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Sequencing-Related NSF Grants Awarded July 17 – Aug. 13, 2007

Construction of Comprehensive Sequence Indexed Transposon Resources for Maize
Start date: Aug. 1, 2007
Expires: July 31, 2008
Awarded amount to date: $967,015
Principal investigator: Donald McCarty
Sponsor: University of Florida
Funds development of a sequence-based index of the location of each transposon insertion site in the maize genome for the UniformMu inbred maize population. The sequence index database is expected to contain annotations of up to 100,000 unique transposon insertion sites in a collection of 8,050 maize lines. Benefits of the project will include “providing rich research experiences in bioinformatics, state-of-the-art DNA sequencing technologies, [and] maize genetics and transposon biology to diverse undergraduates,” according to the grant abstract.

Synthesis and Restructuring of a Yeast Chromosome
Start date: Aug. 1, 2007
Expires: July 31, 2008
Awarded amount to date: $216,000
Principal investigator: Jef Boeke
Sponsor: Johns Hopkins University
Supports the design of a synthetic organism based on Saccharomyces cerevisiae that will be used to answer “a wide variety of profound biological questions, including the minimum gene set compatible with free-living eukaryotic life and the fundamental requirements for genome and chromosome stability.” Initially, the investigators will synthesize a medium sized chromosome, IX, which is about 440 kb long. The project will use an iterative recombinational approach in which segments of between 30 kb and 100 kb sequentially replace wild-type segments. “If any particular segment is inviable, it can be resynthesized after the nature of the growth defect is mapped and diagnosed,” according to the grant abstract. Specific genomic features to be deleted or relocated in the genome include telomeric regions, repeats such as transposon sequences, tRNA genes, introns, silenced regions, and certain nonessential genes. In addition, “an internal genome reshuffling mechanism will be built into the synthetic yeast chromosome, and tested.”

Acquisition of a Genetic Analyzer for Research, Research Training, and Education at Indiana University South Bend
Start date: Aug. 1, 2007
Expires: July 31, 2009 
Awarded amount to date: $86,873
Principal investigator: Andrew Schnabel
Sponsor: Indiana University
Funds the purchase of a genetic analysis system for research and education in molecular biology and biotechnology. The system will be used for DNA sequencing and genotyping in several projects, including studies of pollen gene flow in acacia trees, to identify fungi infecting plants, and in the study of genes controlling metabolism in fruit flies and freshwater hydras, according to the grant abstract.

Nano-Enhanced Epigenetics Research (NE^2R) in Nebraska
Start date: Aug. 1, 2007
Expires: July 31, 2009
Awarded amount to date: $6,000,000
Principal investigator: Fred Choobineh
Sponsor: University of Nebraska
Supports a center to study how chromatin and its structure influence global gene expression patterns within an organism. The center will have three specific aims: investigating the relationship of chromatin modification and remodeling on global gene expression patterns in plants and animals; studying structural features of chromatin and its associated proteins; and understanding physical properties of the plant cell wall, developing nano-devices for intracellular delivery, and testing experimental approaches of intracellular delivery in both animal and plant systems.

rE.coli ─ Recoding the E. coli Genome
Start date: Aug. 1, 2007
Expires: July 31, 2008
Awarded amount to date: $256,000
Principal investigator: Joseph Jacobson
Sponsor: Massachusetts Institute of Technology
Funds the development of a set of tools and technologies to re-engineer the bacterial genome of Escherichia coli. In the first phase, the project plans to recode all instances of the rarest stop codons (amber, UAG) to the most common stop codon (UAA), “creating a free completely unused codon which can be repurposed for a number of applications, including the introduction of non-natural amino acids and for applications in protein based therapeutics,” according to the grant abstract. The investigators plan to meet this goal by introducing around 300 specific point mutants at sites widely distributed throughout the genome. “Later phases will pursue more extensive codon reassignments, constituting thousands of changes to the genome,” the abstract states.

The Evolutionary Genomics of Rice Domestication
Start date: July 15, 2007
Expires: June 30, 2008
Awarded amount to date: $935,592
Principal investigator: Michael Purugganan
Sponsor: New York University
Supports a project to fine-map domestication genes in rice (Oryza sativa) and identify genomic regions that show signatures of positive selection in approximately 53 Mb of the rice genome associated with 15 quantitative trait loci for six domestication traits. Among other goals, the project will provide genomic sequence for approximately 5 Mb of O. rufipogon spanning 10 regions that contain domestication loci and undertake a comparative genomic analyses of domestication genomic regions between cultivated and wild rice.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.