Selected category: Genomics

Dr Sam Abraham is an associate professor at Murdoch University, Australia, with a research interest in antimicrobial resistance and drug discovery. His presentation at Tecan’s virtual Genomics Symposium can be viewed here.

The human gut microbiome has been found to affect metabolic health and nutrient absorption, and preliminary research also suggests that it contributes to the development of the immune response, food allergies and intolerances, obesity, and a wide range of other conditions. This field is the focus of Ortho-Analytic, an integrative medicine laboratory based in Wallisellen, Switzerland, that identifies bacterial, fungal and parasite DNA found in stool samples. The company uses molecular genetic analyses to build a detailed picture of a patient’s gut microbiome, aiding practitioners in formulating specific treatment plans.

Precision medicine is potentially revolutionizing diagnostics and treatment by targeting mutations that are specific to individual patients with various diseases, including cancer. The Institute of Pathology and Neuropathology at the Essen University Hospital, Germany, is following this ethos, relying on NGS to look for biomarkers associated with a number of key malignancies.

Interest and research into the human microbiome have boomed in recent years, and it is now known that the bacteria that colonize the gut of animals and humans play vital functions in health and disease. Despite this, scientists have only just begun to skim the surface of microbiome knowledge, and there is still so much to learn. Researchers in the Adams Lab at the Jackson Laboratory for Genomic Medicine are focused on the creation of different assays and analyses to help study the microbiome.

It has been estimated that, by 2050, the world will need to produce 70% more food than in 2005, and will need 50% more fresh water and fuel, while reducing CO₂ emissions by 100%. These are massive global challenges that are not going to be solved by current technologies, which is why international teams at the Centre for Solar Biotechnology, based at the Institute for Molecular Bioscience (IMB) at The University of Queensland, Australia, are working with a wide range of industry partners to advance novel algae-based solutions to tackle these issues.

The potential of ‘omics’ to further our understanding of cell biology and disease progression has been discussed for over 30 years, but these technologies have so far failed to translate to a healthcare setting. One of the major challenges has been the lack of reproducible results, making it difficult to distinguish between true discoveries and experimental artifacts. ProtiFi was founded to overcome these challenges: to solve the bottlenecks around sampling, sample preparation and data interpretation in order to accelerate the deployment of omics technologies in real-world clinical applications.

The emergence and outbreak of the novel coronavirus SARS-CoV-2 at the end of 2019 has created an urgent need for testing to help limit the spread of COVID-19. AusDiagnostics has used its patented, multiplexed-tandem PCR technology to develop a test to detect SARS-CoV-2 and distinguish between the different causes of coronavirus-like infections.

The COVID-19 pandemic has required an unprecedented level of collaboration within the scientific community, as labs around the world aim to characterize and understand the SARS-CoV-2 virus in order to develop and implement new diagnostic tests, therapeutics and vaccines. This cooperative approach has led to some unexpected partnerships, as techniques and knowhow from across numerous disciplines are brought together to accelerate research and testing activities. Professor Nir Friedman’s team at the Hebrew University of Jerusalem has been at the center of one such situation, using its knowledge of workflow automation from investigating yeast genomics to develop a novel large-scale sequencing-based assay for the detection of SARS-CoV-2.

The COVID-19 pandemic sweeping the globe has highlighted the need for the rapid development of new diagnostic tests, therapeutics and vaccines in response to emerging infectious diseases. Advanced gene assembly techniques represent a powerful tool to aid these efforts, and are currently allowing the construction of synthetic SARS-CoV-2 genomes for research and development activities. Codex DNA is at the forefront of this approach, using its knowhow and BioXp™ 3200 system to supply labs across the globe with the gene constructs required to accelerate the design and optimization of vaccines and treatments.

DNA isolation and PCR set-up can be laborious and time consuming when performed manually. Dutch pathology and microbiology services provider PAMM has overcome this issue by automating its molecular testing protocols for sexually transmitted infections and gastrointestinal conditions, freeing up staff to perform other tasks.

Genetic testing is at the forefront of modern medicine, and powerful tools are now available to identify inherited DNA characteristics that are potentially detrimental to health or conversely show susceptibility to targeted therapies. One such service, the Sanford Chip, has been developed by Sanford Health as a screening tool to identify pathogenic and likely pathogenic genetic variations that can be used to estimate the risk of some cancers and cardiac conditions.

Genetic testing to screen for congenital defects is useful to identify susceptibility to, or the cause of, many diseases. The medical genetics department at the Policlinico di Milano – a teaching hospital in Italy’s Lombardy region – is using automation to improve the throughput of its genetic screening workflow, aiming to increase the number of diseases it can test for, and the number of samples it can handle.

CNS disorders are often seen as the greatest area of unmet medical need, and are characterized by changes or degeneration in specific subsets of neurons and other cell types in the brain. Pharmaceutical start-up Cerevance is using a new sequencing method to study specific cell types from post-mortem brain tissue, helping the company to understand the pathology of these conditions in more detail than previously possible.

Quality control of milk is important to ensure compliance with regulations and to support dairy farmers in their herd management. However, analyzing multiple milk samples from many individual cows is a time-consuming process. French laboratory AGRANIS is using a new, automated genotyping technique to analyze bulk tank milk samples, saving time and money on its testing services.

NuGEN Technologies – a specialist in NGS and genomic sample preparation products – joined the Tecan Group in September 2018, opening up exciting new opportunities for integrated NGS workflow solutions.

Automation is helping the University Hospital Münster to streamline its molecular diagnostics workflows, increasing throughput for Sanger sequencing and NGS library preparation.

Next generation sequencing is now in widespread use throughout the life sciences sector, but the commonly used short-read sequencing methods are often subject to GC base pair bias. Combined with the inherent mapping ambiguity of the short reads, this often results in fragmented genome assemblies, creating a demand for technologies offering longer reads that simplify analysis and yield more complete sequences. Using its proprietary technology, Pacific Biosciences is able to offer longer reads, more uniform coverage and high accuracy, supporting advanced genomics, full-length transcript sequencing and epigenetics.

Canada’s Molecular Genetics Laboratory at the Pacific Biological Station uses DNA analysis to identify and track salmon from different hatcheries. Automated NGS has enabled the laboratory to introduce parentage-based tagging, a cost-effective alternative to the coded wire tag system.

Microbiome research is still in its infancy, with little currently understood about the role micro-organisms play in both maintaining our day-to-day health and the genesis of disease. Researchers at the Karolinska Institute are using next generation sequencing to establish a baseline of the microbiota present in healthy individuals as a starting point for the development of new therapeutic strategies for a wide range of diseases.

Automation has an important role to play in molecular diagnostic workflows, minimizing manual interventions to help enhance throughput. Mobidiag has developed a CE-marked, automated platform for nucleic acid extraction and PCR plate set-up, enabling high volume screening and antibiotic resistance testing for gastrointestinal pathogens.

PTP’s Genomics Platform has automated all the steps from DNA/RNA extraction to the preparation of sequencing pools. Using three Freedom EVO® platforms, comprehensive automated workflows ensure high quality data and complete sample traceability, with a daily throughput of up to 288 genomic DNA samples.

A Freedom EVO® platform is helping scientists at Italy’s Stazione Zoologica Anton Dohrn, one of the world’s top marine biology and ecology research institutions, to provide a range of automated genomics services for marine biologists.

Human genetics and drug discovery are now inextricably linked, with large pharmaceutical companies, small biotech and even academic laboratories turning to sequencing data to identify potential targets for new therapies. But is this information being used to the best effect? And does genetic testing have a role to play in helping today's patients as well as tomorrow’s? Dr Pierre-Alain Menoud, Scientific Manager for Molecular Diagnostics at Unilabs in Lausanne, Switzerland, discusses the potential benefits of genetic testing for both the understanding and treatment of disease.

The Leiden University Medical Center has integrated the Freedom EVO® NGS workstation into its molecular diagnostic testing and clinical research workflows. Taking advantage of this preconfigured solution, the center was quickly able to commission the platform for routine testing, while still having the flexibility to develop new protocols and conduct research studies.

The GeT genomics facility near Toulouse has been developing a series of automated NGS protocols in collaboration with Tecan – including Illumina’s TruSeq® DNA and RNA kits, as well as Bioo Scientific’s NEXTflex™ PCR-Free Modules – on two Freedom EVO® workstations, helping to improve throughput and reliability for a wide range of projects.

Researchers in the Synthetic Biology Center at the Massachusetts Institute of Technology are using a Freedom EVO® workstation to aid the development of genetic circuits. By automating the laborious liquid handling protocols, the platform has increased throughput from just a few samples to hundreds of experiments a day.

The Swedish national biobanking infrastructure, BBMRI.se (BioBanking and Molecular Resource Infrastructure of Sweden), has initiated a pilot study for the improvement and national harmonization of biobanking procedures in clinical cytology. Following a national procurement process, the first of 10Freedom EVO® liquid handling platforms has been installed in the Clinical Cytology Biobank at the Karolinska University Hospital.