Biomedical subjects

Heping Zhang

Publications and source records attributed to Heping Zhang.

At least 37 records · Page 2Linked to original sources

PubMed2005

A genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking.

Genetic mechanisms underlying alcoholism are complex. Understanding the etiology of alcohol dependence and its comorbid conditions such as smoking is important because of the significant health concerns. In this report, we describe a method based on classification trees and deterministic forests for association studies to perform a genome-wide joint association analysis of alcoholism and smoking. This approach is used to analyze the single-nucleotide polymorphism data from the Collaborative Study on the Genetics of Alcoholism in the Genetic Analysis Workshop 14. Our analysis reaffirmed the importance of sex difference in alcoholism. Our analysis also identified genes that were reported in other studies of alcoholism and identified new genes or single-nucleotide polymorphisms that can be useful candidates for future studies.

Alcoholism↗

PubMed2005

Linkage analysis and association analysis in the presence of linkage using age at onset of COGA alcoholism data.

Complex disease mapping usually involves a combination of linkage and association techniques. Linkage analysis can scan the entire genome in a few hundred tests. Association tests may involve an even greater number of tests. However, association tests can localize the susceptibility genes more accurately. Using a recently developed combined linkage and association strategy, we analyzed a subset of the Collaborative Study on the Genetics of Alcoholism (COGA) data for the Genetic Analysis Workshop 14 (GAW14). In this analysis, we first employed linkage analysis based on frailty models that take into account age of onset information to establish which regions along the chromosome are likely to harbor disease susceptibility genes for alcohol dependence. Second, we used an association analysis by exploiting linkage disequilibrium to narrow down the peak regions. We also compare the methods with mean identity-by-descent tests and transmission/disequilibrium tests that do not use age of onset information.

Age of Onset↗

PubMed2005

Comparison of survival times in a transplant study of hematologic disorders.

Bone marrow transplantation including autologous, allogeneic and syngeneic has evolved over the past 30 years into an effective therapy for patients with a variety of hematologic malignancies. A total of 51 patients with hematologic disorders were treated with myeloablation and transplantation with either unrelated human leucocyte antigen (HLA) partially matched umbilical cord blood or HLA-matched unrelated donor grafts during 1997-2003. In evaluation of survival of these patients, the log rank and Wilcoxon tests lead to ambiguous results, which also happen in other applications. While the asymptotic properties of these tests are well understood, it is not clear how they behave in a small and specific sample. To resolve the ambiguity and to better understand our patient sample, we compare the power of the two tests by simulation in small samples with piecewise log-logistic and Weibull distributions and with different censoring distributions. Our simulation study confirms the well known fact that when the hazards of underlying survival distributions are non-proportional early on, say t < t(0), but proportional when t> or = t(0), the Wilcoxon test has more power than log rank test. But the importance of our simulation is to gain insight into the time point and impact of t(0) with respect to our transplantation study of leukemia cancer patients. We now conclude that overall survivals of patients with two graft sources are statistically significantly different, in part due to the delay of neutrophil recovery of one patient population immediately after transplantation. Thus, we recommend that Wilcoxon test should be used in future studies of similarly designed clinical trials.

Adolescent↗

PubMed2005

Detection of genes for ordinal traits in nuclear families and a unified approach for association studies.

There is growing interest in genomewide association analysis using single-nucleotide polymorphisms (SNPs), because traditional linkage studies are not as powerful in identifying genes for common, complex diseases. Tests for linkage disequilibrium have been developed for binary and quantitative traits. However, since many human conditions and diseases are measured in an ordinal scale, methods need to be developed to investigate the association of genes and ordinal traits. Thus, in the current report we propose and derive a score test statistic that identifies genes that are associated with ordinal traits when gametic disequilibrium between a marker and trait loci exists. Through simulation, the performance of this new test is examined for both ordinal traits and quantitative traits. The proposed statistic not only accommodates and is more powerful for ordinal traits, but also has similar power to that of existing tests when the trait is quantitative. Therefore, our proposed statistic has the potential to serve as a unified approach to identifying genes that are associated with any trait, regardless of how the trait is measured. We further demonstrated the advantage of our test by revealing a significant association (P = 0.00067) between alcohol dependence and a SNP in the growth-associated protein 43.

Alcoholism↗

PubMed2005

Increased serum levels of interleukin-12 and tumor necrosis factor-alpha in Tourette's syndrome.

BACKGROUND: The hypothesis that common infections can modulate the onset and course of tic disorders and early-onset obsessive-compulsive disorder (OCD) in pediatric populations is longstanding. To date, most investigations have focused on the hypothesis of molecular mimicry and humoral immune responses. This study was carried out to investigate whether cytokines associated with the innate immune response or T cell activation were altered under baseline conditions and during periods of symptom exacerbation. METHODS: Forty-six patients with Tourette's syndrome and/or early-onset OCD, aged 7-17 years, and 31 age-matched control subjects participated in a prospective longitudinal study. Ratings of clinical severity and serum were collected at regular intervals, and serum concentrations of 10 cytokines were measured repeatedly. RESULTS: Interleukin-12 and tumor necrosis factor alpha concentrations at baseline were elevated in patients compared with control subjects. Both of these markers were further increased during periods of symptom exacerbation. CONCLUSIONS: These findings suggest that symptom exacerbations are associated with an inflammatory process propagated by systemic and local cytokine synthesis that might involve the central nervous system. We conclude that, in the future, longitudinal studies of children with neuropsychiatric disorders should examine the involvement of innate and T cell immunity.

Adolescent↗

PubMed2005

Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3.

The papers in presentation groups 1-3 of Genetic Analysis Workshop 14 (GAW14) compared microsatellite (MS) markers and single-nucleotide polymorphism (SNP) markers for a variety of factors, using multiple methods in both data sets provided to GAW participants. Group 1 focused on data provided from the Collaborative Study on the Genetics of Alcoholism (COGA). Group 2 focused on data simulated for the workshop. Group 3 contained analyses of both data sets. Issues examined included: information content, signal strength, localization of the signal, use of haplotype blocks, population structure, power, type I error, control of type I error, the effect of linkage disequilibrium, and computational challenges. There were several broad resulting observations. 1) Information content was higher for dense SNP marker panels than for MS panels, and dense SNP markers sets appeared to provide slightly higher linkage scores and slightly higher power to detect linkage than MS markers. 2) Dense SNP panels also gave higher type I errors, suggesting that increased test thresholds may be needed to maintain the correct error rate. 3) Dense SNP panels provided better trait localization, but only in the COGA data, in which the MS markers were relatively loosely spaced. 4) The strength of linkage signals did not vary with the density of SNP panels, once the marker density was approximately 1 SNP/cM. 5) Analyses with SNPs were computationally challenging, and identified areas where improvements in analysis tools will be necessary to make analysis practical for widespread use.

Alcoholism↗

PubMed2005

Data mining.

Group 14 used data-mining strategies to evaluate a number of issues, including appropriate diagnosis, haplotype estimation, genetic linkage and association studies, and type I error. Methods ranged from exploratory analyses, to machine learning strategies (neural networks, supervised learning, and tree-based methods), to false discovery rate control of type I errors. The general motivations were to find the "story" in the data and to summarize information from a multitude of measures. Several methods illustrated strategies for better trait definition, using summarization of related traits. In the few studies that sought to identify genes for alcoholism, there was little agreement among the different strategies, likely reflecting the complexities of the disease. Nevertheless, Group 14 found that these methods offered strategies to gain a better understanding of the complex pathways by which disease develops.

Alcoholism↗

PubMed2005

Socioeconomic status and diagnosed diabetes incidence.

AIMS: To investigate the association between socioeconomic status (SES) and incidence of diabetes. METHODS: We investigated three measures of SES and incidence of diagnosed diabetes among women and men in the NHANES I Epidemiologic Followup Study, 1971-1992, who were free of diagnosed diabetes in 1980. RESULTS: Among women, diabetes incidence was inversely associated with income (measured as percent of the poverty level), education, and occupational status, adjusting for age and race/ethnicity. The hazard ratio (HR) for women with > 16 years education was 0.26 (95% confidence interval (CI) 0.13-0.54) relative to those with < 9 years of education. Adjustment for potential mediators, including body size variables, diet, physical activity, and alcohol and tobacco use, substantially attenuated the associations with income and education. Among men a trend toward lower diabetes incidence with higher income and higher education was evident (the HR for men with household income > 5 times the poverty level was 0.44 (95% CI 0.19-0.98) relative to those under the poverty line), but there was no inverse association of diabetes incidence with occupational status. CONCLUSIONS: SES, assessed with any of three common measures, is a risk factor for diagnosed diabetes in women. Among men these associations are less consistent.

Adult↗

PubMed2005

Localizing value of ictal-interictal SPECT analyzed by SPM (ISAS).

PURPOSE: The goal of neuroimaging in epilepsy is to localize the region of seizure onset. Single-photon emission computed tomography with tracer injection during seizures (ictal SPECT) is a promising tool for localizing seizures. However, much uncertainty exists about how to interpret late injections, or injections done after seizure end (postictal SPECT). A widely available and objective method is needed to interpret ambiguous ictal and postictal scans, with changes in multiple brain regions. METHODS: Ictal or postictal SPECT scans were performed by using [99mTc]-labeled hexamethyl-propylene-amine-oxime (HMPAO), and images were analyzed by comparison with interictal scans for each patient. Forty-seven cases of localized epilepsy were studied. We used methods that can be implemented anywhere, based on freely downloadable software and normal SPECT databases (http://spect.yale.edu). Statistical parametric mapping (SPM) was used to localize a single region of seizure onset based on ictal (or postictal) versus interictal difference images for each patient. We refer to this method as ictal-interictal SPECT analyzed by SPM (ISAS). RESULTS: With this approach, ictal SPECT identified a single unambiguous region of seizure onset in 71% of mesial temporal and 83% of neocortical epilepsy cases, even with late injections, and the localization was correct in all (100%) cases. Postictal SPECT, conversely, with injections performed soon after seizures, was very poor at localizing a single region based on either perfusion increases or decreases, often because changes were similar in multiple brain regions. However, measuring which hemisphere overall had more decreased perfusion with postictal SPECT, lateralized seizure onset to the correct side in approximately 80% of cases. CONCLUSIONS: ISAS provides a validated and readily available method for epilepsy SPECT analysis and interpretation. The results also emphasize the need to obtain SPECT injections during seizures to achieve unambiguous localization.

Adolescent↗

PubMed2004

Linkage analysis of ordinal traits for pedigree data.

Linkage analysis is used routinely to map genes for human diseases and conditions. However, the existing linkage-analysis methods require that the diseases or conditions either be dichotomized or measured by a quantitative trait, such as blood pressure for hypertension. In the latter case, normality is generally assumed for the trait. However, many diseases and conditions, such as cancer and mental and behavioral conditions, are rated on ordinal scales. The objective of this study was to establish a framework to conduct linkage analysis for ordinal traits. We propose a latent-variable, proportional-odds logistic model that relates inheritance patterns to the distribution of the ordinal trait. We use the likelihood-ratio test for testing evidence of linkage. By means of simulation studies, we find that the power of our proposed model is substantially higher than that of the binary-trait-based linkage analysis and that our test statistic is robust with regard to certain parameter misspecifications. By using our proposed method, we performed a genome scan of the hoarding phenotype in a data set with 53 nuclear families, which were collected by the Tourette Syndrome Association International Consortium for Genetics (TSAICG). Standard linkage scans using hoarding as a dichotomous trait were also performed by using GENEHUNTER and ALLEGRO. Both GENEHUNTER and ALLEGRO failed to reveal any marker significantly linked to the binary hoarding phenotypes. However, our method identified three markers at 4q34-35 (P = 0.0009), 5q35.2-35.3 (P = 0.0001), and 17q25 (P = 0.0005) that manifest significant allele sharing.

Genetic Linkage↗

PubMed2004

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.

The rapid advances in high-throughput biotechnologies such as DNA microarrays and mass spectrometry have generated vast amounts of data ranging from gene expression to proteomics data. The large size and complexity involved in analyzing such data demand a significant amount of computing power. High-performance computation (HPC) is an attractive and increasingly affordable approach to help meet this challenge. There is a spectrum of techniques that can be used to achieve computational speedup with varying degrees of impact in terms of how drastic a change is required to allow the software to run on an HPC platform. This paper describes a high- productivity/low-maintenance (HP/LM) approach to HPC that is based on establishing a collaborative relationship between the bioinformaticist and HPC expert that respects the former's codes and minimizes the latter's efforts. The goal of this approach is to make it easy for bioinformatics researchers to continue to make iterative refinements to their programs, while still being able to take advantage of HPC. The paper describes our experience applying these HP/LM techniques in four bioinformatics case studies: (1) genome-wide sequence comparison using Blast, (2) identification of biomarkers based on statistical analysis of large mass spectrometry data sets, (3) complex genetic analysis involving ordinal phenotypes, (4) large-scale assessment of the effect of possible errors in analyzing microarray data. The case studies illustrate how the HP/LM approach can be applied to a range of representative bioinformatics applications and how the approach can lead to significant speedup of computationally intensive bioinformatics applications, while making only modest modifications to the programs themselves.

Amino Acid Sequence↗

PubMed2004

Gigantic cavernous hemangioma of the liver treated by intra-arterial embolization with pingyangmycin-lipiodol emulsion: a multi-center study.

PURPOSE: To evaluate the therapeutic effect and safety of pingyangmycin-lipiodol emulsion (PLE) intra-arterial embolization for treating gigantic cavernous hemangioma of the liver (CHL). METHODS: Three hospitals (Nanfang Hospital, Inner Mongolia Autonomous Region's Hospital and Huai He Hospital) participated in the study during 1997-2001. A total of 98 patients with CHL were embolized with PLE via the hepatic artery. The therapeutic effects including changes in tumor diameter, symptomatic improvement and occurrence of complications were evaluated for a period of 12 months after the procedure. RESULTS: The tumor diameters decreased significantly from 9.7 +/- 2.3 cm to 5.6 +/- 1.6 cm 6 months after the treatment ( P < 0.01), and then to 3.0 +/- 1.2 cm at 12 months ( P < 0.01). Transient impairment of liver function was found in 77 cases after embolization, 69 cases of which returned to normal in 2 weeks, and the other eight cases of which recovered 1 month later. The clinical symptoms were significantly relieved in all 53 symptomatic patients. Persistent pain in the hepatic region was found in two cases, and these two patients resorted to surgery eventually. CONCLUSION: Intra-arterial PLE embolization proves to be effective and safe in treating patients with CHL.

Adult↗

PubMed2004

Results of a genomewide linkage scan: support for chromosomes 9 and 11 loci increasing risk for cigarette smoking.

UNLABELLED: Cigarette smoking is highly destructive to individuals and society, and is moderately heritable. We completed a genomewide linkage scan to map loci increasing risk for cigarette smoking in a set of families originally identified because they segregate panic disorder (PD). One hundred forty two genotyped individuals in a total of 12 families were studied (214 subjects analyzed, including non-genotyped individuals). Of these individuals, 69 were "affected" with habitual cigarette smoking (i.e., they smoked more than one pack per day for at least a year, or at least 1/2 pack per day for at least 10 years), 49 were "unaffected" (i.e., they smoked less than 1/2 pack per day for less than 1 year), and 24 were scored as "unknown." Nine families from the panic series were excluded from these analyses because they lacked multiple affected individuals with habitual cigarette smoking. In an initial genomewide scan, we genotyped a total of 416 markers (398 autosomal, 18 X-chromosome) with an average spacing of less than 10 cM, spanning the genome. Linkage analysis (pairwise, or single-point, and multi-point) was performed using ALLEGRO. An additional 14 markers were genotyped in a high-density panel to follow-up on an identified region of interest on chromosome 11p. The three highest multi-point Zlr scores (3.43, 3.04, and 3.01; P = 0.0003, P = 0.0012, and P = 0.0013, respectively), which each reflect "suggestive" evidence for linkage, were observed in multi-point linkage analyses using Allegro on chromosomes 11p and 9, near markers D11S4046, D9S283, and D9S1677, respectively. D11S4046 is in a region where linkage to alcohol dependence and linkage disequilibrium to substance dependence have previously been identified. The chromosome 9 region we identified as possibly linked to cigarette smoking in anxiety families, was previously identified as significantly linked to PD in Icelandic pedigrees. We also identified evidence supporting linkage (Zlr score > 2.3, P < 0.01) to regions of chromosomes 14, 16, and X. There was a significant phenotypic association between PD and cigarette smoking (P < 0.001). CONCLUSIONS: We identified evidence for two loci increasing risk for cigarette smoking that map to chromosomes 9 and 11. There is now evidence supporting linkage or association of chromosome 11 markers with alcohol dependence, illegal drug abuse and dependence, and cigarette smoking. Interestingly, one of our most promising linkage regions, includes a region previously identified as linked to PD.

Alcoholism↗

PubMed2004

Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights.

MOTIVATION: Due to the existence of the loss of synchrony in cell-cycle data sets, standard clustering methods (e.g. k-means), which group open reading frames (ORFs) based on similar expression levels, are deficient unless the temporal pattern of the expression levels of the ORFs is taken into account. METHODS: We propose to improve the performance of the k-means method by assigning a decreasing weight on its variable level and evaluating the 'weighted k-means' on a yeast cell-cycle data set. Protein complexes from a public website are used as biological benchmarks. To compare the k-means clusters with the structures of the protein complexes, we measure the agreement between these two ways of clustering via the adjusted Rand index. RESULTS: Our results show the time-decreasing weight function--exp[-(1/2)(t(2)/C(2))]--which we assign to the variable level of k-means, generally increases the agreement between protein complexes and k-means clusters when C is near the length of two cell cycles.

Algorithms↗

PubMed2004

Neonatal hypoxia suppresses oligodendrocyte Nogo-A and increases axonal sprouting in a rodent model for human prematurity.

Premature human infants frequently suffer from periventricular leukomalacia (PVL) characterized by the loss of central myelinated tracts in the brain [Neuropathology, 22 (2002) 193]. Rodent chronic sublethal hypoxia (CSH) from P3 to 33 (postnatal day 3-33) provides a model for PVL characterized by cerebral ventriculomegaly and reductions in cerebral white matter volume [Brain Res. Dev. Brain Res. 111 (1998) 197; Proc. Natl. Acad. Sci. USA 100 (2003) 11718]. Here, we demonstrate that mice exposed to CSH from P3 to P33 followed by normoxia from P33 to P75 continue to exhibit a locomotor hyperactivity that resembles behavioral changes observed in some human children with very low birth weights. Because periventricular white matter is specifically lost in PVL, we examined the expression of oligodendrocyte proteins. Hypoxic rearing dramatically decreases the level of the axon outgrowth inhibitor Nogo-A in oligodendrocytes of CNS white matter at P12. The Nogo-A decrease exceeds the moderate decrease in another myelin protein, myelin associated glycoprotein (MAG). Although myelin protein expression returns to normal by maturity (P75), persistent abnormalities in axonal trajectories are detectable. Anterograde axonal tracing from motor cortex demonstrates ectopic corticofugal fibers in the corticospinal tract (CST), corpus callosum, and caudate nucleus of adult animals reared in CSH. Thus, hypoxia-induced reduction in myelin-derived axon outgrowth inhibitors appears to contribute axonal misconnection to the pathology of very low birth weight infants.

Age Factors↗

PubMed2004

Mixed effects multivariate adaptive splines model for the analysis of longitudinal and growth curve data.

In this article, I review the use of nonparametric methods in the analysis of longitudinal and growth curve data, particularly the multivariate adaptive splines models for the analysis of longitudinal data (MASAL). These methods combine nonparametric techniques (B-splines, kernel smoothing, piecewise polynomials) and models with random effects, and provide fruitful alternatives to mixed effects linear models. Similarities, differences, strengths and limitations among these methods are presented. The analysis of a real example is also presented to illustrate the application and interpretation of MASAL. Open questions are posed for further investigation.

Biomedical Research↗

PubMed2004

Preoperative anxiety and emergence delirium and postoperative maladaptive behaviors.

Based on previous studies, we hypothesized that the clinical phenomena of preoperative anxiety, emergence delirium, and postoperative maladaptive behavioral changes were closely related. We examined this issue using data obtained by our laboratory over the past 6 years. Only children who underwent surgery and general anesthesia using sevoflurane/O(2)/N(2)O and who did not receive midazolam were recruited. Children's anxiety was assessed preoperatively with the modified Yale Preoperative Anxiety Scale (mYPAS), emergence delirium was assessed in the postanesthesia care unit, and behavioral changes were assessed with the Post Hospital Behavior Questionnaire (PHBQ) on postoperative days 1, 2, 3, 7, and 14. Regression analysis showed that the odds of having marked symptoms of emergence delirium increased by 10% for each increment of 10 points in the child's state anxiety score (mYPAS). The odds ratio of having new-onset postoperative maladaptive behavior changes was 1.43 for children with marked emergence status as compared with children with no symptoms of emergence delirium. A 10-point increase in state anxiety scores led to a 12.5% increase in the odds that the child would have a new-onset maladaptive behavioral change after the surgery. This finding is highly significant to practicing clinicians, who can now predict the development of adverse postoperative phenomena, such as emergence delirium and postoperative behavioral changes, based on levels of preoperative anxiety.

Adaptation, Psychological↗

PubMed2003

Cell and tumor classification using gene expression data: construction of forests.

The advent of gene chips has led to a promising technology for cell, tumor, and cancer classification. We exploit and expand the methodology of recursive partitioning trees for tumor and cell classification from microarray gene expression data. To improve classification and prediction accuracy, we introduce a deterministic procedure to form forests of classification trees and compare their performance with extant alternatives. When two published and commonly used data sets are used, we find that the deterministic forests perform similarly to the random forests in terms of the error rate obtained from the leave-one-out procedure, and all of the forests are far better than the single trees. In addition, we provide graphical presentations to facilitate interpretation of complex forests and compare our findings with the current biological literature. In addition to numerical improvement, the main advantage of deterministic forests is reproducibility and scientific interpretability of all steps in tree construction.

Cells↗