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). In a diverse human population set, we found that SNP alleles with higher frequencies were more likely to be ancestral than less frequently occurring alleles. There were, however, exceptions. We also found three shared human/pygmy chimpanzee polymorphisms, all involving CpG dinucleotides, and two shared human/gorilla polymorphisms, one involving a CpG dinucleotide. We demonstrate that microarray-based assays allow rapid comparative sequence analysis of intra- and interspecies genetic variation.

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. A total of 3241 candidate SNPs were identified. A genetic map was constructed showing the location of 2227 of these SNPs. Prototype genotyping chips were developed that allow simultaneous genotyping of 500 SNPs. The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs.

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.

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. Utilizing electron beam computed tomography, one can accurately determine the degree of coronary artery calcification, which is reflective of coronary atherosclerosis. METHODS: We performed a study of 35 men who had no clinical evidence of coronary heart disease. Twenty exhibited severe type A behavior and 15 exhibited type B behavior. All subjects were given an Electron Beam Computed Tomography scan of their coronary arteries and a treadmill electrocardiogram. RESULTS: Eight of the 20 (40%) type A subjects were found to have coronary calcification compared to none of the type B subjects (P=0.005). The correlation coefficient between type A score and coronary calcium score was 0.39 (P=0.09). CONCLUSIONS: The pathophysiology by which type A behavior increases the risk for coronary heart disease may involve the premature development of coronary atherosclerosis.

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. Daily dietary sodium intake fell by 38%, from 3,393 to 2,088 mg (p = 0.0001); average daily medication doses increased significantly (lisinopril: 17 to 23 mg, p <0.001; hydralazine: 140 to 252 mg, p = 0.01). Functional status and exercise capacity improved significantly (p = 0.01). Compared with the 6 months before enrollment and normalized for variable follow-up, the frequency of general medical and cardiology visits declined by 23% and 31%, respectively (both p <0.03); emergency room visits for heart failure and for all causes declined 67% and 53%, respectively (both p <0.001). Hospitalization rates for heart failure and for all causes declined 87% and 74%, respectively (p = 0.001), compared with the year before enrollment. The MULTIFIT system enhanced the effectiveness of pharmacologic and dietary therapy for heart failure in clinical practice, improving clinical outcomes and reducing medical resource utilization.

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. These studies enabled progressive refinement of (a) a food frequency questionnaire used to assess food intake in the preceding month; (b) computer-generated progress reports, based on questionnaire responses, offering dietary change subgoals and strategies for change; and (c) a dietary workbook providing detailed information on how to achieve goals. SUBJECTS/SETTING: Persons with hyperlipidemia (n=814) were enrolled from worksite and clinical settings in the San Francisco Bay area of California. The attrition rate after randomization was 5%. INTERVENTION: Elements of the dietary intervention evolved in response to the results of five clinical studies. In each study, patients underwent a form of baseline assessment of dietary intake followed by counseling/instruction by various means. Follow-up dietary assessments were provided at specific intervals to facilitate subjects' progress toward their dietary goals. A dietary workbook provided the detailed instruction required to implement the recommendations contained in the periodic progress reports. STATISTICAL ANALYSES PERFORMED: Changes in plasma cholesterol level were measured by paired and unpaired t tests. The relationship between the reported reduction in dietary fat and cholesterol level assessed by food frequency questionnaires and the directly measured change in plasma cholesterol level was measured by multiple linear regression. RESULTS: The three major elements of the final computerized system (food frequency questionnaires, computer-generated progress reports, and dietary workbook) were developed and refined in the course of the five clinical studies. Reductions in total plasma cholesterol level of 5.0% to 6.5% achieved by participants in all five studies were consistent with self-reported reductions in intake of dietary saturated fat and cholesterol. Therefore, the computerized self-management system appears to be an effective tool for reducing plasma cholesterol levels. APPLICATIONS/CONCLUSIONS: A computer-based system for dietary self-management of hyperlipidemia, implemented by mail, was effective in short-term studies. This self-management system can potentially provide health-promoting services to large numbers of people at low cost.

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. Each physical sign and symptom was given an arbitrarily weighted score (according to its observed frequency of occurrence in previously studied and authenticated type A behavior). These total scores were then statistically analyzed to obtain a critical "diagnostic score" for the presence of type A behavior. The medically oriented videotaped clinical examination detected the presence of type A behavior in 97 of 99 (98%) successively examined postinfarction patients and in 14 of 15 (93%) subjects who were clinically well at the time of their videotaped clinical examination but who subsequently had clinical coronary heart disease. Conversely type A behavior was diagnosed by videotaped clinical examination in only 1 of 23 (4%) healthy men who previously had been found to exhibit type B behavior by prior diagnostic procedures.

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

Concepts and methods [Karlin, S. & Ghandour, G. (1985) Proc. Natl. Acad. Sci. USA 82, 5800-5804] for the analysis of patterns and relationships are extended to multiple DNA and protein sequences. Functionals include multiple sequence common word occurrence distributions, characterizations of high frequency shared words, and ascertainment of long block identities. Various comparisons of sequences using natural alphabets obtained from grouping nucleotides or amino acids by their chemical and functional characteristics are described. Specific applications are given to globin genes, mitochondrial genomes, and a variety of mammalian viruses.

The use of multiple alphabets in kappa-gene immunoglobulin DNA sequence comparisons.

Comparisons within and between the human, mouse and rabbit immunoglobulin-kappa gene (J-C region) DNA sequences are carried out in terms of three two-letter nucleotide alphabets: (i) S-W alphabet (W = A or T; S = G or C); (ii) P-Q alphabet which distinguishes purines (P = A or G) from pyrimidines (Q = C or T); and (iii) a 'control' E-F alphabet (E = A or C; F = G or T). All statistically significant direct repeats within each of the three sequences and all significant block identities (a set of consecutive matching letters) shared by two or more sequences are determined for each alphabet. By contrast to the S-W and E-F alphabets, the P-Q alphabet comparisons reveal an abundance of statistically significant block identities not seen at the nucleotide level. Various interpretations of these P-Q structures with respect to control and functional roles are considered.

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.

Alignment maps and homology analysis of the J-C intron in human, mouse, and rabbit immunoglobulin kappa gene.

The statistically significant shared oligonucleotides (block identities) of the intervening region (J5-C) in the human, mouse, and rabbit immunoglobulin (Ig)-kappa gene were determined. These identities maintain their order (do not cross) and never connect with any Ig-kappa segment external to the intron region. The two regions of pronounced similarity are (1) the vicinity of the established enhancer element (Queen and Baltimore 1983) and (2) a 200-bp region approximately 1 kb upstream that we have labeled the second enhancer element. Similarity is strong between the human and mouse sequences in the neighborhood of the first enhancer element and more pronounced between the human and rabbit sequences in the vicinity of the second enhancer region. The overall extent of similarity between the mouse and rabbit sequences is less than that between the human and mouse sequences and that between the human and rabbit sequences. All close and large dyad-symmetry pairings were ascertained and their possible relations to the enhancer elements discussed.

DNA sequence patterns in human, mouse, and rabbit immunoglobulin kappa-genes.

DNA sequences of the human, mouse, and rabbit immunoglobulin kappa-gene (J-C regions) are compared with respect to various DNA patterns, including dyad symmetry pairings, runs of nucleotides, repeat clusters, and repeats that occur with unusually high frequency. The significant dyad symmetry pairings within each of the sequences emphasize the two "control-enhancer" elements of the J5-C intron. Dyad symmetry pairs between the J-C region and a number of kappa variable (V)-gene domains suggest differences in the affinities between the V and J segments. It is the "consensus heptamer" rather than the "consensus nonamer" that embodies the longest V-J dyad symmetry combinations. In the rabbit there are long runs and repeat clusters of the sequences that identify regions of high duplication; these regions are absent in the human and mouse sequences. High-frequency oligonucleotides feature the consensus nonamer 5' to the J segments, especially in the mouse sequence.

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. Residues 22-29 are highly conserved among the three species in the chemical and functional alphabets but do not show any three-sequence significant amino acid block identities. These results are discussed in terms of transcript processing, effector functions, and structural interactions within the constant domain and with the heavy chain.

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. The relation between insecurity and type A behavior was examined in a sample of 3013 people. In this large population insecurity showed a strong positive correlation to type A behavior and to each of the two overt behavioral components, time urgency and free-floating hostility.

DNA sequence comparisons of the human, mouse, and rabbit immunoglobulin kappa gene.

A comparative analysis between human, mouse, and rabbit immunoglobulin (Ig) kappa-gene DNA sequences is presented. New formulas for determining the expected length and variance of the longest block identity (a succession of matching nucleotides) between multiple random sequences are given and are used to establish statistical criteria for ascertaining the significance of block identities shared in r out of s sequences. The statistically significant block identities within and between the Ig-kappa-gene sequences are ascertained, and alignment maps based on these similarities are constructed. The human and rabbit sequences (especially in the noncoding regions) and the human and mouse sequences (on the coding regions) show a similarity much stronger than that between the mouse and rabbit sequences. The existence of several highly significant shared oligonucleotides occurring in alignment with each other or with respect to the J- and C-gene segments suggests a configuration of multiple control sites. Discussion and interpretations of the form and distribution of the block identities are given.

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.

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. Specific oligonucleotide probe arrays have been designed to rapidly screen human STSs, known genes and full-length cDNAs. This has led to the identification of several thousand biallelic single-nucleotide polymorphisms (SNPs). Meanwhile, a rapid and robust method has been developed for genotyping these SNPs using oligonucleotide arrays. Each allele of an SNP marker is represented on the array by a set of perfect match and mismatch probes. Prototype genotyping chips have been produced to detect 400, 600 and 3000 of these SNPs. Based on the preliminary results, using oligonucleotide arrays to genotype several thousand polymorphic loci simultaneously appears feasible.

New approaches for computer analysis of nucleic acid sequences.

A new high-speed computer algorithm is outlined that ascertains within and between nucleic acid and protein sequences all direct repeats, dyad symmetries, and other structural relationships. Large repeats, repeats of high frequency, dyad symmetries of specified stem length and loop distance, and their distributions are determined. Significance of homologies is assessed by a hierarchy of permutation procedures. Applications are made to papovaviruses, the human papillomavirus HPV, lambda phage, the human and mouse mitochondrial genomes, and the human and mouse immunoglobulin kappa-chain genes.

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. Many genes with known or predicted inhibitory functions are highly expressed in naive, quiescent B cells, notably the signal inhibitor SLAP and DNA-binding proteins of the Kruppel family (LKLF, BKLF, GKLF), Tsc-22, GILZ, Id-3, and GADD45. Activation of naive B cells, triggered by acute binding of antigen to the B-cell receptor, involves a rapid decrease in expression of these inhibitory genes. Promitotic genes are induced in parallel, including c myc, LSIRF/IRF4, cyclin D2, Egr-1 and Egr-2, as are the anti-apoptotic gene A1 and genes for the T-cell-attracting chemokines MIP-1alpha and beta. B-cell tolerance through the process of anergy, induced by chronic binding of self antigen, maintains expression of the inhibitory genes found in quiescent B cells and induces an additional set of inhibitory genes. The latter include inhibitors of signaling - CD72, neurogranin, pcp4 - and additional inhibitors of gene expression such as SATB1, MEF2C, TGIF and Nab-2. The effects of tolerance, the immunosuppressive drug FK506 and other modulators of calcium or MAPK signaling allow individual gene responses to be linked to different signal transduction pathways. The global molecular profiles obtained illustrate how quiescence and anergy are actively maintained in circulating B cells, how these states are switched to clonal expansion and how they could be better emulated by pro-tolerogenic drugs.