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Archives for July 2012

Population Genetics Validates GenomePooling for Cancer

Population Genetics Technologies Ltd., creator of innovative methods for genetic analyses and biomarker discovery, has successfully completed a pilot study to prove that its GenomePooling™ method is sensitive and accurate enough to detect even small percentages of gene variants within cancer tissue. This validates the method’s suitability for use in IntReALL, the world’s largest genetic analysis of acute lymphoblastic leukaemia (ALL) relapse cases. ALL is the most common childhood malignant disease.

Cancer tissues are problematic because they can contain multiple tissue types and multiple cancer variants that may respond differently to treatment. Being able to identify associations between genotype and treatment responsiveness matters because, if a tumour contains highly drug resistant variants, or the patient has a genetic predisposition to relapse, alternative treatments may be appropriate. In order to demonstrate their ability to detect variants in mixed tumour tissue, Population Genetics mixed two different DNA samples and showed using their novel molecular counting technology that they could identify variants with high sensitivity.

The pilot compared data derived by Population Genetics from ALL patients and cell-line derived samples with data generated in a parallel study. The parallel study was undertaken by Dr Julie Irving, Reader in Experimental Haematology at Newcastle University, who used the conventional mutational screening method, called DHPLC (denaturing high-performance liquid chromatography).

Explained Julie Irving: “Our comparative study showed that Population Genetics’ methodology is accurate, more sensitive and thus superior to the standard DHPLC method. This gives us confidence that it is the right workflow to use for interrogating data from the large population IntReALL study which is just getting underway”.

Population Genetics sequenced 28 discrete genomic regions across a total of 50 human genomic DNA samples, 40 derived from patients suffering ALL and 10 derived from cell lines containing a mix of mutated and wild type phenotypes of two known genes. The Population Genetics method identified all the known mutations and an additional five that were not detected by DHPLC; these novel variants were then confirmed by Sanger sequencing and allele specific polymerase chain reaction.

ALL affects 4 per 100,000 children per year in Europe but intensive combination chemotherapy with stem cell transplantation has improved survival from under 20% in the 1970s to over 80% today. However treatment is complex and prolonged and it is unclear why some children do not respond to, or relapse after, existing treatments.

IntReALL 2010 comprises 23 research teams, led by Vaskar Saha, Professor of Paediatric Oncology at The University of Manchester, gathering DNA across Europe, Japan, Israel and Australia from children who have relapsed after treatment for ALL. Funded by IntReALL’s EU FP7 grant, Population Genetics will study the resulting biobank of leukaemia samples using proprietary GenomePooling workflows to identify and validate associations between genetic risk factors and treatment efficacy. It is hoped that the IntReALL study will aid in the optimisation of therapy based on genetic stratification and allow randomised controlled trials of potential new drugs.

Alan Schafer, CEO of Population Genetics, commented: “Accurately and sensitively detecting genetic variants in large numbers of samples is critical for developing genetic biomarkers for cancer. For this collaboration we created a version of GenomePooling suited to the study needs, and have established cancer as another application in which our population-scale genetic analysis methods have demonstrated their utility. Our approach enables the generation of statistically rich information from thousands of genomes with resolution down to the level of the individual. We look forward to working with the IntReALL consortium to potentially improve treatment outcomes for children suffering ALL”.

Source: Population Genetics

The PROOF Centre of Excellence Partners with OriGene Technologies on Heart & Kidney Transplant Biomarker Program

OriGene Technologies, Inc. and Canada’s Centre of Excellence for the Prevention of Organ Failure (PROOF Centre) recently announced the selection of OriGene Technologies as a major collaboration and development partner to implement blood-based protein assays in heart and kidney transplantation. This multi-year, collaborative project funded by multiple partners will provide monitoring and predictive blood tests, based upon OriGene’s extensive expertise in immunoassay and antibody development, to improve the care of heart and kidney transplant patients worldwide.

EPA Awards $27 Million Contract to EA for Expansion of ToxCast’s Genomic Data

The Environmental Protection Agency’s (EPA) ToxCast™ Program, launched to forecast the toxicity of chemical compounds for humans and the environment, is expanding genomic data collection through a renewed five-year contract with Expression Analysis (EA), which will serve as the program’s primary contractor for RNA biomarker analysis.

Great Point Partners Announces Sale of Caprion Proteomics

Great Point Partners, LLC recently announced the sale of Caprion Proteomics, Inc., a Great Point Partners I portfolio company. Caprion is a leading provider of proteomic services to the pharmaceutical industry that include: (i) biomarker discovery, (ii) biomarker validation, (iii) drug target discovery, (iv) advanced immune monitoring services, and (v) in-vitro diagnostics development. Under Great Point’s investment, Caprion grew EBITDA by over 300x. The growth was primarily driven through strong organic growth, industry leadership and accretive tuck-in acquisitions.

Cambridge Healthtech Associates Announces Results of Survey on Trends in Safety Biomarkers

Cambridge Healthtech Associates™ (CHA™), today announced results of industry survey of biotech and pharmaceutical companies on the use of safety biomarkers in the development of new medications.

Recently, Cambridge Healthtech Associates, through the Drug Safety Executive Council™ (DSEC™), completed interviews with preclinical safety experts from large and small biotech and pharmaceutical companies, focusing on middle and senior level managers in preclinical safety and toxicology groups.

The goal of the research was to identify trends in biomarkers and their utilization in these top tier companies. The survey builds on CHA’s seven year history of technology evaluation projects in the life sciences.

Ernie Bush, Ph.D., Scientific Director in drug safety and development, for DSEC and CHA, led this research project. Dr. Ernie Bush has nearly 30 years of biomedical research, focused on:

  • Preclinical safety assessment; and the
  • Navigation, evaluation and prioritization of biopharmaceutical research initiatives.

Some of the key findings of the safety biomarkers research include the following:

  • Biomarkers of organ toxicity are consistently rated as one of the most desired new tools by this industry segment. In this current study, most interviewees found the inclusion of systems or pathway modeling into the selection and interpretation of safety biomarkers to be an attractive new element. We have also seen this pattern emerge in CHA’s annual New Technology Adoption surveys.
  • In theory, knowing the levels and profiles of various safety biomarkers will improve the understanding of the mechanism and relevance of the animal studies relative to human clinical safety prediction.
  • The following trends emerged in ’early’ safety tests in drug discovery (tests that companies use more than 50% of the time):
    • Small companies are far less aggressive than larger companies in terms of the volume of tests conducted, and how early those tests are administered.
    • Most companies are running physical chemical prediction software, and about half are using DEREK or other forms of gene or DART prediction software. Most companies conduct HCA cell health parameter screening of some form, with the exception of small companies.
    • Surprisingly, most companies, large and small, did a form of off-target screening (usually CEREP), with smaller companies performing the screens later in the process.
    • The range of early safety tests run at large and small pharmas was from about 20% to over 90%, but the average was about 60%.

“We are always interested in trends in the life sciences industry and our recent surveys indicate a growing interest in the use of biomarkers in early drug safety testing. We believe this is one of several areas of growth for the future,” said Dawn Van Dam, General Manager for Cambridge Healthtech Associates and the Drug Safety Executive Council.

Source: Cambridge Healthtech Associates