This grant submission is to request funding for the Roche Genome Sequencer (GS) FLX and the GS FLX Computer Cluster required for its dedicated software applications. In an overnight run, this equipment can generate over a million sequence reads at an average read-length of 400 base pairs with a single-base read accuracy of >99.99% at the 400th base pair position, yielding over 400,000 high quality sequences. The output is then analyzed by imbedded GS FLX software to generate manageable datafiles of only 50GB. The instrument's long read length capability is uniquely suited to several applications of particular interest to investigators at Tufts Medical Center and Tufts University School of Medicine. The metagenomic studies in this application which will characterize the intestinal microbiota in a wide range of study populations (children with pneumonia or cystic fibrosis or infected with Cryptosporidium, recipients of bone marrow transplants, patients colonized with antibiotic resistant bacteria, carriers of Shiga-toxin producing E. coli, HIV and Hepatitis C infected drug users, and patients with inflammatory bowel disease) can only be done using the GS FLX system. The platform's ability to re-sequence entire prokaryote mutant genomes at a read length sufficient to identify small RNAs, resolve the novel endpoints in duplications, and identify any other unanticipated genome rearrangements will be used in studies of the infectious agents Vibrio cholera, Streptococcus pneumoniae and Legionella pneumophila. Research on genetic markers of cardiac disease susceptibility, the association of G protein-coupled receptor variants with obesity, genetic risk factors for pulmonary vascular disease and genetic regulation of craniofacial skeletal and tooth development and regeneration as well as a search for endogenous retroviruses in cancer tissue will depend on its unique transcriptome sequencing and analysis capability. In addition, deep sequencing will be used to achieve full length HIV sequencing to assess HIV drug resistance mutations and regions of HIV-1 envelope protein related to long term non-progression. The equipment will be housed in a pre-existing Core facility, a plan for its management has been developed, and institutional support has been pledged by both Tufts Medical Center and Tufts University School of Medicine.
|Volpe, Gretchen E; Ward, Honorine; Mwamburi, Mkaya et al. (2014) Associations of cocaine use and HIV infection with the intestinal microbiota, microbial translocation, and inflammation. J Stud Alcohol Drugs 75:347-57|