This past week the the RE Children’s Project (www.rechildrens.org) provided a research grant to Dr. Charles Chiu at the University of California, San Francisco for an initial amount of $25,000.  Below is a description of the research taken from the research proposal.

“We will analyze 20-50 brain tissue specimens from RE patients using (1) the Virochip, a pan-viral microarray designed to detect all known as well as novel viruses, and (2) deep sequencing on an Illumina Hi-Seq 2000 Genetic Analyzer.   The samples will be kindly provided by Dr. Christian Bien and Jan Bauer  at the University of Bonn in Germany and Dr. Gary Mathern at University of California, Los Angeles.

We will adopt a two-pronged approach to comprehensively identify viruses or other infectious agents in these specimens.  First, we will analyze all of the specimens using the Virochip.  Analysis of samples by the Virochip is a stepwise process of nucleic acid extraction and amplification, hybridization, and microarray interpretation, for which we now have standardized and well-described protocols in place.

Second, we will subject all specimens to deep sequencing on an Illumina Hi-Seq 2000 Genetic Analyzer/Om.  Clinical metagenomics, nucleic acid (RNA and /or DNA) are extracted from specimens and amplified libraries are generated.  “Deep sequencing” of these libraries is then performed.   We now have the capacity to produce, per lane, ~50-80 million sequence reads per run with read lengths of 200 base pairs (100 bp paired end).  The use of deep sequencing is complementary to microarrays, as deep sequencing, although labor and cost-intensive, has the capability of detecting nearly all known infectious agents (i.e. viruses, bacteria, fungi, parasites, etc.) by alignment to large sequence databases such as GenBank.  We have also developed a computational protocol for automated analysis of Illumina deep sequencing data.

Ultimately, we aim to use comprehensive technologies to answer the question of whether RE as an infectious cause, or whether RE is more likely to be a non-infectious inflammatory or autoimmune disease.  These results will help guide diagnosis, therapy, and further research into the causes of this devastating illness.”

For more information contact Seth Wohlberg; swohlberg@rechildrens.com

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