Reforms Random Fragments
Rubicon Genomics' (www.rubicongenomics. com) OmniPlex technology, GenomePlex, reformats random fragments of genomic DNA into plexisomes, which are defined size DNA fragments, structured to allow large regions of a genome to be amplified simultaneously from a single locus or multiple loci. These plexisomes, called OmniPlex libraries, can amplify the entire human genome in a single reaction and also use a high processive, high-fidelity DNA polymerase, according to the company.
Rubicon has extended Omni-Plex technology into two areas: whole methylome amplification (WMA), which amplifies only methylated DNA sequences, and whole transcriptome amplification (WTA), which amplifies total RNA.
"WGA, WMA, and WTA are related technologies for amplifying nanograms of starting genomic DNA or RNA by a thousand-fold in fewer than three hours," notes John Langmore, Ph.D., vp of commercial development at Rubicon.
"WGA, WMA, and WTA produce amplified products that have been proven to perform as well or better than the template nucleic acids on most of the currently available genotyping, expression, and CGH platforms, including homogeneous assays such as TaqMan, and all the microarray and bead-based assays," claims Dr. Langmore.
Rubicon WGA can correctly amplify limited samples with degraded DNA such as serum, plasma, CSF, buccal swabs, blood spots, urine and formalin-fixed biopsies, with no background, Dr. Langmore continues.
"Rubicon's WGA, WMA, and WTA technologies can enable drug companies and institutions to discover novel drug targets from archived patient samples collected up to 50 years ago, as well as to evaluate effectiveness and toxicities for current drug development studies and clinical trials," according to Dr. Langmore.
"Samples, typically collected before the genomics era, and used for purposes other than gene analysis and gene expression, are unique because they are linked with extensive data on disease or treatment outcomes, but their usefulness is limited because there is insufficient DNA or RNA, and the DNA and RNA are often highly degraded or contain PCR inhibitors.
"These limitations in sample quantity and quality can cause substantial frequencies of allele or locus drop-out as well as total sample failure," Dr. Langmore asserts.
These technologies also allow amplification of DNA or RNA copy number and can dilute inhibitors in the sample if they are present.
"Genotyping, resequencing, methylation analysis, and abundance analysis of amplified materials are used to identify gene sequence, promoter methylation, and expression patterns associated with disease, which can lead to discovering new drug targets and predicting treatment outcomes," adds Dr. Langmore.