Assaf Grunwald
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View article: Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing
Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing Open
An exciting feature of nanopore sequencing is its ability to record multiomic information on the same sequenced DNA molecule. Well-trained models allow the detection of nucleotide-specific molecular signatures through changes in ionic curr…
View article: Brain tumor classification from FFPE samples using nanopore methylation sequencing
Brain tumor classification from FFPE samples using nanopore methylation sequencing Open
Oxford Nanopore Technology (ONT)-based methylation sequencing is emerging as a powerful approach for the rapid and accurate classification of brain tumors, an essential component of precision oncology. However, its broader clinical adoptio…
View article: Enzymatic profiling of cfDNA methylation for detection and monitoring of lung cancer
Enzymatic profiling of cfDNA methylation for detection and monitoring of lung cancer Open
We present a highly sensitive, low-cost approach for detecting lung cancer and monitoring response to therapy, based on sequencing-free detection of methylation biomarkers in cell-free DNA. An engineered methyltransferase is used to fluore…
View article: Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing
Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing Open
An exciting feature of nanopore sequencing is its ability to record multi-omic information on the same sequenced DNA molecule. Well-trained models allow the detection of nucleotide-specific molecular signatures through changes in ionic cur…
View article: Optical genome and epigenome mapping of clear cell renal cell carcinoma
Optical genome and epigenome mapping of clear cell renal cell carcinoma Open
Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily captured by short-read sequencing. This study presents a novel approach for simultaneous profili…
View article: Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping
Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping Open
Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic te…
View article: PATH-01. ACCURATE AND RAPID PAEDIATRIC BRAIN TUMOR CLASSIFICATION (PBT) BY METHYLATION PROFILING USING NOVEL NATIVE REAL TIME OXFORD NANOPORE TECHNOLOGY SEQUENCING TECHNOLOGY
PATH-01. ACCURATE AND RAPID PAEDIATRIC BRAIN TUMOR CLASSIFICATION (PBT) BY METHYLATION PROFILING USING NOVEL NATIVE REAL TIME OXFORD NANOPORE TECHNOLOGY SEQUENCING TECHNOLOGY Open
BACKGROUND Pediatric brain tumors (PBTs) pose a significant challenge being the leading cause of cancer related mortality in children. The existing classification process is time-consuming and fails to capture the heterogeneity of PBTs. Ur…
View article: Towards accesible brain-tumor classification at the point of care: Nanopore methylation sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) pathology samples
Towards accesible brain-tumor classification at the point of care: Nanopore methylation sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) pathology samples Open
Oxford Nanopore Technology (ONT) based methylation sequencing is increasingly recognized for its rapid and accurate classification of brain tumors. A process that is crucial for optimal patient treatment. However, widespread clinical utili…
View article: Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping
Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping Open
Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogene…
View article: Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays Open
Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expressio…
View article: Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma
Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma Open
Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily characterized by short-read sequencing. We present a method for simultaneous profiling of long-r…
View article: Long-read single-molecule maps of the functional methylome
Long-read single-molecule maps of the functional methylome Open
We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provi…
View article: Microfluidic DNA combing for parallel single-molecule analysis
Microfluidic DNA combing for parallel single-molecule analysis Open
DNA combing is a widely used method for stretching and immobilising DNA molecules on a surface. Fluorescent labelling of genomic information enables high-resolution optical analysis of DNA at the single-molecule level. Despite its simplici…
View article: Reduced representation optical methylation mapping (R<sup>2</sup>OM<sup>2</sup>)
Reduced representation optical methylation mapping (R<sup>2</sup>OM<sup>2</sup>) Open
Reduced representation methylation profiling is a method of analysis in which a subset of CpGs is used to report the overall methylation status of the probed genomic regions. This approach has been widely adopted for genome-scale bisulfite…
View article: Reduced representation optical methylation mapping (R<sup>2</sup>OM<sup>2</sup>)
Reduced representation optical methylation mapping (R<sup>2</sup>OM<sup>2</sup>) Open
Reduced representation methylation analysis utilizes a subset of CpGs in order to report the overall methylation status of the probed genomic regions. Here, we use this concept in order to create fluorescent optical methylation profiles al…
View article: Super-Resolution Genome Mapping in Silicon Nanochannels
Super-Resolution Genome Mapping in Silicon Nanochannels Open
Optical genome mapping in nanochannels is a powerful genetic analysis method, complementary to deoxyribonucleic acid (DNA) sequencing. The method is based on detecting a pattern of fluorescent labels attached along individual DNA molecules…