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Jianping Dong

Publications and source records attributed to Jianping Dong.

5 recordsLinked to original sources
PubMed2005

Haplotype sharing transmission/disequilibrium tests that allow for genotyping errors.

The present study introduces new Haplotype Sharing Transmission/Disequilibrium Tests (HS-TDTs) that allow for random genotyping errors. We evaluate the type I error rate and power of the new proposed tests under a variety of scenarios and perform a power comparison among the proposed tests, the HS-TDT and the single-marker TDT. The results indicate that the HS-TDT shows a significant increase in type I error when applied to data in which either Mendelian inconsistent trios are removed or Mendelian inconsistent markers are treated as missing genotypes, and the magnitude of the type I error increases both with an increase in sample size and with an increase in genotyping error rate. The results also show that a simple strategy, that is, merging each rare haplotype to a most similar common haplotype, can control the type I error inflation for a wide range of genotyping error rates, and after merging rare haplotypes, the power of the test is very similar to that without merging the rare haplotypes. Therefore, we conclude that a simple strategy may make the HS-TDT robust to genotyping errors. Our simulation results also show that this strategy may also be applicable to other haplotype-based TDTs.

Algorithms↗
PubMed2005

Tests of association between quantitative traits and haplotypes in a reduced-dimensional space.

Candidate gene association tests are currently performed using several intragenic SNPs simultaneously, by testing SNP haplotype or genotype effects in multifactorial diseases or traits. The number of haplotypes drastically increases with an increase in the number of typed SNPs. As a result, large numbers of haplotypes will introduce large degrees of freedom in haplotype-based tests, and thus limit the power of the tests. In this study we propose using the principal component method to reduce the dimension, and then construct association tests on the lower-dimensional space to test the association between haplotypes and a quantitative trait using population-based samples. The proposed method allows ambiguous haplotypes. We use simulation studies to evaluate the type I error rate of the tests, and compare the power of the proposed tests with that of the tests without dimension reduction, and the tests with dimension reduction by merging rare haplotypes. The simulation results show that the proposed tests have correct type I error rates and are more powerful than other tests in most cases considered in our simulation studies.

Computer Simulation↗
PubMed2003

Transmission/disequilibrium test based on haplotype sharing for tightly linked markers.

Studies using haplotypes of multiple tightly linked markers are more informative than those using a single marker. However, studies based on multimarker haplotypes have some difficulties. First, if we consider each haplotype as an allele and use the conventional single-marker transmission/disequilibrium test (TDT), then the rapid increase in the degrees of freedom with an increasing number of markers means that the statistical power of the conventional tests will be low. Second, the parental haplotypes cannot always be unambiguously reconstructed. In the present article, we propose a haplotype-sharing TDT (HS-TDT) for linkage or association between a disease-susceptibility locus and a chromosome region in which several tightly linked markers have been typed. This method is applicable to both quantitative traits and qualitative traits. It is applicable to any size of nuclear family, with or without ambiguous phase information, and it is applicable to any number of alleles at each of the markers. The degrees of freedom (in a broad sense) of the test increase linearly as the number of markers considered increases but do not increase as the number of alleles at the markers increases. Our simulation results show that the HS-TDT has the correct type I error rate in structured populations and that, in most cases, the power of HS-TDT is higher than the power of the existing single-marker TDTs and haplotype-based TDTs.

Computer Simulation↗
PubMed2002

[Effect of antisense-tissue inhibitor of metalloproteinase-1 gene transfer on tubulointerstitial lesion in rats with unilateral ureteral obstruction].

OBJECTIVE: To observe the effect of antisense- human tissue inhibitor of metalloproteinase-1 (hTIMP-1) on tubulointerstitial lesion induced by unilateral ureteral obstruction (UUO). METHODS: Forty-two SD rats, divided into 3 groups equally, underwent UUO and received intra-ureteral injection of normal saline, empty retroviral vectors and recombinant retroviral vectors containing antisense- hTIMP-1 respectively, and were sacrificed 3 and 7 days after the operation. The expression of antisense h-TIMP-1 in rat kidney was detected by RT-PCR. Immunohistochemistry was used to detect the expression of rat TIMP-1, alpha-SMA actin (alpha-SMA), and proliferating cell nucleus antigen (PCNA) in tubulointerstitium. The relative area of renal tubulointerstitium was calculated. RESULTS: The expression of antisense-hTIMP-1 mRNA was detected in rat renal tubulointerstitum. The expressions of rat TIMP-1, alpha-SMA and PCNA were lower in the obstructed kidneys of rats treated with antisense-hTIMP-1 than those in the rats in empty vectors group and normal saline group (3 day after: 0.75 +/- 0.07 vs 1.18 +/- 0.12, 1.14 +/- 0.14, P < 0.05; 7 days after: 2.02 +/- 0.16 vs 4.07 +/- 0.57, 4.13 +/- 0.60, P < 0.01). The relative area of renal tubulointerstitium in rats treated with antisense-hTIMP-1 was smaller than those in the empty vetors group and normal saline group (3 days after: 6.0 +/- 0.7 vs 8.2 +/- 1.2, 8.2 +/- 1.3, P < 0.01; 7 days after: 16.2 +/- 1.0 vs 21.2 +/- 2.6, 21.0 +/- 2.4, P < 0.01). More renal tubules were dilated, infiltration of inflammatory cells was seen focally or diffusely, and the relative area of renal tubulointerstitium was smaller in the antisense-hTIMP-1 group than in the empty vectors group and normal saline group. No difference was seen among the degrees of dilation/atrophy of renal tubules and infiltration of inflammatory cells in the three groups. No difference was seen between the relative area of renal tubulointerstitium in empty vectors group and normal saline group. CONCLUSION: Antisense-hTIMP-1 may have beneficial effects on the tubulointerstitial lesion of obstructive nephropathy through inhibiting the expression of TIMP-1 in tubulointerstitum and the proliferation of interstitial and tubular cells.

Animals↗