Shree Lekha Kandasamy
McKinney
Summary
- Dedicated bioinformatician with 7 years of experience in genomic data analysis, specializing in Next-Generation Sequencing (NGS) workflows.
- Experienced in designing and implementing scalable bioinformatics pipelines, integrating software development and workflow automation to streamline data analysis.
- Expertise in human genomics and WGTS data analysis across constitutional and oncology domains.
- Hands-on experience with clinical and research-grade samples, ensuring data integrity and HIPAA compliance with QC and regulatory standards (CLIA).
- Skilled in managing large-scale genomic workflows in HPC (SLURM) and cloud environments (AWS, GCP) Proficient in Python, WDL workflow management, and containerization (Docker) for automation and reproducible pipelines.
- Experienced with Git/Bitbucket version control, Jira/Confluence for project tracking, and collaboration with interdisciplinary teams.
- Proficient in working with Illumina NGS data, DRAGEN pipelines and Illumina tool Emedgene.
- Strong organizational, project management, and collaborative skills, with a proven record of effective communication in interdisciplinary teams.
Overview
11
11
years of professional experience
Work History
Bioinformatics Analyst
New York Genome Center
04.2023 - Current
- Developed and maintained CLIA compliant bioinformatics pipelines for tumor-normal analysis (SNV, Indel, CNV, SV).
- Supported and optimized oncology data pipelines across HPC and cloud (AWS/GCP) environments.
- Diagnosed, debugged, and refined pipelines to ensure reproducible, accurate results.
- Benchmarked and integrated new sequencing tools, improving pipeline efficiency and accuracy.
- Managed large-scale genomic and clinical datasets in Google BigQuery for aggregation and downstream analysis.
- Performed and evaluated sequencing QC measures to ensure data quality and compliance with clinical standards.
- Collaborated with clinical teams to generate annotated VCFs, CNV calls, and curated variant summaries for reporting.
- Analyzed tumor RNA-seq data for fusion and variant detection, supporting integrated genomic interpretation.
- Analyzed validation experiments for Laboratory Developed Tests (LDTs) and contributed to the preparation of validation reports and supporting documentation for assay submissions in compliance with CLIA standards.
- Participated in CAP proficiency testing for WGS and RNA fusion assays to ensure accuracy, reproducibility, and regulatory compliance.
- Supported validation and benchmarking of variant-calling pipelines for both constitutional and oncology assays.
- Area of work: Oncology WGTS analysis
Research Associate
University of Missouri
04.2022 - 03.2023
- Gathered, curated, and analyzed genomic data from multiple sources to support biomarker and drug target discovery.
- Developed computational algorithms in Python and R for SNP analysis and genomic interpretation.
- Designed figures, tables, and analytical content for grants and peer-reviewed publications.
- Area of work: Coronavirus, Monkey pox and HIV
Senior Data Analyst
VClinBio Labs Private Limited
06.2014 - 08.2017
- Performed end-to-end NGS data analysis and pipeline development for clinical and research applications in HPC and cloud environments.
- Experienced in clinical exome panel analysis to identify disease-causing mutations using the TruSight One panel.
- Analyzed marine microbial samples through genome sequencing, assembly, and functional annotation.
- Designed and implemented Python-based analysis pipelines ensuring accuracy, QC, and reproducibility.
- Provided technical guidance for data profiling, pipeline optimization, and process improvement.
- Area of work: NGS data analysis
Education
Master of Science - Bioinformatics
SRM University
05.2014
Bachelor of Engineering - Computer Science and Engineering
Anna University
04.2011
Skills
- Programming: Python, bash scripting
- NGS Tools and Analysis: SNV, Indel, CNV, SV analysis, transcriptome analysis, WDL pipeline development
- NGS Quality Control: Familiarity with QC principles and practices
- Public Genomic Datasets: 1000 Genomes, ExAC, OMIM, ClinVar, HGMD, CIViCDB, and OncoKB
- HPC / Cloud: SLURM, Linux/MAC environments, AWS, GCP
- Version Control: Git, Bitbucket
- Documentation / Collaboration: Jira, Confluence
- Regulatory Compliance: CLIA/CAP standards, HIPAA
PUBLICATIONS
- Saathvik R. Kannan, Shrikesh Sachdev, Athreya S. Reddy, Shree Lekha Kandasamy, Siddappa N. Byrareddy, Christian L Lorson, Kamal Singh. “Mutations in the monkeypox virus replication complex: Potential contributing factors to the 2022 outbreak”, Journal of Autoimmunity Volume December 2022, 102928
- Austin N. Spratt, Saathvik R. Kannan, Kalicharan Sharma, Shrikesh Sachdev, Shree Lekha Kandasamy, Anders Sonnerborg, Christian L. Lorson, Kamal Singh. “Continued Complexity of Mutations in Omicron Sublinages”, Biomedicines 2022,10,259
Timeline
Bioinformatics Analyst
New York Genome Center
04.2023 - Current
Research Associate
University of Missouri
04.2022 - 03.2023
Senior Data Analyst
VClinBio Labs Private Limited
06.2014 - 08.2017
Bachelor of Engineering - Computer Science and Engineering
Anna University
Master of Science - Bioinformatics
SRM University