflows.
• Familiarity with open-source and GitHub-based bioinformatics tools and pipelines.
• Experience with structural-variant and somatic-variant callers such as Lumos, Human Variation Caller (HVC), or comparable genomic analysis tools preferred.
• Strong experience with workflow optimization and troubleshooting complex genomic datasets.
• Ability to evaluate analytical outputs from multiple workflows and identify inconsistencies, artifacts, or clinically meaningful genomic alterations.
• Experience developing data visualizations or graphical representations of genomic findings.
• Familiarity with programming, scripting, or computational tools such as Python, R, Linux/Unix, Bash, SQL, or similar technologies preferred.
• Experience with Cytogenetics, FISH, chromosome analysis, or cancer cytogenetics is highly desirable but not required for candidates with strong genomics/bioinformatics expertise.
• Strong analytical, problem-solving, and troubleshooting skills.
• Excellent documentation and communication skills.
• Experience working within a regulated clinical laboratory, cancer genomics laboratory, research laboratory, or diagnostic environment preferred.
• New York State clinical laboratory licensure is not necessarily required for this position and will depend on the specific scope of testing responsibilities.

Ideal Candidate

The ideal candidate will have a strong background in bioinformatics and cancer genomics, with particular experience in long-read sequencing, germline and somatic variant calling, structural variation, chromosomal abnormalities, and complex genomic datasets.

Candidates who can integrate multiple existing sequencing and variant-calling workflows, troubleshoot difficult datasets, optimize pipelines, and translate results into meaningful visual and analytical outputs will be especially well suited for this role. Experience with Cytogenetics and/or FISH is valuable because of the position's emphasis on identifying large-scale chromosomal and structural genomic abnormalities.