Robert B. Norgren, PhD
Rob Norgren of The University of Nebraska Medical Center and Katja Nowick of Lawrence Livermore National Laboratory discuss the innovation behind the development of the Affymetrix GeneChip® Rhesus Macaque Genome Array
Researchers at the University of Nebraska Medical Center (UNMC), in collaboration with scientists at Affymetrix, have discovered a novel way to derive sequences for microarrays, resulting in the first ever commercially available whole-genome rhesus macaque microarray. This advance in primate genome research may help researchers to better understand the evolutionary relationship between humans and other primates, and will increase the utility of rhesus macaque as a model organism for disease research.
Rob Norgren and his collaborators used human transcript annotation to design primers to amplify and sequence rhesus genes. In collaboration with Affymetrix, this strategy was extended to an in silico approach using information from the Baylor Rhesus Genome Project. This project resulted in a set of probes representing 18,296 rhesus/human orthologs, including transcript variants and more than 17,000 genes for the GeneChip® Rhesus Macaque Genome Array. The resulting human genome-derived macaque array was the first whole-genome rhesus expression array. The array design was published in the January 23, 2007, issue of BMC Genomics. Experiments illustrating the reliability and validity of the array were published in the February 28, 2007, issue of BMC Genomics.
"The normal way a microarray is developed, you have to wait until you have a complete genome project and then you cluster the ESTs [expressed sequence tags] and come up with a consensus sequence to align with the genome project. By using our method, we were able to get the orthologous rhesus macaque sequence using human sequences to design primers," said Norgren. "It was a nice shortcut. As far as I know, this is the only Affymetrix microarray that has been made in this way."
More Scientist Spotlights
- Mady Hornig, MD Mady Hornig, MA, MD, Director of Translational Medicine at Columbia University, discusses the use multiplexed immunoassays for studying chronic fatigue syndrome, known as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).
- Jizeng Jia, PhD Jizeng Jia, PhD, from the Institute of Crop Sciences, Chinese Academy of Agriculture Science, Beijing, discusses the limitations of current technologies and how they were overcome to develop the highest density wheat array commercially available.
- Gordon Mills, MD Gordon Mills, MD, PhD, of the University of Texas MD Anderson Cancer Center and "Dream Team" co-leader in Stand Up To Cancer®, discusses the importance of genomic profiling in the discovery of novel predictive markers to improve the effectiveness of cancer treatment.
- Mark I. McCarthy, MD Professor Mark McCarthy, from the University of Oxford, UK, outlines how the intersection of biobank capabilities, new study designs, and technological advances will improve our understanding of complex trait genetics.
- Bruno Stuhlmüller, PhD Bruno Stuhlmüller, PhD, head of the scientific laboratory and team leader at the Institute of the Rheumatology and Clinical Immunology department at the Charité Free University and Humboldt University, Berlin, discusses working with whole blood samples to identify mRNA and miRNA biomarkers for predictive rheumatoid arthritis treatments.
- Peter Ambros, PhD Peter Ambros, PhD, Associate Professor at the Children's Cancer Research Institute (CCRI) in Vienna, Austria discusses the way in which arrays are helping to unravel the complexities of the cancer genome and guiding patient-tailored treatment strategies.
- Austin Tanney, PhD Austin Tanney, PhD, Scientific Liaison Manager for Almac Diagnostics, UK, discusses the opportunities and challenges of working with FFPE tissue, and his visions for technologies driving towards personalized medicine.
- Jay Tiesman, PhD Procter & Gamble Company's Jay Tiesman, PhD, discusses the role of genomics in the cosmetics industry.
- Joshua Schiffman, MD The University of Utah's Joshua Schiffman, MD, discusses the use of molecular inversion probe (MIP) technology for studying copy number alterations in pediatric cancers.
- Lisa Baumbach, MD The University of Miami's Lisa Baumbach and Maastricht University's Torik Ayoubi discuss how ethnicity-specific genetic changes govern aggressive breast cancer risks.
- Chris Smith, PhD Chris Smith of Cambridge University, Tyson Clark of Affymetrix and Melissa Cline of UCSC discuss EURASNET's approach for comparing commercial microarrays.
- Robert Norgren, PhD Rob Norgren of The University of Nebraska Medical Center and Katja Nowick of Lawrence Livermore National Laboratory discuss the development of the Rhesus Macaque Genome Array.
- Yong-Jie Lu, PhD Yong-Jie Lu of Queen Mary, University of London and Colleen Elso of the Walter and Eliza Hall Institute discuss a method for rapidly identifying chromosome rearrangements.
- Novel approach results in first ever rhesus macaque whole-genome array (pdf, 206 KB) Rob Norgren of the University of Nebraska Medical Center and Katja Nowick of Lawrence Livermore National Laboratory discuss the innovation behind the development of the Affymetrix GeneChip® Rhesus Macaque Genome Array.
Intercenter reliability and validity of the rhesus macaque GeneChip
Duan, F. H.; Spindel, E. R.; Li, Y. H.; Norgren, R. B. Jr BMC Genomics 8(), NPG, 2007 PubMed
Leveraging human genomic information to identify nonhuman primate sequences for expression array development
Spindel, E. R.; Pauley, M. A.; Jia, Y. B.; Gravett, C.; Thompson, S. L.; Boyle, N. F.; Ojeda, S. R.; Norgren, R. B. Jr BMC Genomics 6(), NPG, 2005 PubMed