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Harold R Garner

Publications and source records attributed to Harold R Garner.

11 recordsLinked to original sources
PubMed2003

Low hanging fruit: a subset of human cSNPs is both highly non-uniform and predictable.

We present a point mutation classification method that contrasts SNP databases and has the potential to illuminate the relative mutational load of genes caused by codon bias. We group point variation gleaned from public databases by their wild-type and mutant codons, e.g. codon mutation classes (CMCs, 576 possible such as ACG-->ATG), whose frequencies in a database are assembled into a BLOSUM-style matrix describing the likelihood of observing all possible single base codon changes as tuned by the intertwined effects of mutation rate and selection. The rankings of the CMCs in any database are reshuffled according to the population stratification of the typical genotyping experiment producing that resource's data. Analysis of four independent databases reveals that a considerable fraction of mutation in functional genes can be described by a few CMCs regardless of gene identity or population stratification in the genotyping experiment. For example, the top 5% (29/576) of CMCs account for 27.4% of the observed variants in dbSNP while the bottom 5% account for only 0.02%. For non-synonymous disease-causing mutation, 40.8% are described by the top 5% of all possible non-silent CMCs (22/438). Overall, the most observed polymorphism is a G-->A transition at CpG dinucleotides causing ACG, TCG, GCG, and CCG to frequently undergo silent mutation in any gene due to the putative lack of impact on the protein product. In order to assess how well CMC spectrums estimate the aggregate non-synonymous mutational trends of a single gene, a CMC matrix was applied to seven unrelated genes to compute the most likely point mutations. In excess of 87% of these mutation predictions are historically known to play an important role in a disease state according to published literature. CMC-based mutation prediction may aid design and execution of direct association genotyping studies.

Base Sequence↗
PubMed2003

Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts.

Only a small fraction of short oligonucleotide probes bind efficiently to complementary segments in long RNA transcripts. Technologies such as array-based transcript profiling and antisense control of gene expression would benefit greatly from a method for predicting probes that bind well to a given target RNA. To develop an algorithm for prioritizing selection of probes, we have analyzed predicted thermodynamic parameters for the binding of several large sets of probes to complementary RNA transcripts. The binding of five of these sets of probes to their RNA targets has been reported by others. In addition, we have used a method for light-directed synthesis of oligonucleotide arrays that we developed to generate two new arrays of surface-bound probes and measured the binding of these probes to their RNA targets. We considered predicted free energies for intramolecular base pairing of the oligonucleotide and its RNA target as well as the predicted free energy of intermolecular hybridization of probe and target. We find that a reliable predictor of probes that will hybridize significantly with their targeted transcripts is the predicted free energy of hybridization minus the predicted free energy for intramolecular folding of the probe.

Green Fluorescent Proteins↗
PubMed2003

Methodologic quality and genotyping reproducibility in studies of tumor necrosis factor -308 G-->A single nucleotide polymorphism and bacterial sepsis: implications for studies of complex traits.

OBJECTIVE: Studies of genetic associations with common diseases, such as between cytokine gene polymorphisms and severe bacterial sepsis, have reached conflicting conclusions. Failure to follow methodologic standards may have contributed to discordant findings. The -308 G-->A transition in the tumor necrosis factor-alpha promoter has been genotyped by a variety of methods. Based on our observation of genotyping inaccuracies, we sought to determine whether published studies followed a series of acceptable methodologic standards and whether failure to follow the standard of genotyping reproducibility could lead to erroneous conclusions about gene-disease associations. DESIGN: Systematic review and reanalysis of banked genetic material. We applied a published series of seven methodologic standards to five reports of the association between this variant and bacterial sepsis. We then studied the accuracy of restriction fragment length polymorphism for the -308 site using DNA from a cohort of injury victims. SETTING: Surgery research laboratory. MEASUREMENTS AND MAIN RESULTS: We observed that methodologic quality was not uniform and that reproducibility of genotyping was infrequently met. In our subjects, we found that 4 of 46 heterozygotes analyzed by restriction fragment length polymorphism were actually GG-homozygotes (9% misclassified) according to alternative genotyping methods. CONCLUSIONS: Failure to confirm genotype may have led to conclusions that this polymorphism is not associated with sepsis or outcome. Our observations have implications for the conduct and evaluation of studies of complex genetic disease.

Genetic Techniques↗
PubMed2002

Parallel assessment of CpG methylation by two-color hybridization with oligonucleotide arrays.

We have developed a method for the parallel analysis of multiple CpG sites in genomic DNA for their state of methylation. Hypermethylation of CpG islands within the promoters and 5' exons of genes has been found to be a mechanism of transcriptional inactivation associated with a variety of tumors. The method that we developed relies on the differential reactivity of methylated and unmethylated cytosines with sodium bisulfite, which exclusively converts unmethylated cytosines to deoxyuracils. The resulting sequence changes are determined with single-nucleotide resolution by hybridization to an oligonucleotide array. Cohybridization with a reference sample containing a different label provides an internal standard for assessment of methylation state. This method provides advantages in parallelism over existing methods of methylation analysis. We have demonstrated this technique with a region from the promoter of the tumor suppressor gene p16, which is hypermethylated in many cancers.

Base Sequence↗
PubMed2002

SIGNAL-Sequence Information and GeNomic AnaLysis.

An integrated software package has been developed to provide convenient graphical and textual analysis of a variety of genomic sequence features, free of charge to the biomedical research community. This package, called sequence information and genomic analysis, is available as either a stand-alone or a web-based version to enable greater versatility in access and utilization. The package can be accessed or downloaded at the following URL: http://innovation.swmed.edu/signal.htm.

Algorithms↗
PubMed2002

ARROGANT: an application to manipulate large gene collections.

ARROGANT (ARRay OrGANizing Tool) is a software tool developed to facilitate the identification, annotation and comparison of large collections of genes or clones. The objective is to enable users to compile gene/clone collections from different databases, allowing them to design experiments and analyze the collections as well as associated experimental data efficiently. ARROGANT can relate different sequence identifiers to their common reference sequence using the UniGene database, allowing for the comparison of data from two different microarray experiments. ARROGANT has been successfully used to analyze microarray expression data for colon cancer, to compile genes potentially related to cardiac diseases for subsequent resequencing (to identify single nucleotide polymorphisms, SNPs), to design a new comprehensive human cDNA microarray for cancer, to combine and compare expression data generated by different microarrays and to provide annotation for genes on custom and Affymetrix chips.

Base Sequence↗
PubMed2002

Toward a universal standard: comparing two methods for standardizing spotted microarray data.

DNA microarray technology has allowed the transcriptome to be studied to a depth that was inconceivable only 10 years ago. Until recently these studies were isolated because, without a universal standard, the results from experiment to experiment and laboratory to laboratory were not directly comparable. For human microarrays, this problem has been addressed by numerous methods, but only two are truly universal. The first method uses genomic DNA as a standard for comparison since it is, by definition, complete and universally available. The second method employs a highly representative total RNA pool such as the one currently available from Stratagene. To determine the advantages and disadvantages of both methods, they were directly compared by hybridization to the University of Texas Southwestern Medical Center's 4000- or 10800-member human cDNA array, using typical microarray techniques. The labeled analytes were 2 microg normal human genomic DNA labeled by nick translation or 20 microg total RNA pool labeled by reverse transcription. The resulting data were then background-subtracted, analyzed, and the number of spots above a background threshold was compared in each sample. Using the McNemar test and a Yate's correction with one degree of freedom, the samples were statistically identical with chi2 = 3.72.

DNA↗