Publications by authors named "Zoe Steinsnyder"
Article Synopsis
- The Genome in a Bottle Consortium (GIAB) is creating matched tumor-normal samples that are publicly consented for sharing genomic data and cell lines, focusing on pancreatic ductal adenocarcinoma (PDAC).
- They provide a comprehensive genomic dataset from the first individual, combining high-depth DNA from tumor and normal cells using advanced whole genome sequencing technologies.
- This open-access resource aims to help develop benchmarks for detecting genetic variants in cancer, fostering innovation in genome measurement and analysis tools.
In solid tumor oncology, circulating tumor DNA (ctDNA) is poised to transform care through accurate assessment of minimal residual disease (MRD) and therapeutic response monitoring. To overcome the sparsity of ctDNA fragments in low tumor fraction (TF) settings and increase MRD sensitivity, we previously leveraged genome-wide mutational integration through plasma whole-genome sequencing (WGS). Here we now introduce MRD-EDGE, a machine-learning-guided WGS ctDNA single-nucleotide variant (SNV) and copy-number variant (CNV) detection platform designed to increase signal enrichment.
View Article and Find Full Text PDFPurpose: To explore the role of NBN as a pan-cancer susceptibility gene.
Experimental Design: Matched germline and somatic DNA samples from 34,046 patients were sequenced using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets and presumed pathogenic germline variants (PGV) identified. Allele-specific and gene-centered analysis of enrichment was conducted and a validation cohort of 26,407 pan-cancer patients was analyzed.
SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death.
Cancer Epidemiol Biomarkers Prev
July 2022
Background: A previous genome-wide association study identified several loci with genetic variants associated with prostate cancer survival time in two cohorts from Sweden. Whether these variants have an effect in other populations or if their effect is homogenous across the course of disease is unknown.
Methods: These variants were genotyped in a cohort of 1,298 patients.
Article Synopsis
- A correction has been issued for the paper referenced by the DOI 10.1038/s41467-021-23162-4.
- The correction addresses specific errors or inaccuracies found in the original research.
- Readers are encouraged to review the correction to understand the updated findings and implications.
Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies.
View Article and Find Full Text PDFPurpose: Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities.
Experimental Design: We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes.
Article Synopsis
- The study examined how polygenic risk scores (PRS) for breast and ovarian cancers relate to risks for women with BRCA1 and BRCA2 gene variants.
- It used data from nearly 32,000 female carriers to evaluate different versions of BC and EOC PRS, finding that specific scores were strongly linked to cancer risk.
- Results indicated stronger associations between certain PRS and cancer risks, with implications for understanding absolute risk differences among women in different PRS groups.
Importance: The limited data on cancer phenotypes in men with germline BRCA1 and BRCA2 pathogenic variants (PVs) have hampered the development of evidence-based recommendations for early cancer detection and risk reduction in this population.
Objective: To compare the cancer spectrum and frequencies between male BRCA1 and BRCA2 PV carriers.
Design, Setting, And Participants: Retrospective cohort study of 6902 men, including 3651 BRCA1 and 3251 BRCA2 PV carriers, older than 18 years recruited from cancer genetics clinics from 1966 to 2017 by 53 study groups in 33 countries worldwide collaborating through the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA).
Purpose: Despite advances in DNA sequencing technology and expanded medical guidelines, the vast majority of individuals carrying pathogenic variants of common cancer susceptibility genes have yet to be identified. An alternative to population-wide genetic screening of healthy individuals would exploit the trend for genetic testing at the time of cancer diagnosis to guide therapy and prevention, combined with augmented familial diffusion or "cascade" of genomic risk information.
Methods: Using a multiple linear regression model, we derived the time interval to detect an estimated 3.