Genomic diagnostics beyond the sequence
BeyondSeq. Genomic diagnostics beyond the sequence.
Project BeyondSeq have participated, along with other two "sister" H2020 projects (MRG-GRammar 664918 and PROSEQO 687089), in a specialised interactive workshop called Common Dissemination Booster (CDB). It resulted in a common flier that you can find here.
December 31, 2018
I was contacted by artist Anna Dumitriu as a result of the work I was doing on the large, collaborative BeyondSeq project (an EU Horizon 2020 project, grant number 634890). As a result of this, Anna and I applied for external funding for her to develop an artistic interpretation of the work we were carrying out for the BeyondSeq project.
3rd Consortium Meeting
January 31, 2017
The 3rd project meeting was held in Chalmers University, Gothenburg, Sweden at the end of January 2017
During the meeting, each of the partners presented his team's work of the past few months, as well as upcoming expected progress and mutual projects were discussed.
July 14, 2017
Using a single-molecule approach, we observed a significantly reduced level of 5hmC in blood and colon cancers, and could distinguish between colon tumor and colon tissue adjacent to the tumor based on the global levels of this molecular biomarker.
To view the paper in open access click the "Read More" below
Irys Extract published in Bioinformatics
July 11, 2017
Irys Extract is a software tool for generating genomic information from data collected by the BioNano Genomics Irys platform. The tool allows the user easy access to the raw data in the form of cropped images and genetically aligned intensity profiles. The latter are also made compatible with the BED format for using with popular genomic browsers such as the UCSC Genome Browser.
Reduced representation optical methylation mapping (R2OM2) - published in bioRxiv
March 6, 2017
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 sequencing since it requires fewer sequencing reads and uses significantly less starting material than whole-genome analysis. Consequently, this method is suitable for profiling medical samples and single cells at high throughput and reduced costs. Here, we use this concept in order to create a pattern of fluorescent optical methylation profiles along individual DNA molecules. Reduced representation optical methylation mapping (R2OM2) in combination with Bionano Genomics next generation genome mapping (NGM) technology provides a hybrid genetic/epigenetic genome map of individual chromosome segments spanning hundreds of kilobase pairs (kbp). These long reads, along with the single-molecule resolution, allow for epigenetic variation calling and methylation analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell next generation sequencing (NGS).
Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping - published in bioRxiv
February 22, 2017
Variations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformation. Next-generation sequencing analyses are unable to reliably capture aberrations larger than the typical sequencing read length of several hundred bases. Long-read, single-molecule sequencing methods such as SMRT and nanopore sequencing can address larger variations, but require costly whole genome analysis. Here we describe a method for isolation and enrichment of a large genomic region of interest for targeted analysis based on Cas9 excision of two sites flanking the target region and isolation of the excised DNA segment by pulsed field gel electrophoresis. The isolated target remains intact and is ideally suited for optical genome mapping and long-read sequencing at high coverage. In addition, analysis is performed directly on native genomic DNA that retains genetic and epigenetic composition without amplification bias. This method enables detection of mutations and structural variants as well as detailed analysis by generation of hybrid scaffolds composed of optical maps and sequencing data at a fraction of the cost of whole genome sequencing.
Optical DNA mapping in nanofluidic devices: principles and applications - published in Lab on a Chip
January 10, 2017
In this review, we highlight the recent development in using nanofluidic channels for optical DNA mapping. We discuss the different labelling protocols that have been used and highlight examples of applications. We also discuss how the devices used can be tailored for the specific study of interest and discuss future applications beyond the DNA sequence.
December 30, 2016
Anna Dumitriu will undertake a 2017 Leverhulme Artist in Residence project engaging with the School of Chemistry at The University of Birmingham, collaborating with Dr Robert K Neely and colleagues to creatively explore the impact of new developments in chemistry on biotechnology.
Another paper published in Scientific Reports: Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping
November 1, 2016
The paper Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping demonstrates how genes coding for antibiotic resistance can be identified in optical maps of bacterial plasmids, using the CRISPR/Cas9 system.
Paper publication in Scientific Reports: Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules
July 27, 2016
The paper Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules was published in Scientific Reports.
This paper demonstrates how optical DNA mapping can be used to identify bacterial plasmids, that make bacteria resistant to antibiotics.
To see the full paper click the "Read Article" button below.
May 2016
Read about the BeyondSeq Project in the May 2016 edition of Adjacent Government!
Paper publication in ACS Infectious Diseases
March 23, 2016
The paper Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping was published in ACS Infectious Diseases.
This paper demonstrates how we can follow the spread of resistant bacteria during an outbreak of resistance at a hospital ward, using optical DNA mapping.
To see the full paper click the "Read Article" button below.
February 5, 2016
Read about the Beyonseq Project in EU Research Magazine!
2nd Consortium Meeting
February 2016
The 2nd project meeting was held in Paris on February 2016.
During the meeting, each partner presented the team's ongoing work in the past few months, as well as upcoming expected progress. Open sessions raised important issues related to future working techniques and discussions were made regarding the next steps of the project's execution.
Nanotech - It Will End in Blood... (Article in Ynet, Heb)
November 26, 2015
Dr. Ebenstein explains that this nanometric capability allows to accurately identify and quantify these chemical changes: "The therapeutic aspect of this development is that in the same blood test we would be able to evaluate the patient's own reaction to a specific treatment. Currently, one of the biggest problems is that while some of the patients react to one type of treatment, others react to a different type. This is a long and possibly fatal process for the patient, so in that sense, we have here a theoretical possibility to first test the potential treatment on the patient’s blood rather than on the patient itself, and see how the cells react".
Kick-off meeting hosted in Tel-Aviv
June 23, 2015
The BeyondSeq Kick-off Meeting took place on June 22-23, 2015 in Tel Aviv, Israel.
May 1, 2015
BeyondSeq's project details in the European Commission CORDIS portal
May 1, 2015
BeyondSeq, a new project in the area of Genomic Diagnostics is launched. It has been selected for funding by the highly-competitive Horizon 2020 Framework Programme of the European Union and will be launched this month. BeyondSeq, acronym stands for “genomic diagnostics beyond the sequence”, and is aiming to develop new diagnostic tools based on emerging optical DNA mapping technologies.