Jason Mundin, MBA, Director of Collaborations at Population Genetics, gave a Knowledge and Technology Transfer seminar, presenting his company, last 25th July in IDIBELL. Population Genetics, created in 2005 by Dr Sydney Brenner, Nobel Laureate in Medicine, has developed novel sequencing approaches to identify variants in candidate genomic regions in populations ranging in size from hundreds to thousands of individuals.
Population Genetics has developed a novel, proprietary approach for the rapid identification of genetic variants in large populations of interest. “It was a simple idea, but the most complicated was to make it work”, said Mundin. Based on concepts proposed by Sydney Brenner, this approach is applicable to DNA from any source. It can simultaneously re-sequence candidate genomic regions of interest in populations of thousands of individual genomes suspected of characterizing a particular phenotype. This enables the identification of variants that correlate with phenotype, whether they are already known, novel or rare, in applications ranging from human healthcare to agbiotech.
The approach of Population Genetics avoids the need to laboriously sequence thousands of samples individually. The proprietary technology it uses tags and pools multiple genomes into a single population library. Specific genomic regions can then be extracted from the library into a single sample that can be sequenced using the latest technologies to identify variants, all the while preserving their association with individual genomes from within the population.
The benefits of this approach include savings in time and cost and also a significant reduction in the bioinformatic problems, typically associated with genomic analyses.
The Genetics Space: Needs and Opportunities
The main objective of the company is to provide solutions in genetics research partnerships. “We also work in biomarkers discovery and validation, to understand the illnesses”, said Jason Mundin.
Population Genetics has developed proprietary technologies designed to support hypothesis led genetic investigation, which are being used in the context of strategic partnerships. The two approaches are GenomePooling™, for targeted sequencing of non-contiguous regions across large populations of genomes for the identification of genetic variations that correlate with phenotype, and Reflex™, for targeted sequencing of long contiguous regions across large populations.
GenomePooling™ begins with the construction of a mixed population library. Each genomic DNA sample to be included in the mixed population library is individually fragmented and tagged with a unique DNA sequence tag (a DNA bar-code). All of the tagged genomic DNA fragments are then pooled into a mixed population library that may contain hundreds to thousands of individuals together in a single tube. Each individual’s DNA fragments within the mixed population library can be identified via its unique sample-specific DNA bar-code. In addition, the tags include a degenerate base run sequence such that, within each individual’s genomic DNA sample within the mixed population library, different input genomic DNA molecules can be identified. This allows bona-fide variants present on multiple input DNA molecules to be distinguished from false positives, such as PCR errors, that would only be present on single input DNA molecules. Regions of interest are selected for sequencing across the mixed population library based upon collective insights into the biology of the disease or drug response.
“In GenomePooling™ we use a uniquely barcode individual genomes, we amplify and store, we target and enrich fragments (as desired) from genes / genomic regions retaining barcodes”, continued Mundin.
The technology used is very precise. “We have identified five additional patient mutations not detected by DHPLC. All these applications can be used in heterogeneous tumour samples”, said Mundin.
The other technology is Reflex™, a novel and highly effective method for sequencing long contiguous regions, such as whole genes (including coding and non-coding regions), across large populations of interest for the identification of genetic variants that correlate with phenotype. This technology has applications in human healthcare, such as the identification of multiple variants within pathogenic viruses such as HIV and hepatitis B.
Population Genomics has collaborated in different projects like IntReALL 2010: acute lymphoblastic leukeamia relapse study (FP7); University of Cardiff: Alzheimer Disease study; Oxford University in a research/technology collaboration; Major Pharma in mouse models; and UK academic research group in renal cell carcinoma, among others.