Biomedical subjects

Momiao Xiong

Publications and source records attributed to Momiao Xiong.

18 recordsLinked to original sources

PubMed2003

A mathematical programming approach for gene selection and tissue classification.

MOTIVATION: Extracting useful information from expression levels of thousands of genes generated with microarray technology needs a variety of analytical techniques. Mathematical programming approaches for classification analysis outperform parametric methods when the data depart from assumptions underlying these methods. Therefore, a mathematical programming approach is developed for gene selection and tissue classification using gene expression profiles. RESULTS: A new mixed integer programming model is formulated for this purpose. The mixed integer programming model simultaneously selects genes and constructs a classification model to classify two groups of tissue samples as accurately as possible. Very encouraging results were obtained with two data sets from the literature as examples. These results show that the mathematical programming approach can rival or outperform traditional classification methods.

Algorithms↗

PubMed2003

SamCluster: an integrated scheme for automatic discovery of sample classes using gene expression profile.

MOTIVATION: Feature (gene) selection can dramatically improve the accuracy of gene expression profile based sample class prediction. Many statistical methods for feature (gene) selection such as stepwise optimization and Monte Carlo simulation have been developed for tissue sample classification. In contrast to class prediction, few statistical and computational methods for feature selection have been applied to clustering algorithms for pattern discovery. RESULTS: An integrated scheme and corresponding program SamCluster for automatic discovery of sample classes based on gene expression profile is presented in this report. The scheme incorporates the feature selection algorithms based on the calculation of CV (coefficient of variation) and t-test into hierarchical clustering and proceeds as follows. At first, the genes with their CV greater than the pre-specified threshold are selected for cluster analysis, which results in two putative sample classes. Then, significantly differentially expressed genes in the two putative sample classes with p-values < or = 0.01, 0.05, or 0.1 from t-test are selected for further cluster analysis. The above processes were iterated until the two stable sample classes were found. Finally, the consensus sample classes are constructed from the putative classes that are derived from the different CV thresholds, and the best putative sample classes that have the minimum distance between the consensus classes and the putative classes are identified. To evaluate the performance of the feature selection for cluster analysis, the proposed scheme was applied to four expression datasets COLON, LEUKEMIA72, LEUKEMIA38, and OVARIAN. The results show that there are only 5, 1, 0, and 0 samples that have been misclassified, respectively. We conclude that the proposed scheme, SamCluster, is an efficient method for discovery of sample classes using gene expression profile. AVAILABILITY: The related program SamCluster is available upon request or from the web page http://www.sph.uth.tmc.edu:8052/hgc/Downloads.asp.

Algorithms↗

PubMed2003

Haplotype block linkage disequilibrium mapping.

Linkage disequilibrium (LD) mapping is emerging as a powerful alternative approach to identifying genes for complex disease. However, the feasibility and success of LD mapping depend largely on the extent and pattern of LD. Erratic pattern of pair-wise LD seriously compromises LD mapping. Recently discovered haplotype block structure dramatically alleviates the irregular pattern of LD and holds the promise for mapping complex disease genes. To facilitate applications of the haplotype block LD mapping, in this report we conduct theoretical analysis for haplotype block LD mapping. We present an overall LD measure of the haplotype to quantify the LD level of the haplotype block, between the haplotype blocks, and between the haplotype block and the marker locus. Most theoretical and empirical studies of the extent of LD and evaluation of the power of LD mapping have focused on pair-wise LD and single marker LD mapping. There is a lack of systematic and integrative analysis for the haplotype block LD mapping. In this report, we develop population genetic models of the haplotype blocks and analytic tools for calculation of noncentrality parameter of the statistic for the haplotype block LD mapping. We evaluate the impact of the population parameters and disease models on the power of the haplotype block LD mapping in the hope to improve its study design. We compare the powers of the single marker LD and haplotype block LD mapping. Haplotype block structure is an important discovery. Our preliminary results of theoretic analysis further demonstrate that the haplotype block LD analysis is a breakthrough in LD mapping and is a promising tool for genome-wide association studies.

Chromosome Mapping↗

PubMed2003

Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift.

There is considerable interest in identifying and characterizing block-like patterns of linkage disequilibrium (LD; haplotype blocks) in the human genome as these may facilitate the identification of complex disease genes via genome-wide association studies. Although recombination hot-spots have been suggested as the primary mechanism to explain the block-like pattern of LD, other forces, such as genetic drift, may also be important. To this end, we have studied the effect of various recombination models on patterns of LD by using extensive simulations. As expected, haplotype blocks were observed under a model allowing recombination hot-spots. However, we also observed similar block-like patterns in the models where recombination crossovers are randomly and uniformly distributed, and we demonstrate that these blocks are generated by genetic drift. We caution that genetic drift may be an alternative mechanism (in addition to recombination hot-spots) that can lead to block-like patterns of LD. Our findings highlight the necessity of characterizing haplotype blocks in world-wide populations.

Computer Simulation↗

PubMed2003

Genome-wide association study for regions of systemic sclerosis susceptibility in a Choctaw Indian population with high disease prevalence.

OBJECTIVE: Systemic sclerosis (SSc) is a complex, multisystem connective tissue disease in which genetic factors contribute to disease susceptibility. The aim of this study was to localize chromosome regions associated with susceptibility to SSc in a relatively isolated and homogeneous population of Choctaw Indians with a high prevalence of SSc. METHODS: A genome-wide microsatellite screen at 10 cM resolution (400 markers) was performed in 20 Choctaw patients with SSc and 76 ethically matched controls. Based on the results of the initial screen, fine-scale microsatellite mapping at < or =1 cM resolution was performed in 10 selected chromosome regions. Allele and marker haplotype frequencies were compared between SSc patients and controls. RESULTS: From the genome-wide screen, 12 markers showed evidence of highly significant associations with SSc in this population (P < 0.01), while 5 other markers showed significant associations (0.01 < P < 0.05). Among these markers, loci D5S410, D6S422, D15S978, and D20S107 are near the SPARC, MHC, FBN1, and TOPOI genes, respectively, confirming the results of our previous studies, which used different markers. D1S2800 and D14S63 have been reported to show linkage to systemic lupus erythematosus (SLE) in family-based studies, and D1S206, D6S422, and D6S264 are loci on 1p21.2, 6p22.3, and 6q23-27, respectively, which are in regions reported as showing linkage to SLE and other autoimmune diseases. Other markers showing unique associations with SSc were D7S510 (7p12-11), D7S661 (7q35), D8S514 (8q24.12), D19S221 (19p13.2), D19S220 (19q13.2), D22S423 (22q13.1), DXS1068 (Xp11.4), and DXS8055 (Xq21-23). Further analysis with fine-scale microsatellite mapping revealed at least 14 potential haplotypes associated with SSc. CONCLUSION: Our findings indicate that a number of genetic loci may contribute to the high prevalence of SSc in the Choctaw and are consistent with the paradigm that some autoimmune rheumatic diseases are likely to share genetic determinants.

Chromosomes, Human↗

PubMed2003

Combination of TRAIL gene therapy and chemotherapy enhances antitumor and antimetastasis effects in chemosensitive and chemoresistant breast cancers.

We recently found that breast cancer cell lines that are resistant to chemotherapy or to the recombinant TRAIL protein are susceptible to TRAIL gene therapy. However, it is unclear whether a combination of TRAIL gene therapy and chemotherapy will have enhanced antitumor activity or can be used for the treatment of metastasis. In this study, we investigated the combined effect of TRAIL gene therapy and chemotherapeutic agents, including doxorubicin, paclitaxel, vinorelbine, gemcitabine, irinotecan, and floxuridine, in different breast cancer cell lines. In all the cell lines tested, including a breast cancer cell line that is resistant to chemotherapy, the combination of TRAIL gene therapy and cytotoxic agents had either a synergistic or an additive effect. An in vivo study showed that aerosolized administration of an adenovector expressing the GFP-TRAIL fusion protein from the human telomerase reverse transcriptase promoter (designated Ad/gTRAIL) also decreased the number of lung metastases from both doxorubicin-sensitive and doxorubicin-resistant breast cancer cell lines. The combination of TRAIL gene therapy and chemotherapy resulted in a further reduction of lung metastatic nodules with minimal toxicity. These results suggest that a combination of TRAIL gene therapy and chemotherapy is effective in the treatment of metastatic diseases.

Antibiotics, Antineoplastic↗

PubMed2003

Comparison of gene expression between metastatic derivatives and their poorly metastatic parental cells implicates crucial tumor-environment interaction in metastasis of head and neck squamous cell carcinoma.

Metastasis of human head and neck cancer is a multistep and highly heterogeneous process requiring activation and deactivation of multiple and specific genes. To identify these genes, we established highly metastatic head and neck squamous cell carcinoma (HNSCC) cell lines from poorly metastatic HNSCC cells through in vivo selection using a lymph node metastatic mouse model. The very close genetic relationship between these highly metastatic cell lines and the parental cell line provided an excellent model for differential gene expression analysis using cDNA microarrays. Comparison of 6 cell lines established individually from the lymph node metastases with their poorly metastatic parental cell line revealed 33 differentially expressed genes. Some of these genes are involved in cellular signal transduction and matrix modeling. Differences in expression of members of the tumor necrosis factor, interleukin, caspase, and matrix metalloproteinase families were also examined. We found that two upregulated genes participated in the NF-kappaB regulatory pathway. Furthermore, differences in gene expression between six cell lines derived from primary tumors and six cell lines derived from lymph node metastases in the mouse model were analyzed statistically. Tissue growth factor-beta and tumor necrosis factor-related genes showed significantly altered expression in cells derived from lymph node metastases as compared with cells derived from primary tumors, suggesting that the differential growth advantage of metastatic cells requires more aggressive responses to their environment, such as a lymph node tissue.

Animals↗

PubMed2003

Combined high resolution linkage and association mapping of quantitative trait loci.

In this paper, we investigate variance component models of both linkage analysis and high resolution linkage disequilibrium (LD) mapping for quantitative trait loci (QTL). The models are based on both family pedigree and population data. We consider likelihoods which utilize flanking marker information, and carry out an analysis of model building and parameter estimations. The likelihoods jointly include recombination fractions, LD coefficients, the average allele substitution effect and allele dominant effect as parameters. Hence, the model simultaneously takes care of the linkage, LD or association and the effects of the putative trait locus. The models clearly demonstrate that linkage analysis and LD mapping are complementary, not exclusive, methods for QTL mapping. By power calculations and comparisons, we show the advantages of the proposed method: (1) population data can provide information for LD mapping, and family pedigree data can provide information for both linkage analysis and LD mapping; (2) using family pedigree data and a sparse marker map, one may investigate the prior suggestive linkage between trait locus and markers to obtain low resolution of the trait loci, because linkage analysis can locate a broad candidate region; (3) with the prior knowledge of suggestive linkage from linkage analysis, both population and family pedigree data can be used simultaneously in high resolution LD mapping based on a dense marker map, since LD mapping can increase the resolution for candidate regions; (4) models of high resolution LD mappings using two flanking markers have higher power than that of models of using only one marker in the analysis; (5) excluding the dominant variance from the analysis when it does exist would lose power; (6) by performing linkage interval mappings, one may get higher power than by using only one marker in the analysis.

Chromosome Mapping↗

PubMed2003

Multiple transporters associated with malaria parasite responses to chloroquine and quinine.

Mutations and/or overexpression of various transporters are known to confer drug resistance in a variety of organisms. In the malaria parasite Plasmodium falciparum, a homologue of P-glycoprotein, PfMDR1, has been implicated in responses to chloroquine (CQ), quinine (QN) and other drugs, and a putative transporter, PfCRT, was recently demonstrated to be the key molecule in CQ resistance. However, other unknown molecules are probably involved, as different parasite clones carrying the same pfcrt and pfmdr1 alleles show a wide range of quantitative responses to CQ and QN. Such molecules may contribute to increasing incidences of QN treatment failure, the molecular basis of which is not understood. To identify additional genes involved in parasite CQ and QN responses, we assayed the in vitro susceptibilities of 97 culture-adapted cloned isolates to CQ and QN and searched for single nucleotide polymorphisms (SNPs) in DNA encoding 49 putative transporters (total 113 kb) and in 39 housekeeping genes that acted as negative controls. SNPs in 11 of the putative transporter genes, including pfcrt and pfmdr1, showed significant associations with decreased sensitivity to CQ and/or QN in P. falciparum. Significant linkage disequilibria within and between these genes were also detected, suggesting interactions among the transporter genes. This study provides specific leads for better understanding of complex drug resistances in malaria parasites.

Animals↗

PubMed2003

Linkage and association studies of QTL for nuclear families by mixed models.

The transmission disequilibrium test (TDT) has been utilized to test the linkage and association between a genetic trait locus and a marker. Spielman et al. (1993) introduced TDT to test linkage between a qualitative trait and a marker in the presence of association. In the presence of linkage, TDT can be applied to test for association for fine mapping (Martin et al., 1997; Spielman and Ewens, 1996). In recent years, extensive research has been carried out on the TDT between a quantitative trait and a marker locus (Allison, 1997; Fan et al., 2002; George et al., 1999; Rabinowitz, 1997; Xiong et al., 1998; Zhu and Elston, 2000, 2001). The original TDT for both qualitative and quantitative traits requires unrelated offspring of heterozygous parents for analysis, and much research has been carried out to extend it to fit for different settings. For nuclear families with multiple offspring, one approach is to treat each child independently for analysis. Obviously, this may not be a valid method since offspring of one family are related to each other. Another approach is to select one offspring randomly from each family for analysis. However, with this method much information may be lost. Martin et al. (1997, 2000) constructed useful statistical tests to analyse the data for qualitative traits. In this paper, we propose to use mixed models to analyse sample data of nuclear families with multiple offspring for quantitative traits according to the models in Amos (1994). The method uses data of all offspring by taking into account their trait mean and variance-covariance structures, which contain all the effects of major gene locus, polygenic loci and environment. A test statistic based on mixed models is shown to be more powerful than the test statistic proposed by George et al. (1999) under moderate disequilibrium for nuclear families. Moreover, it has higher power than the TDT statistic which is constructed by randomly choosing a single offspring from each nuclear family.

Asthma↗

PubMed2003

The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium.

At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide polymorphism (SNP) marker map has been constructed. Many of the SNPs on this map, however, were identified by sampling a small number of chromosomes from a single population, and inferences drawn from studies using such SNPs may be influenced by ascertainment bias (AB). Through extensive simulations, we have found that AB is a potentially significant problem in estimating and comparing LD within and between populations. Specifically, the magnitude of AB is a function of the SNP discovery strategy, number of chromosomes used for SNP discovery, population genetic characteristics of the particular genomic region considered, amount of gene flow between populations, and demographic history of the populations. We demonstrate that a balanced SNP discovery strategy (where equal numbers of chromosomes are sampled from multiple subpopulations) is the optimal study design for generating broadly applicable SNP resources. Finally, we validate our theoretical predictions by comparing our results to publicly available data from ten genes sequenced in 24 African American and 23 European American individuals.

Biological Evolution↗

PubMed2002

Long-term tumor-free survival from treatment with the GFP-TRAIL fusion gene expressed from the hTERT promoter in breast cancer cells.

We evaluated anti-tumor activity and toxic effect of an adenoviral vector expressing the GFP/TRAIL fusion gene from the hTERT promoter (designated Ad/gTRAIL) on human breast cancer cell lines and on normal human breast cells. Treatment with Ad/gTRAIL elicited high levels of transgene expression and apoptosis in a variety of breast cancer cell lines. Furthermore, treatment with Ad/gTRAIL was effective in killing breast cancer lines resistant to doxorubicin or soluble TRAIL protein. In contrast, only minimal transgene expression and toxicity was detected in normal human primary mammary epithelial cells after treatment with this vector. An in vivo study further showed that the intralesional administration of Ad/gTRAIL effectively suppressed the growth of human tumor xenografts derived from both doxorubicin-sensitive and doxorubicin-resistant breast cancer lines. Specifically, about 50% of animals bearing doxorubicin-sensitive and doxorubicin-resistant breast cancer xenografts showed complete tumor regression and remained tumor-free for over 5 months. These results suggest that the adenovirus encoding the GFP/TRAIL gene driven by the hTERT promoter has potential application in cancer therapy.

Apoptosis Regulatory Proteins↗

PubMed2002

Generalized T2 test for genome association studies.

Recent progress in the development of single-nucleotide polymorphism (SNP) maps within genes and across the genome provides a valuable tool for fine-mapping and has led to the suggestion of genomewide association studies to search for susceptibility loci for complex traits. Test statistics for genome association studies that consider a single marker at a time, ignoring the linkage disequilibrium between markers, are inefficient. In this study, we present a generalized T2 statistic for association studies of complex traits, which can utilize multiple SNP markers simultaneously and considers the effects of multiple disease-susceptibility loci. This generalized T2 statistic is a corollary to that originally developed for multivariate analysis and has a close relationship to discriminant analysis and common measure of genetic distance. We evaluate the power of the generalized T2 statistic and show that power to be greater than or equal to those of the traditional chi2 test of association and a similar haplotype-test statistic. Finally, examples are given to evaluate the performance of the proposed T2 statistic for association studies using simulated and real data.

Algorithms↗

PubMed2002

High resolution mapping of quantitative trait loci by linkage disequilibrium analysis.

Two methods, linkage analysis and linkage disequilibrium (LD) mapping or association study, are usually utilised for mapping quantitative trait loci (QTL). Linkage mapping is appropriate for low resolution mapping to localise trait loci to broad chromosome regions within a few cM (<10 cM), and is based on family data. Linkage disequilibrium mapping, on the other hand, is useful in high resolution or fine mapping, and is based on both population and family data. Using only one marker, one may carry out single-point linkage analysis and linkage disequilibrium mapping. Using two or more markers, it is possible to flank the QTL by multipoint analysis. The development and thus availability of dense marker maps, such as single nucleotide polymorphisms (SNP) in human genome, presents a tremendous opportunity for multipoint fine mapping. In this article, we propose a regression approach of mapping QTL by linkage disequilibrium mapping based on population data. Assuming that two marker loci flank one quantitative trait locus, a two-point linear regression is proposed to analyse population data. We derive analytical formulas of parameter estimations, and non-centrality parameters of appropriate tests of genetic effects and linkage disequilibrium coefficients. The merit of the method is shown by the power calculation and comparison. The two-point regression model can capture much more linkage and linkage disequilibrium information than that derived when only one marker is used. For a complex disease with heritability h(2)> or =0.15, a study with sample size of 250 can provide high power for QTL detection under moderate linkage disequilibria.

Chromosome Mapping↗

PubMed2002

[Linkage analysis of cytokine and cytokine-related receptor gene loci and essential hypertension in Chinese].

OBJECTIVE: To investigate the genetic linkage between several cytokine and cytokine-related receptor gene loci and essential hypertension (EH) in Chinese. METHODS: Linkage between seven genetic markers and EH in 95 Chinese nuclear families with EH (including 477 subjects) was analyzed using a technique of fluorescence-based gene scan with DNA short tandem repeat loci. These markers were selected from the chromosomal regions nearby eight cytokines and their receptor genes. The two-point non-parametric linkage analysis (NPL), maximum Lod score and transmission/disequilibrium test (TDT) with GENEHUNTER software package were used in this study. RESULTS: Result of TDT showed significant transmission disequilibrium between D14S61 and EH (Chi square 14.29,P=0.00016) although NPL and Lod score revealed no significant linkage (Z=0.78, P>0.05 and Lod score =0.72 respectively) at this locus. No linkage between other loci typed and EH was found by the three genetic analysis methods (P>0.05 or Lod score<-1). CONCLUSION: Alleles at D14S61 were of significant transmission disequilibrium in affected siblings. Transforming growth factor beta 3 is 0.1 cM away from D14S61, which suggests that the relationship between genes at or near this regions and EH needs to be further explored.

Adult↗

PubMed2002

[Linkage analysis of 13 vasoactivity-regulating short tandem genes loci in essential hypertension in Chinese].

OBJECTIVE: To investigate whether linkage between essential hypertension (EH) and genetic loci near renin-angiotensin system, endothelin system, nitric oxide synthase, adrenergic receptor genes in Chinese. METHODS: Linkage analysis of thirteen candidate gene loci and EH was performed in 95 Chinese nuclear families including 477 subjects using a technique of fluorescence-based gene scan with DNA short tandem repeat. The markers were selected on the chromosomal regions containing candidate genes regulating vasoactivity. GENEHUNTER package were used for two-point, non-parametric linkage analysis (NPL), maximum Lod score and transmission/disequilibrium test (TDT) in this study. RESULTS: The results of TDT indicated relatively small P values at D1S1678, D3S1744, D4S1604, D13S800, D7S483 and D8S255 (0.01 < P < 0.05). No significant linkages was found at any locus by Lod score and NPL analysis (Lod </= -1, P >/= 0.05). CONCLUSIONS: TDT is considered as a sensitive test for detecting linkage disequilibrium. Significant linkage was found at 6 of the 13 loci typed in Chinese nuclear families with hypertension by using TDT, but no evidence suggested linkage of any locus to EH by NPL and Lod score. It is worthwhile to pay attention to chromosomal regions near the loci with small P values.

Asian People↗

PubMed2002

Linkage analysis of a region on chromosome 2 with essential hypertension in Chinese families.

OBJECTIVE: To verify the linkage of the candidate regions identified in a previous study (markers D2S168, D2S151, D2S142 on chromosome 2) with hypertension in Chinese families. METHODS: A genetic linkage study focused on chromosome 2 was performed on 240 Chinese families containing 856 patients with essential hypertension. A total of 1080 individuals were genotyped using 9 highly polymorphic microsatellite markers around the candidate regions on chromosome 2 with an average spacing of 5 cM. Non-parametric linkage (NPL), parametric linkage analysis and transmission-disequilibrium test (TDT) with the GENEHUNTER software were used to assess evidence for linkage. RESULTS: Linkage of a region on chromosome 2 around D2S151 and D2S142 with hypertension was confirmed by different statistical methods (NPL, LOD score and TDT). However, the linkage of D2S168 could not be replicated in this extension study. CONCLUSIONS: The data suggest that a region on chromosome 2 at or near the loci of D2S142 and D2S151 may harbor genes responsible for the development of essential hypertension in Chinese.

Alleles↗

PubMed2002

Clues to pathogenesis of spondyloarthropathy derived from synovial fluid mononuclear cell gene expression profiles.

OBJECTIVE: To use gene expression profiles of spondyloarthropathy (SpA) synovial fluid mononuclear cells (SFMC) to determine if there are transcripts that support the unfolded protein response (UPR) hypothesis, and to identify which cytokines/chemokines are being expressed and which cell fractions are involved. METHODS: Gene expression profiles were generated by microarray screening of SFMC of 5 patients with SpA, 5 patients with rheumatoid arthritis (RA), and peripheral blood mononuclear cells (PBMC) of 6 controls. Results were validated by reverse transcription polymerase chain reaction using samples from a larger panel of subjects. RESULTS: The repertoires of proinflammatory cytokines/chemokines expressed by SpA and RA SFMC were very similar: monocyte chemotractant protein 1 (MCP-1), interleukin 8 (IL-8), IL-1beta, endothelial-monocyte activating polypeptide II, interferon-gamma, and tumor necrosis factor-alpha. MCP-1 was highly expressed in SpA SFMC. There was enhanced expression of immunoglobulin heavy chain binding protein (BiP) in SpA, which is compatible with the UPR hypothesis. BiP was most highly expressed in the adherent fraction of SpA SFMC. CONCLUSION: Previous data postulating UPR in SpA are based on in vitro experiments with transfected cell lines. Our patient derived data suggest that it also occurs in vivo in the macrophages of SpA joints.

Adolescent↗