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NIH, ParagonDx, Iverson Genetic Diagnostics, DeCode Genetics, US Preventive Medicine, PerkinElmer, Cerep, Dana-Farber Cancer Institute, Memorial Sloan-Kettering Cancer Center, Signature Genomic Laboratories

NIH Seeks Suggestions on Problems Facing Pharmacogenomics
The National Institutes of Health is seeking information about the barriers and challenges confronting the fields of pharmacogenomics and pharmacogenetics and wants to hear suggestions about how to address them, the institute said in a request for information posted on its website last week.
To find out more about these challenges, NIH is inviting responses from the scientific community, pharmaceutical companies, federal agencies, and other parties. The agency also wants to hear “transformative ideas and approaches” about how to address the difficulties facing these new branches of medical science.
“Collectively, we want to identify ways in which NIH can effectively and efficiently address these barriers,” NIH said in the RFI. More specifically, the agency continued, the “best ideas will have great potential to dramatically affect how biomedical research is conducted over the next decade, yet will be concrete and achievable tasks.”
Examples of the type of ideas NIH is seeking include those that would address challenges that “no other entity is likely to be able to successfully conduct,” those that will generate publicly accessible knowledge, and those that clearly benefit public health.
The National Institute of General Medical Sciences will collect the suggestions on behalf of the Trans-NIH Pharmacogenomics Working Group. Suggestions are to be sent to the NIGMS website by April 30.

ParagonDx Signs on Partner for Warfarin PGx Test
ParagonDx said this week that Iverson Genetic Diagnostics will use its pharmacogenomics test to determine warfarin sensitivity among patients taking the blood thinner.
IGD is a Seattle-based CLIA-certified lab that had been using a blood-based method for determining warfarin dosing, Research Triangle Park, NC-based ParagonDx said. Now, it will use a saliva-based test that incorporates ParagonDx’s technology and provides results the same day, as opposed to in two to three days with the blood-based test.
Terms of the alliance were not disclosed.

DeCode to Team with US Preventive Medicine on Genetic Test Offering
DeCode Genetics and US Preventive Medicine announced last week that they have signed a letter of intent to collaborate on offering genetic testing to US Preventive Medicine customers.
Dallas-based US Preventive Medicine offers preventive care, wellness, and disease-management services to employers, consumers, and government agencies. The privately held firm said that it is building a personalized medicine business in the US.
“The signing of the letter of intent with DeCode is significant because we will be the first entity in the US and internationally to offer a full continuum of geographically dispersed, comprehensive solutions for personalized medicine,” Christopher Fey, chairman and CEO of US Preventive Medicine, said in a statement.
Terms of the alliance were not disclosed.

PerkinElmer, Cerep Partner on Drug Discovery Tools
PerkinElmer this week announced that it has signed a co-marketing agreement with Cerep to provide custom drug discovery tools and services to customers.
Under the agreement, PerkinElmer will exclusively market Cerep’s target screening and profiling services to its customers. The firms also will jointly promote PerkinElmer’s assay technologies and Cerep’s high-throughput screening and profiling services to the drug discovery market.
PerkinElmer said that the alliance provides its customers with an option to work with a single vendor throughout the entire drug discovery process.
“This agreement represents the latest step in our strategy to build the most comprehensive offering in biochemical and cellular screening for drug discovery,” PerkinElmer President and CEO Robert Friel said in a statement.
The firm rapidly expanded its cellular analysis and screening business early in 2007 with the acquisitions of Evotec Technologies, Euroscreen Products, and Improvision.
Paris-based Cerep specializes in custom binding, cellular, and tissue assay services. It also has developed the BioPrint pharmacoinformatics platform.

Algorithm Helps Researchers Sort Brain Cancer Genomic Data
Researchers from the Dana-Farber Cancer Institute, Memorial Sloan-Kettering Cancer Center, and elsewhere have developed the so-called genome topography scan, or GTS, algorithm to rank mutations associated with a type of brain cancer called glioblastoma and finger those mutations most likely to affect cancer development and progression. In the process, they identified a new functional pathway involved in glioblastoma’s tumorigenesis.
The results appear online this week in the journal Cancer Cell
“We have demonstrated here that GTS can address one critical need in the development of a functional map of [glioblastoma] genetic targets: namely, to prioritize those genomic alterations that are likely to be of importance from among those that are more likely to be bystanders of the cancer process,” co-lead authors Ruprecht Wiedemeyer, a post-doctoral fellow at Dana-Farber, and Cameron Brennan, a neurosurgeon and researcher affiliated with Memorial Sloan-Kettering and Weill-Cornell Medical College, and colleagues wrote.
Although many genes have been implicated in different types of cancer, determining which mutations are really relevant to the condition being studied is often daunting.
The GTS approach involves combining several types of data about chromosomal copy aberrations found in cancerous cells — including the level of variation, how often they occurred, and whether they were specifically focused or covered a wide region on the chromosome.
For this study, the team applied this three-dimensional, high-resolution genome topography scan to glioblastoma, a type of adult brain cancer that is notoriously aggressive and difficult to treat.
First, they identified genes of interest in 28 related tumor samples and 18 cell lines using array-comparative genomic hybridization profiling on Agilent’s 60-mer 44K or 244K density microarrays.
They then analyzed the data to determine factors such as amplitude and width of copy number aberrations and their frequency in different parts of the genome. By putting this information into the algorithm, the team was able to rank the top 50 amplification and deletion mutations associated with glioblastoma.
Although they picked up some genes that had previously been associated with glioblastoma, the approach allowed them to uncover a new glioblastoma-related gene, called p18INK4C, whose depletion is linked to the cancer. As it turns out, this gene seems to function in a cellular pathway that’s parallel to another gene often missing from brain cancer cells: p16INK4A, a gene that codes for a tumor suppressor protein.
Subsequent experiments supported the notion that these two related genes function in parallel pathways, curbing glioblastoma. On the other hand, when both genes are absent or mutated, glioblastoma develops or becomes more dangerous. For instance, when the researchers used short hairpin RNAs to knock down p18INK4C in cells lacking p16INK4A, the cells became more tumorigenic.
“Just a few years ago, the view was that pathways were largely linear,” senior author Lynda Chin, a dermatologist and oncologist affiliated with the Dana-Farber Cancer Institute and the Belfer Institute for Innovative Cancer Science, said in a statement. “We’re increasingly coming to appreciate, however, that they operate in concert — that each one has multiple tentacles reaching out to other pathways and they function collectively as a network.”
And, researchers say, the algorithm may also prove useful for interpreting data collected from large-scale cancer genome research projects. It is also expected to be added to the BioConductor website, which hosts open-source bioinformatics software.

Signature Genomics Launches Program to Advocate For Insurance Coverage For Patients' Lab Testing
Signature Genomic Laboratories has introduced a patient advocacy program to assist patients and their families with obtaining insurance coverage for microarray analysis. Through the program's advocacy staff, Signature will negotiate with patients' insurance carrier on their behalf to determine the benefits available for clinical laboratory testing.
“If the insurance carrier refuses to pay for all or part of the charge, the Patient Advocacy Team will work with the patient to submit an appeal or develop an alternate payment plan,” the company said in a statement this week.

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