Comparative Assessment of Diagnostic Homologous Recombination Deficiency associated mutational signatures in ovarian cancer
Clinical Cancer Research, 2021
About Zsofia Sztupinszki
Boston, MA
zsofia[dot]sztupinszki[at]childrens[dot]harvard[dot]edu
Harvard Medical School
Boston Children's Hospital, Computational Health Informatics Program
Danish Cancer Institute
Zsofia Sztupinszki, M.D., Ph.D., is a Research Fellow at Harvard Medical School and Boston Children's Hospital (Computational Health Informatics Program), and an affiliate researcher at the Danish Cancer Institute. She is a physician-scientist specializing in cancer genomics, DNA repair deficiencies, and precision medicine. Her work focuses on identifying homologous recombination deficiency (HRD) and nucleotide excision repair (NER) defects through computational and statistical methods, and translating these findings into clinical biomarkers. She developed the scarHRD R package for HRD estimation from tumor sequencing, which has been cited in over 160 publications, and created TCGA Explorer, a no-code platform enabling pan-cancer analysis across all 30 TCGA cancer types. As of 2025, she has authored 47 peer-reviewed publications, accumulated 1,561 citations, and holds an h-index of 22 (Google Scholar). She holds patent WO2021195390A2 for a method for treating cancer.
- Machine Learning in Cancer Genomics
- Biomarker Discovery
- NGS Data Analysis
- Statistical Modeling
- DNA Repair Deficiencies
- Cancer Immunology
- Precision Medicine
- Clinical Diagnostics
Research
My research aims to identify DNA repair deficiencies and develop companion diagnostics through computational approaches. I integrate medical expertise with machine learning and statistical modeling to advance cancer treatment.
- — Developed a bioinformatics method to estimate homologous recombination deficiency (cited in over 160 publications)
- — Identified HR- and NER-deficient prostate, bladder, and ovarian cancers
- — Led research in oncoimmunology, exploring the gut microbiome's role in checkpoint inhibitor therapy
- — Translating genomic insights into clinical applications and biomarker development
Research Tools
TCGA Explorer
No-Code Cancer Genomics Platform
A browser-based platform for cancer genomics research — type a gene, run pan-cancer analyses across all 30 TCGA cancer types, and download comprehensive HTML reports. No coding required. Designed for researchers, bioinformaticians, and clinicians.
Gene Expression
Pan-cancer expression across 30 TCGA cohorts + GTEx normal tissue comparisons
Survival Analysis
Cox regression and Kaplan-Meier curves across 4 survival endpoints
Molecular Features
Immune infiltration scores, mutational signatures (COSMIC v2/v3/Indel)
Differential Expression
DESeq2 analysis with GSEA enrichment and pathway annotation
Pathway Enrichment
ssGSEA explorer using MSigDB pathways; async background jobs (10–90 min) with downloadable HTML reports
Coverage: All 30 TCGA cancer types · GTEx normal tissue · COSMIC v2/v3/Indel · MSigDB pathways
scarHRD R Package ↗
Open-source R package for estimating homologous recombination deficiency from tumor sequencing data
Selected Publications
ALK peptide vaccination restores the immunogenicity of ALK-rearranged non-small cell lung cancer
Nature Cancer, 2023
Detection of Molecular Signatures of Homologous Recombination Deficiency in Prostate Cancer with or without BRCA1/2 Mutations
Clinical Cancer Research, 2020
Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage
Science, 2020
Total publications: 47 · Citations: 1,561 · h-index: 22
Patent: WO2021195390A2 — Method for treating cancer