Morphometric analysis in ethnic neonates from multiple substance exposure.

In the United States, approximately 10% of newborn infants are exposed prenatally to alcohol and/or illicit substances. However, no studies have evaluated the compounding effects of multiple illicit substances exposure as potential teratogen (s). The potential teratogenic effects of nicotine and illicit substances (e.

Batch Model for Batched Timestamps Data Analysis with Application to the SSA Disability Program.

The Office of Disability Adjudication and Review (ODAR) is responsible for holding hearings, issuing decisions, and reviewing appeals as part of the Social Security Administration's disability determining process. In order to control and process cases, the ODAR has established a Case Processing and Management System (CPMS) to record management information since December 2003. The CPMS provides a detailed case status history for each case.

Detecting case-control expression quantitative trait loci using locally most powerful or maximin robust rank tests.

In testing genome-wide gene expression quantitative trait loci, efficiency robust statistical methods and their computational convenience are most relevant. For this purpose, we propose to use a modified locally most powerful rank test for the analysis of case-control expression data. This modified rank test statistic is computationally simple, robust for non-normally distributed expression data, and asymptotically locally most powerful.

Global pattern of pairwise relationship in genetic network.

In recent times genetic network analysis has been found to be useful in the study of gene-gene interactions, and the study of gene-gene correlations is a special analysis of the network. There are many methods for this goal. Most of the existing methods model the relationship between each gene and the set of genes under study.

Molecular constitution of breast but not other reproductive tissues is rich in growth promoting molecules: a possible link to highest incidence of tumor growths.

In the current study we tested if highest incidence of benign as well as cancer growths in breast tissue is due to constitutive molecular composition of this tissue. To delineate the molecular basis, we compared the expression of nine functional gene modules (total 578 genes) that regulate major positive growth and negative inhibitory signals in normal breast with two other reproductive tissues, ovary and uterus. We present data to demonstrate that breast tissues constitutively have very highly elevated levels of several growth promoting molecules and diminished levels of inhibitory molecules which may, in part, contribute for highest incidence of tumor growths in this tissue.

Molecular risk assessment for breast cancer development in patients with ductal hyperplasias.

Purpose: It has been reported that approximately a million women are diagnosed with benign breast lesions that include ductal hyperplasias per year in the United States. Recent studies that followed women with benign lesions have established that about 8% to 9% of them will subsequently develop invasive breast cancer (IBC). However, currently, there are no means of identifying a subclass of "true precancerous tissues" in women with ductal hyperplasias who will subsequently develop cancer.

An extension of the weighted dissimilarity test to association study in families.

Association studies for complex diseases based on pedigree haplotype or genotype data have received increasing attention in the last few years. The similarity tests are appealing for these studies because they take into account of the DNA structure, but they have blind areas on which significant association can not be detected. Recently, we developed a dissimilarity method for this problem based on independent haplotype data, which eliminates the blind areas of the existing methods.

Estrogen receptor alpha (ER alpha) mRNA copy numbers in immunohistochemically ER alpha-positive-, and negative breast cancer tissues.

Background: The presence of ERalpha is the basis for treating breast cancer patients with targeted molecular therapies that block estrogen stimulation of breast cancer cell division. To select patients for the above therapies, currently, the ERalpha presence in breast cancer tissues is determined in clinical laboratories by microscopically scoring the slides subjected to immunohistochemistry (IHC). This method is not quantitative, highly subjective and requires large amount of tumor tissue, therefore, cannot be applied to sterotactic and ultrasound guided biopsy samples.

Expression of carcinoembryonic antigen cell adhesion molecule 6 oncoprotein in atypical ductal hyperplastic tissues is associated with the development of invasive breast cancer.

Background: Epidemiologic studies have established that women with prior atypical ductal hyperplastic (ADH) lesions have a 5-fold increased risk of developing invasive breast cancer (IBC). However, there is currently no means of identifying a subclass of ADH from women who will most likely develop cancer. The purpose of this study is to investigate whether elevated expression of carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) in ADH tissues is associated with the development of IBC.

Detecting disease gene in DNA haplotype sequences by nonparametric dissimilarity test.

Association studies for complex diseases based on haplotype data have received increasing attention in the last few years. A commonly used nonparametric method, which takes haplotype structure into consideration, is to use the U-statistic to compare the similarities between genetic compositions in the case and control populations. Although the method and its variants are convenient to use in practice, there are some areas where the tests cannot detect even large differences between cases and controls.

Which strategy is better for linkage analysis: single-nucleotide polymorphisms or microsatellites? Evaluation by identity-by-state-identity-by-descent transformation affected sib-pair method on GAW14 data.

The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To answer this question we analyzed the simulated data using Duffy's SIB-PAIR program, which can incorporate parental genotypes, and our identity-by-state - identity-by-descent (IBS-IBD) transformation method of affected sib-pair linkage analysis which uses the matrix transformation between IBS and IBD. The advantages of our method are as follows: the assumption of Hardy-Weinberg equilibrium is not necessary; the parental genotype information maybe all unknown; both IBS and its related IBD transformation can be used in the linkage analysis; the determinant of the IBS-IBD transformation matrix provides a quantitative measure of the quality of the marker in linkage analysis. With the originally distributed simulated data, we found that 1) for microsatellite markers there are virtually no differences in types I and II error rates when parental genotypes were or were not used; 2) on average, a microsatellite marker has more power than a SNP marker does in linkage detection; 3) if parental genotype information is used, SNP markers show lower type I error rates than microsatellite markers; and 4) if parental genotypes are not available, SNP markers show considerable variation in type I error rates for different methods.