Nicolas Robine
Kettering University
GeneCancerInternal medicineSomatic cellGenomeOncologymicroRNAPiwi-interacting RNAGene expressionNew York Genome CenterTranscriptomeGenomicsArgonauteWhole genome sequencingSmall RNAComputer scienceMutationCancer researchGeneticsDNARNAComputational biologyMedicineBiologyCell biology
Publications 59
Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes, but the impacts of integration in tumorigenesis remain unclear. Analysis of 105 HPV-positive oropharyngeal cancers by whole genome sequencing detects viral integration in 77%, revealing five statistically significant integration hotspots near genes that regulate epithelial stem cell maintenance (i.e. SOX2, TP63, FGFR, MYC) and immune evasion (i.e. CD274). Somatic hyperamplification is enriched 16...
#1Maria E. Monberg (University of Texas System)H-Index: 3
#2Heather GeigerH-Index: 10
Last. Matthew Hg Katz (University of Texas System)H-Index: 3
view all 13 authors...
Abstract null Intratumoral heterogeneity (ITH) is a hallmark of cancer. The advent of single-cell technologies has helped uncover ITH in a high-throughput manner in different cancers across varied contexts. Here we apply single-cell sequencing technologies to reveal striking ITH in assumptively oligoclonal pancreatic ductal adenocarcinoma (PDAC) cell lines. Our findings reveal a high degree of both genomic and transcriptomic heterogeneity in established and globally utilized PDAC cell lines, cus...
#1Thomas G. PaulsonH-Index: 22
Last. Jennifer M. G. SheltonH-Index: 8
view all 22 authors...
#1Rachel MartiniH-Index: 3
#2Endale Gebregzabher (Cornell University)
Last. Melissa B. Davis (Cornell University)H-Index: 15
view all 13 authors...
Background: Triple-negative breast cancer (TNBC) remains the most aggressive molecular subtype of breast cancer, with worse survival outcomes compared to other breast cancer subtypes. TNBC prevalence is highest among women of African descent worldwide, and through our previous work we have established a connection between West African ancestry (WAa) and higher rates of TNBC. Specifically, we have shown that prevalence rates of TNBC among West African and African American women are similar and hi...
#81Ramaswamy Govindan (WashU: Washington University in St. Louis)H-Index: 92
#82Marcin Imielinski (Cornell University)H-Index: 49
Summary RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(−) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of ...
#1Adam J Widman (MSK: Memorial Sloan Kettering Cancer Center)H-Index: 2
#2Cole C. KhamneiH-Index: 1
Last. Dan A. Landau (Cornell University)H-Index: 25
view all 9 authors...
Background Clearance of circulating tumor DNA (ctDNA) following checkpoint blockade (CB) can precede radiographic response,1 2 though current state of the art ctDNA detection via targeted panels faces limited sensitivity in low burden disease (figure 1). We previously showed that whole genome sequencing (WGS) of plasma can overcome low input of ctDNA to dynamically track low volume malignancy using matched tumor tissue.3 We therefore sought to evaluate ctDNA for tracking early response to checkp...
#1Daniel K. WellsH-Index: 14
#2Marit M. van Buuren (NKI-AVL: Netherlands Cancer Institute)H-Index: 14
Last. Ana Belen Blazquez (ISMMS: Icahn School of Medicine at Mount Sinai)H-Index: 17
view all 145 authors...
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding ...
#5Charalampos Xanthopoulakis (Cornell University)H-Index: 1
#9Madison Darmofal (Cornell University)H-Index: 1
Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated w...
#2Fieke E.M. Froeling (CSHL: Cold Spring Harbor Laboratory)H-Index: 17
view all 10 authors...
Background and aims Recent advances in DNA sequencing technologies have revolutionized approaches to the prevention, risk assessment, early detection, diagnosis, and treatment of cancers. However, many ethnic groups, especially non-European populations, have been significantly under-represented in cancer research, including clinical trials, and have not received equal benefits in clinical practice. As a result, our current knowledge about tumor biology, cancer risk, and response to treatment has...
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