Combining mouse congenic strains and microarray gene expression analyses to study a complex trait: the NOD model of type 1 diabetes.

Combining congenic mapping with microarray expression profiling offers an opportunity to establish functional links between genotype and phenotype for complex traits such as type 1 diabetes (T1D). We used high-density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes-resistant congenic strains, and two nondiabetic control strains. We developed a simple, yet general, method for measuring differential expression that provides an objective assessment of significance and used it to identify >400 gene expression differences and eight new candidates for the Idd9.

Attributes of gammadelta intraepithelial lymphocytes as suggested by their transcriptional profile.

gammadelta T lymphocytes in the intestinal intraepithelial layer (gammadelta IELs) are thought to contribute to immune competence, but their actual function remains poorly understood. Here we used DNA microarrays to study the gene expression profile of gammadelta IELs in a Yersinia infection system to better define their roles. To validate this approach, mesenteric lymph node CD8(+) alphabeta T cells were similarly analyzed.

Type A behavior and coronary atherosclerosis.

Objectives: To evaluate whether the pathogenesis of type A behavior may involve the premature development of coronary atherosclerosis.

Background: Type A or coronary-prone behavior is considered a possible risk factor for the development of coronary heart disease. Premature development of coronary atherosclerosis is suspected to play a role.

B-lymphocyte quiescence, tolerance and activation as viewed by global gene expression profiling on microarrays.

Self-tolerance is achieved by deleting or regulating self-reactive lymphocytes at a series of cellular checkpoints placed at many points along the developmental pathways to plasma cells and effector T cells. At each checkpoint, what are the molecular pathways that determine whether a lymphocyte remains quiescent, begins dividing, differentiates or dies? In splenic B cells, the decision between quiescence, tolerance by anergy, and activation provides a tractable setting to explore these issues by global gene expression profiling on DNA microarrays. Here we discuss the application of microarrays to illuminate a set of cell fate decisions that appear to be determined by summation of numerous small changes in expression of stimulatory and inhibitory genes.

Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays.

Most human cancers are characterized by genomic instability, the accumulation of multiple genetic alterations and allelic imbalance throughout the genome. Loss of heterozygosity (LOH) is a common form of allelic imbalance and the detection of LOH has been used to identify genomic regions that harbor tumor suppressor genes and to characterize tumor stages and progression. Here we describe the use of high-density oligonucleotide arrays for genome-wide scans for LOH and allelic imbalance in human tumors.

Genomic-scale gene expression analysis of lymphocyte growth, tolerance and malignancy.

Immunologists are already comfortable with the need for monitoring many different gene products simultaneously. It is a common challenge to remember what CD-one-hundred-and-something is, and an ever-increasing number of colours are required for identification on the flow cytometer. Gene expression arrays now offer the possibility of extending this approach beyond the cell surface and expanding it dramatically to survey the entire catalogue of gene transcripts in a lymphoid cell.

Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays.

Here we report the application of high-density oligonucleotide array (DNA chip)-based analysis to determine the distant history of single nucleotide polymorphisms (SNPs) in current human populations. We analysed orthologues for 397 human SNP sites (identified in CEPH pedigrees from Amish, Venezuelan and Utah populations) from 23 common chimpanzee, 19 pygmy chimpanzee and 11 gorilla genomic DNA samples. From this data we determined 214 proposed ancestral alleles (the sequence found in the last common ancestor of humans and chimpanzees).

High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays.

A highly reliable and efficient technology has been developed for high-throughput DNA polymorphism screening and large-scale genotyping. Photolithographic synthesis has been used to generate miniaturized, high-density oligonucleotide arrays. Dedicated instrumentation and software have been developed for array hybridization, fluorescent detection, and data acquisition and analysis.

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.

Single-nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, and they provide powerful tools for a variety of medical genetic studies. In a large-scale survey for SNPs, 2.3 megabases of human genomic DNA was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips.

Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays.

High-density oligonucleotide arrays can be used to rapidly examine large amounts of DNA sequence in a high throughput manner. An array designed to determine the specific nucleotide sequence of 705 bp of the rpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis.

Development and evaluation of a computer-based system for dietary management of hyperlipidemia.

Objective: To describe the development of a computer-based system for dietary management of hyperlipidemia and to evaluate its efficacy for lowering plasma cholesterol level.

Design: Using a stepwise approach, we developed and tested a three-part self-management system in five consecutive clinical studies. Each study assessed plasma cholesterol levels before and after dietary intervention using the system.

A comprehensive management system for heart failure improves clinical outcomes and reduces medical resource utilization.

The effectiveness of heart failure management in clinical practice is limited by physicians' suboptimal utilization of effective medications, patients' poor adherence to dietary sodium limitation and optimal drug therapy, and the lack of systematic monitoring of patients after hospitalization. The present study evaluated the feasibility and safety of MULTIFIT, a physician-supervised, nurse-mediated, home-based system for heart failure management that implements consensus guidelines for pharmacologic and dietary therapy using a nurse manager to enhance dietary and pharmacologic adherence and to monitor clinical status by frequent telephone contact. Fifty-one patients with the clinical diagnosis of heart failure were followed for 138 +/- 44 days.

Effect of type A behavioral counseling on frequency of episodes of silent myocardial ischemia in coronary patients.

Thirteen of 32 patients with coronary heart disease who also exhibited symptoms and signs of severe time urgency and hostility (the two overt components of type A behavior [TAB]) were found to exhibit multiple episodes of silent myocardial ischemia over a 48-hour period of Holter monitoring as indicated by electrocardiogram ST depressions. Ten of these 13 patients were given 14 months of TAB counseling in an attempt to diminish the intensity of their time urgency and hostility. The remaining three patients served as controls.

Relation between insecurity and Type A behavior.

This article presents a new Type A Videotaped Clinical Examination scale that measures insecurity. This scale was validated against an existing insecurity measure in a sample of 204 individuals. The results indicated that this new scale is a valid measure of insecurity.

A case-management system for coronary risk factor modification after acute myocardial infarction.

Objective: To evaluate the efficacy of a physician-directed, nurse-managed, home-based case-management system for coronary risk factor modification.

Design: Randomized clinical trial in which patients received a special intervention (n = 293) or usual medical care (n = 292) during the first year after acute myocardial infarction.

Setting: 5 Kaiser Permanente Medical Centers in the San Francisco Bay area.

Medical diagnosis of type A behavior.

The objective of this investigation was to develop a medically oriented examination (including a search for physical signs in addition to elicitation of symptoms) for the accurate diagnosis of type A and type B behaviors. Comprising the study were 99 post-myocardial infarction patients, 15 clinically well persons in whom clinical coronary heart disease subsequently developed, and 23 healthy type B subjects. All participants were subjected to a videotaped clinical examination during which, in addition to eliciting responses to questions, 14 possible physical or psychomotor signs (many of which are newly discovered) of type A behavior were also observed.

Cholesterol-related counseling by registered dietitians in northern California.

Background: An estimated 40 million Americans have serum cholesterol levels that warrant medically supervised dietary intervention. Although registered dietitians are expected to play an important role in treating these patients, current treatment practices in the community are largely unknown.

Methods: A questionnaire concerning treatment practices was mailed to all 377 registered dietitians listed in the directories of the American Dietetic Association for two large California districts.

Algorithms for identifying local molecular sequence features.

Efficient algorithms are described for identifying local molecular sequence features including repeats, dyad symmetry pairings and aligned matches between sequences, while allowing for errors. Specific applications are given to the genomic sequences of the Epstein-Barr virus, Varicella-Zoster virus and the bacteriophages lambda and T7.

Efficient algorithms for molecular sequence analysis.

Efficient (linear time) algorithms are described for identifying global molecular sequence features allowing for errors including repeats, matches between sequences, dyad symmetry pairings, and other sequence patterns. A multiple sequence alignment algorithm is also described. Specific applications are given to hepatitis B viruses and the J5-C (J, joining; C, constant) region of the immunoglobulin kappa gene.

Multiple-alphabet amino acid sequence comparisons of the immunoglobulin kappa-chain constant domain.

We compare the amino acid sequences of the constant domains of the immunoglobulin kappa chain of human, mouse, and rabbit by using four classification schemes ("alphabets") of the 20 amino acids based on their chemical, functional, charge, and structural properties. The comparison reveals three regions of pronounced similarity across the three species, independent of allotype. Two of these regions (residues 65-73 and 99-103) entail a high degree of identity at the DNA level and are distinguished from the rest of the constant domain in codon usage and in the dinucleotide sequence at abutting sites of adjacent codons.

Comparative statistics for DNA and protein sequences: multiple sequence analysis.

Concepts and methods [Karlin, S. & Ghandour, G. (1985) Proc.

Comparative statistics for DNA and protein sequences: single sequence analysis.

Four categories of data representations are used to help interpret structures and similarities of nucleic acid and protein sequences. Statistical significance of the observed relationships revealed by these representations are assessed by a hierarchy of permutation procedures and by comparisons with theoretical random models. Applications are presented for various DNA sequences including papovaviruses, Epstein-Barr virus, mitochondrial genomes, and several globin and immunoglobulin genes.