SEARCH

SEARCH BY CITATION

Genomic Sequencing System Promises Results Within Hours

  1. Top of page
  2. Genomic Sequencing System Promises Results Within Hours
  3. Reference

inline image

Since the platform combines target capture, amplification, and DNA sequencing, a researcher can inject a nucleic acid sample into the system to obtain results.

A new desktop DNA sequencing system may enable physicians to get genetic test results within a few hours as opposed to weeks as is standard.

An early version of the system, designed by Cambridge, Massachusetts-based GnuBIO, is being used at the Université de Montréal Pharmacogenomics Centre at the Montreal Heart Institute to sequence a blinded cohort of clinical cardiomyopathy samples, according to a company news release. In June the company announced that its researchers worked with researchers at City of Hope, a National Cancer Institute-designated Comprehensive Care Center in Duarte, California, to assess the presence of the TP53 gene, which encodes for the protein tumor suppressor p53.

Since the platform combines target capture, amplification, and DNA sequencing, a researcher can inject a nucleic acid sample into the system to obtain results. It also makes it more cost-effective for samples to be sequenced individually rather than in batches.

Researchers Consider Use of Cord Blood for Blood Stem Cell Transplants

A new project will investigate how to make better use of umbilical cord cells as a potential source of blood stem cells for adult patients with hematological cancers and sickle cell anemia.inline image

According to the U.S. Department of Health and Human Services, each year about 70% of patients with blood cancer in the U.S. do not find a matching family donor.

Hematopoietic stem cells from umbilical cord blood have proven to be a viable source of allogeneic transplant for pediatric patients but less so in adult patients because of the limited number of cells available in each cord sample. For the 3-year project, funded by $840,000 from the University of California- San Francisco (UCSF) and Cell Technologies of GE Healthcare Life Sciences, researchers will hunt for chemical compounds that can be added to the stem cells and progenitor cells in cord blood to increase their population to the size needed by a diseased blood system.

“We would like to be able to expand the number of stem cells but we certainly wouldn't be disappointed if we also were able to identify a compound that also gave us a little expansion of progenitor cells, cells that don't last forever but that kind of benefit the patient quickly and transiently until the stem cells set

“Th e system is unique in that you put DNA on one end and you get your results on the other end,” says Jakub Sram, PhD, MBA, director of Business Development at the City of Hope Molecular and Diagnostic Laboratory. “With many other systems, you have to get DNA, you have to share DNA, you have to amplify it, there are many, many steps. With this, you can do it all on one instrument.”

According to GnuBIO, the system will be available commercially by the end of 2012. It is projected to sell for under $50,000.up shop,” says Andrew Levitts, MD, medical director of the Bone Marrow Transplant Laboratory at UCSF. Dr. Levitts adds that while it's becoming more common for adults to be treated with 2 blood cords, there are theoretical concerns that both cords will not match up well with the patients’ immune systems. “That is, in principle, going to be a suboptimal situation than having a single donor. At the end of the day, the observation is that one of the cords wins,” he says.

According to Michelle Arkin, PhD, associate director of the Small Molecule Discovery Center at UCSF, the researchers will use robotic technology with a built-in assay to screen about 120,000 chemicals for those that may trigger the expansion of stem and progenitor cells.

“We can get some preliminary reads on that from this assay,” Dr. Arkin said. “Then we’ll take the compounds that are active in this assay and we’ll test them at multiple doses and multiple time points to get much more complete descriptions of a stem cell and a progenitor cell so that we can really hone in on those compounds, the ones that truly affect only the cell types that we’re interested in.”

The next phase of research, she said, would involve chemical optimization and mechanism of action.

NIH investigators will work with research teams to design experiments that will move the compounds being investigated further down the drug pipeline.

Six NIH-funded Research Projects Aim to Find New Treatments for Rare Diseases

In late 2011, the National Institutes of Health (NIH) announced 6 new drug development projects for rare or neglected diseases. The projects are part of the NIH's Therapeutics for Rare and Neglected Diseases (TRND) program created in 2009 to support the pre-clinical development of new drugs for diseases that affect less than 200,000 patients in the U.S., according to TRND Director John McKew, PhD.

The potential treatments would target: inline image

  • • 
    fibrodysplasia ossifi cans, a progressive, musculoskeletal disorder;
  • • 
    creatine transporter deficiency, a cognitive dysfunction disorder;
  • • 
    neonatal herpes simplex, a virus that affects the central nervous system of newborns;
  • • 
    schistosomiasis, a neglected tropical disease caused by parasitic worm infection;
  • • 
    Duchenne muscular dystrophy, an inherited, rapidly progressive form of muscular dystrophy; and
  • • 
    autoimmune pulmonary alveolar proteinosis, a rare lung disease.

Dr. McKew says internal NIH investigators will work with research teams selected by the TRND program to design experiments that will move the compounds being investigated further down the drug pipeline. The NIH received 120 applications during 2 rounds of solicitations, he says. Applicants were asked to describe their projects and molecules, including a projected development path to move the compounds into early clinical testing.

“We have a matrix that we grade these on that's based on the strength of the current data package, the target validations, and connection to human disease, feasibility for research in humans, what the differentiation is away from standard of care, and then some kind of piece on the endgame strategy for this molecule,” Dr. McKew says. “So, what's going to happen to this molecule after we invest in it? Are there other players in the field? Are there other companies that would be interested in working in it?”

For more information about the next solicitation for TRND projects visit nctt.nih.gov/TRND.

Improved Chemotherapy Response Associated with BRCA2 Mutation

Women with a specific high-grade ovarian cancer who also had BRCA2 mutations had an improved overall survival and response to chemotherapy compared to women with BRCA wild-type, according to a study recently published in the Journal of the American Medical Association.1inline image

Da Yang, PhD, of the University of Texas MD Anderson Cancer Center, and colleagues investigated the association between BRCA1/2 deficiencies in ovarian cancer and patient overall survival (OS), progression free survival (PFS) rates, and chemotherapy response. The study evaluated multidimensional genomics and clinical data on 316 high-grade serous ovarian cancer cases made available between 2009 and 2010 through the Cancer Genome Atlas Project. Patients with both mutations did not differ significantly from each other in regard to tumor stage, grade, and histologic type, but patients with BRCA1 mutations were younger at diagnosis than were those with wild-type BRCA or BRCA2 mutation (35 cases, average age 56; 219 cases, average age 62; and 27 cases, average age 61, respectively.)

The 5-year survival rate for BRCA2 mutation carriers was 61 percent, significantly higher than that of wild-type BRCA cases at 25 percent.

The 5-year survival rate for BRCA2 mutation carriers was 61 percent, significantly higher than that of wild-type BRCA cases at 25 percent. BRCA2 carriers also had significantly longer PFS than wild-type carriers. At the same time, 44 percent of BRCA2 carriers remained progression free 3 years after surgery compared to 22 percent of BRCA1 cases.

BRCA2 cases also were associated with a significantly higher primary chemotherapy sensitivity rate (100 percent versus 82 percent for wild-type and 80 percent for BRCA1), as well as longer platinumfree duration. The latter was 18 months for BRCA2 versus 11.7 months and 12.5 months for BRCA wildtype and BRCA1 mutated cases, respectively. These discoveries may have important implications for clinical predictions and trial design, the researchers note.

Reprinted with permission from Cancer 2012;118(6). Copyright 2012 American Cancer Society. CTS

Reference

  1. Top of page
  2. Genomic Sequencing System Promises Results Within Hours
  3. Reference
  • 1
    D. Yang, S. Khan, Y. Sun, et al . Association of BRCA1 and BRCA2 Mutations with Survival, Chemotherapy Sensitivity, and Gene Mutator Phenotype in Patients with Ovarian Cancer. JAMA 2011;306(14):15571565.