Genetic Analysis News You Can Use

A recent paper “Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples” published online in PLoS ONE details an optimized genotyping platform of 400 somatic mutations in 33 oncogenes and tumor suppressors known to predict response or resistance to targeted therapies. The platform, dubbed OncoMap, utilizes iPLEX Gold single base extension coupled with Sequenom’s MassARRAY® system, and provides an update to the original panel of 17 oncogenes.

Publication highlights include:
-Analysis using DNA derived from frozen and FFPE clinical material
-Discussion of “actionable” cancer gene mutations across diverse cancer types
-Detection of known mutations in common cancers
-Screening of known and novel mutations in adult and pediatric cancers
-Extensive study of adenocarcinomas (n=625) of tumors of the breast, lung, prostate, and GI tract
-Details of the methods and assay design including PCR and primer extension sequences

Grant Application Support Page

On our newly revised grant resources web page you will find a wealth of information to support your applications and grant submissions involving the use of Sequenom MassARRAY products.
Featured are specific funding opportunities, including the NCI’s recently announced Epigenetic Approaches in Cancer Epidemiology grant program. In addition, links will take you to technical assistance documents designed to provide basic grant application information, helpful tips, and information on how Sequenom MassARRAY products can aid your research endeavors.
 

An upstream insulator regulates DLK1 imprinting in AML

Khoury, H, et al., Blood First Edition Paper, prepublished online January 20, 2010; DOI 10.1182/blood-2009-03-212746.
DLK1 is a transmembrane protein of the epidermal growth factor family. It is normally imprinted and expressed only from the paternal allele. Using coding SNPs, expression was found to be biallelic in 76% of AML samples over-expressing DLK1.  To determine whether changes in methylation of CpG-rich regions upstream and downstream of DLK1 were associated with the loss of DLK1 imprinting, the authors assessed the methylation of 7 CpG-rich regions using Sequenom MassARRAY EpiTYPER. A strong association between bi-allelic expression and hypermethylation of a region 18Kb upstream of DLK1 was revealed. This hypermethylation inhibits binding of the insulator protein CTCF. It is proposed that this CpG-rich area acts as an insulator of DLK1 imprinting. Hypermethylation results in the loss of CTCF binding and creates a condition more permissive for transcription.

Plant & Animal Genome XVIII Workshop Recording

Agricultural genomic researchers from the University of Illinois at Urbana-Champaign, Southern Cross University, and Pfizer Animal Health, presented how they validated next-gen sequencing data as well as design SNP panels for large sample screening based on the flexible and cost-effective MassARRAY platform. 
The workshop recording is now available online for those of you who missed the opportunity to attend the workshop.