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Genomics Scholars Program
Overview The Genomics Scholars Program (GSP) is a long-term internship designed to help community college students with a science focus transition to four-year colleges. GSP began in 2014 and is scheduled to end with the last cohort in the summer of 2018. Interns enrolled in the 15-month program had exposure to: Two, 10-week summer research experiences (40 hours/week) One, 12-months semester research experience (10 hours/week) Mentoring by JCVI...
Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites.
Genetic factors modifying the blood metabolome have been investigated through genome-wide association studies (GWAS) of common genetic variants and through exome sequencing. We conducted a whole-genome sequencing study of common, low-frequency and rare variants to associate genetic variations with blood metabolite levels using comprehensive metabolite profiling in 1,960 adults. We focused the analysis on 644 metabolites with consistent levels across three longitudinal data collections....
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Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas.
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey mutational changes in cancer in a high-throughput and comprehensive manner. Here we report on the sequence analysis of members of the receptor tyrosine kinase (RTK) gene family in the genomes of glioblastoma brain tumors. Previous studies have identified a number of molecular alterations in glioblastoma,...
Human BAC ends quality assessment and sequence analyses.
End sequences from bacterial artificial chromosomes (BACs) provide highly specific sequence markers in large-scale sequencing projects. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length of >460 bp for a total of 141 Mb covering approximately 4.7% of the genome. Over 60% of the clones have BAC end sequences (BESs) from both ends representing more than fivefold coverage of the human genome by the paired-end clones. Our quality...
The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.
The generation of large numbers of partial cDNA sequences, or expressed sequence tags (ESTs), has provided a method with which to sample a large number of genes from an organism. More than 25,000 Arabidopsis thaliana ESTs have been deposited in public databases, producing the largest collection of ESTs for any plant species. We describe here the application of a method of reducing redundancy and increasing information content in this collection by grouping overlapping ESTs representing the...
Sequence and analysis of the 60 kb conjugative, bacteriocin-producing plasmid pMRC01 from Lactococcus lactis DPC3147.
The complete sequence of pMRC01, a large conjugative plasmid from Lactococcus lactis ssp. lactis DPC3147, has been determined. Using a shotgun sequencing approach, the 60,232 bp plasmid sequence was obtained by the assembly of 1056 underlying sequences (sevenfold average redundancy). Sixty-four open reading frames (ORFs) were identified. Analysis of the gene organization of pMRC01 suggests that the plasmid can be divided into three functional domains, with each approximately 20 kb region...
Revealing Roles of Uncultivated Species in the Oral Microbiome
Many human microbial infectious diseases including oral caries are polymicrobial in nature, and closely associated with ecological conditions of the microbial communities. Oral caries disease is one of the most prevalent and costly bacterial infections in humans. Understanding the metabolism and gene expression profiles as well as inter-species interactions within these complex microbial communities are necessary steps in studying the diseases and finding new treatment solutions. While...
Human Hair Microbiota
Human hair samples are an important trace evidence type for providing leads in forensic investigations. They are used to determine the race, gender, and identity of the individual responsible for a criminal act. Hair also supports its own microbial habitat that is intra- and inter-personal variable, and as such, this little explored substrate has significant potential in forensics microbiome research due to the unique signatures that are available on an individual. We explored...
Optical mapping of Plasmodium falciparum chromosome 2.
Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered...