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Whole-genome chips; mapping


In our October issue a year ago, GT wrote about the coming wave of microarray chips representing the entire complement of human genes. We compared the offerings in terms of content, platform technology, and price, still understanding that technology advances on the horizon would soon cause the whole-genome chip to fade into obsolescence. Were we right?

Yes and no (sorry about the cop-out answer). On the one hand, vendors have continued to pop out increasingly comprehensive microarray products. Affymetrix has expanded the number of SNPs it offers on its GeneChip platform, and Affymetrix, Applied Biosystems, and Agilent Technologies have increased their offerings of whole-genome chips — human, and now mouse and rat. Significantly, however, none of the major pre-printed microarray chip vendors has taken the next step in terms of chip density: arraying much larger genomes such as that of rice.

Our October issue also reported on OpGen, a Madison, Wis., purveyor of genome mapping technology. A year ago, the company was in the midst of a round of funding worth $3 million, and was moving toward commercializing the restriction enzyme-based technology for applications in cancer clinical trials as a means of predicting responders and non-responders for a particular drug. As this issue of GT went to press, OpGen had recently added James Ogle, CEO of contract research services firm INC Research, to its board of directors, a move the company hopes will help it appeal to big pharma. OpGen also began collaborating with GeoSpiza to build a genome sequencing and assembly tool that incorporates optical mapping data.


The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.