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Funding Update: May 19, 2009

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Electrosonic Ejector Microarray for Development of Cancer Therapies
Start date:
Feb. 15, 2009
Expires: Nov. 14, 2009
Amount awarded to date: $120,586
Principal investigator: John Meacham
Sponsor: Opencell Technologies

Abstract: Atlanta-based Opencell plans to develop a "commercially viable intracellular nanomaterial delivery device" called the "electrosonic ejector microarray," that demonstrates "quantitative performance improvement over currently available nanomaterial delivery technologies." According to the grant's abstract, Opencell specifically plans to develop an EEM platform that is optimized for cell treatment and can demonstrate safe treatment of a variety of cell types and characterization of nanomaterial localization. Additionally, the "transfection capabilities of the EEM will be optimized and its advantages over traditional transfection technologies will be quantified."


Ultrasensitive, Label-free Silicon Nanowire Biosensing Arrays
Start date:
Feb. 15, 2009
Expires: Jan. 31, 2010
Amount awarded to date: $200,000
Principal investigator: Season Wong
Sponsor: Lynntech

Abstract: College Station, Tex.-based Lynntech aims to develop and commercialize a silicon nanowire sensor platform for multiplexed, label-free, biosensing applications. The platform will provide "ultrasensitive, highly specific real-time detection of a wide range of biological species by using addressable NW arrays functionalized with peptide nucleic acid or nucleic acid aptamer capture probes," according to the grant abstract. The binding precision provided by the platform could benefit diagnostics and food testing, the abstract states.


Assessing Variation in mRNA Transcript Levels in Mice Using Microarray Data
Start date:
March 2, 2009
Expires: March 1, 2011
Amount awarded to date: $49,646
Principal investigator: Peter Vedell
Sponsor: Jackson Laboratory

Abstract: This study will assess "variation in mRNA transcript levels in mice using data from three microarray experiments that involve tissue samples from laboratory mice and are designed to quantify sources of variation within and across laboratory mouse strains and tissues." The Jacksob Lab will also "develop variance estimation methods that improve upon existing methods," according to the grant abstract.


Sensitive Microarray Slides Using Silica Colloidal Crystals
Start date:
March 15, 2009
Expires: Sept. 15, 2009
Amount awarded to date: $120,163
Principal investigator: Mary WIrth
Sponsor: Biovidria

Abstract: This study aims to develop a "microscope slide bearing a thin layer of optically transmissive silica colloidal crystal to impart higher sensitivity by more than 10 fold." Tucson, Ariz.-based Biovidria will first create a model of how sensitivity varies with particle size and biomolecule size. Then, it plans to test silane coatings for covalent attachment with minimal loss of function. Thirdly, the company will "minimize spot size and wicking by identifying the optimal silane composition," the grant abstract states.


Label-Free Microarray Profiling of Phosphoinositide-PDZ Domain Interactions
Start date:
April 1, 2009
Expires: March 31, 2011
Amount awarded to date: $207,058
Principal investigator: Quan Cheng
Sponsor: University of California, Riverside

Abstract: According to the grant abstract, surface plasmon resonance imaging has become a "very attractive" detection method in microarray analysis, offering "high detection sensitivity without the need of a label," and enabling "various measurement functions, including real-time detection and kinetic analysis to be carried out with simple instrument configuration and operational procedure." Lipid microarrays, in particular, could enable researchers to "obtain a comparable fingerprint of the proteins from a cell or tissue that bind to lipids, and enable the identification of functionally important lipid-binding proteins." The overall goal of this project is to develop new optical substrates for label-free SPR detection with membrane microarrays, and to carry out a high-throughput analysis to profile interactions of phosphoinositides with postsynaptic density protein, disc-large, zonula occludens domains. Phosphoinositides are "essential regulators of nuclear functions and membrane trafficking and are associated with cancers and type II diabetes," according to the abstract.

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Copy Number Variation as a Cause of Congenital Heart Defects in Down Syndrome
Start date:
April 1, 2009
Expires: March 31, 2014
Amount awarded to date: $706,888
Principal investigator: Michael Zwick
Sponsor: Emory University

Abstract: This project aims to test the hypothesis that copy-number variation causes higher rates of atrioventricular septal defects among individuals with Down Syndrome. The researchers plan to perform array comparative genomic hybridization using a high-density, 385,000-probe microarray covering chromosome 21 at a mean density of one probe per 70 base pairs with a trisomy 21 reference in order to test the role of chr21 CNVs on AVSD. Whole-genome detection of CNVs will be carried out using the Affymetrix SNP Array 6.0 in 400 cases, 400 controls, and 800 parents of cases. A subset of the CNVs detected will be validated with Taqman genotyping. Statistical analyses of common and rare CNVs will then be performed to test the hypotheses. Finally, the genome-wide SNP data will be used to identify common AVSD susceptibility variants in both whole-genome association and transmission disequilibrium test frameworks, the grant abstract states.


Design and Interpretation of SNP Association Studies of Addiction
Start date:
April 15, 2009
Expires: Feb. 27, 2014
Amount awarded to date: $139,303
Principal investigator: Frank Saccone
Sponsor: Washington University

Abstract: The project will study a priori biological hypotheses and develop systematic methods of testing these hypotheses using data from genome-wide association studies. Data will specifically be utilized from multiple domains, including SNP-gene functional properties such as promoters and synonymy, transcription-factor binding sites, evolutionary-conserved regions, biochemical pathways, and gene expression. The researchers will develop methods designed for maximum viability and interpretability with the ultimate goal of discovering novel genetic variants that influence disease.


Applied Statistics to a Secondary Analysis of Public Repositories for Microarray
Start date:
May 1, 2009
Expires: April 30, 2011
Amount awarded to date: $228,949
Principal investigator: Haiyan Huang
Sponsor: University of California Berkeley

Abstract: This project aims to develop "systematic approaches on a firm statistical footing to conduct a secondary analysis of the public microarray databases." The developed methods will be particularly applied to the retinal expression data to "gain additional insights on the mechanisms that govern the normal and pathological processes of the eye." The results may translate into effective diagnostic, therapeutic and preventive strategies for retinal diseases, according to the grant abstract.


Glycophage Arrays for the Discovery of Biomarkers in Disease
Start date: May 1, 2009
Expires: April 30, 2010
Amount awarded to date: $200,000
Principal investigator: Adam Fisher
Sponsor: Glycobia

Abstract: Ithaca, NY-based Glycobia seeks to synthesize a functional microarray of phage-displayed glycans and use the microarray to detect basic protein-carbohydrate interactions. These studies could "lay the necessary foundation for future work in expanding the diversity of phage-displayed glycans and analyzing carbohydrate signatures in complex serum," according to the grant abstract. The studies are also "significant" because they will provide an "analytical tool that overcomes the current bottlenecks of glycan microarray synthesis and enable the future synthesis of novel glycoconjugates for research, industrial, and therapeutic applications."


Genome-wide SNP Genotyping and Expression Analysis in Human Livers
Start date:
May 1, 2009
Expires: April 30, 2011
Amount awarded to date: $234,000
Principal investigator: Federico Innocenti
Sponsor: University of Chicago

Abstract: This project will assess the pattern of genome-wide mRNA expression and genetic variation in 220 normal human livers from Caucasian donors with goal of obtaining the genomic signature of the regulation of gene expression in the human liver, according to the grant abstract. The genome-wide SNP scan of DNA will be performed by using the Affymetrix SNP Array 6.0, while mRNA expression will be measured by using Affy's GeneChip Human Gene 1.0 ST Array. "Using standard and novel statistical techniques," the researchers will "identify and characterize cis- and trans-acting eQTLs and the regulatory networks of gene expression in the human liver."

The Scan

Removal Inquiry

The Wall Street Journal reports that US lawmakers are seeking additional information about the request to remove SARS-CoV-2 sequence data from a database run by the National Institutes of Health.

Likely to End in Spring

Free lateral flow testing for SARS-CoV-2 may end in the UK by next spring, the head of Innova Medical Group says, according to the Financial Times.

Searching for More Codes

NPR reports that the US Department of Justice has accused an insurance and a data mining company of fraud.

Genome Biology Papers on GWAS Fine-Mapping Method, COVID-19 Susceptibility, Rheumatoid Arthritis

In Genome Biology this week: integrative fine-mapping approach, analysis of locus linked to COVID-19 susceptibility and severity, and more.