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Sequencing-Related NSF Grants Awarded Jan. 1 — Feb. 28, 2007

Amplification-by-Polymerization in DNA Biosensing
Start date:2/1/07
Expires: 1/31/08
Principal investigator: He, Lin
Organization: North Carolina State University
Awarded amount to date: $260,000
Supports a project to develop a molecular amplification method to detect DNA hybridization. The method is based on a process called atom transfer radical polymerization, which grows polymer brushes at DNA hybridization sites that indicate the presence of specific DNA targets.

Novel Nanotechnology for Multiplexed Analysis of Genes and Proteins with PCR-like Sensitivity
Start date:2/1/07
Expires: 1/31/12
Principal investigator: Gao, Xiaohu
Organization: University of Washington
Awarded amount to date: $400,000
Proposal to develop a nanoparticle-based encoding technology for multiplexed detection of genes, proteins, viruses, and bacteria "with PCR-like sensitivity, which is not possible for the existing techniques such as PCR, ELISA, microfluidics and mass spectrometry," according to the abstract. The method uses a barcoding technology in which target molecules are detected by sandwich assays involving nanoparticle-doped microbeads. "This versatile and powerful technology platform allows simultaneous analysis of DNA, RNA and protein cancer markers with unprecedented sensitivity and reduced cost," according to the grant abstract.

Simple Methods for Oligonucleotide Purification
Start date:3/1/07
Expires: 2/28/10
Principal investigator: Fang, Shiyue
Organization: Michigan Technological University
Awarded amount to date: $195,000
Supports the development of methods for the large-scale purification of oligonucleotides. Project aims include developing an oligonucleotide purification method using a polymerizable capping agent to cap failure sequences and developing an oligonucleotide purification method that uses a polymerizable phosphoramidite to functionalize the 5'-end of full-length sequences. The first approach is designed for the purification of large quantities of 5- to 20-mers oligonucleotides while the second one is designed for the purification of 20- to 100-mers, according to the abstract.

High Resolution Single Molecule Study of RecA
Start date:4/1/07
Expires: 3/31/10
Principal investigator: Ha, Taekjip
Organization: University of Illinois at Urbana-Champaign
Awarded amount to date: $303,279
Follows on an earlier project to develop a single-molecule fluorescence approach that can follow the entire lifecycle of the RecA filament, which forms around DNA, with single-monomer resolution and milliseconds time resolution. In this continuation, the grantees will develop single-molecule assays to probe the homology search, homologous pairing, and strand exchange reactions by RecA. "It is expected that these studies will inspire the next wave of applications of single molecule approaches to more complex biological problems," according to the grant abstract.

Dynamics of DNA during Electrophoresis in Artificial Sieving Matrices
Start date:4/1/07
Expires: 3/31/12
Principal investigator: Dorfman, Kevin
Organization: University of Minnesota-Twin Cities
Awarded amount to date: $400,002
Funds theoretical modeling and experimental investigation of microfluidic electrophoresis of DNA, with the goal of leading to improved DNA separation devices. "Artificial matrices are poised to replace pulsed-field gel electrophoresis for important applications in genome mapping and DNA fingerprinting, but the incomplete understanding of the dynamics of DNA in artificial matrices has prevented this technique from moving beyond the proof-of-principle stage and into routine use," according to the grant abstract.

A Community Genomics Investigation of Fungal Adaptation to Cold
Start date:7/1/07
Expires: 6/30/10
Principal investigator: Taylor, Donald
Organization: University of Alaska Fairbanks Campus
Awarded amount to date: $743,697
Funds large-scale community genomics analysis of fungi in the Arctic to provide insights into the diversity, metabolism, and seasonal dynamics of cold-adapted fungi. Goals include revealing which fungal species are most adapted to extreme arctic environmental conditions by characterizing the changes in fungal communities along three latitudinal gradients using high-throughput, DNA-based clone-library sequencing.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.