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1.  Pathways systematically associated to Hirschsprung’s disease 
Despite it has been reported that several loci are involved in Hirschsprung’s disease, the molecular basis of the disease remains yet essentially unknown. The study of collective properties of modules of functionally-related genes provides an efficient and sensitive statistical framework that can overcome sample size limitations in the study of rare diseases. Here, we present the extension of a previous study of a Spanish series of HSCR trios to an international cohort of 162 HSCR trios to validate the generality of the underlying functional basis of the Hirschsprung’s disease mechanisms previously found. The Pathway-Based Analysis (PBA) confirms a strong association of gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other processes related to the disease. In addition, network analysis recovers sub-networks significantly associated to the disease, which contain genes related to the same functionalities, thus providing an independent validation of these findings. The functional profiles of association obtained for patients populations from different countries were compared to each other. While gene associations were different at each series, the main functional associations were identical in all the five populations. These observations would also explain the reported low reproducibility of associations of individual disease genes across populations.
doi:10.1186/1750-1172-8-187
PMCID: PMC3879038  PMID: 24289864
2.  A multilevel model to address batch effects in copy number estimation using SNP arrays 
Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of base pairs in the genome. Genomewide association studies (GWAS) may simultaneously screen for copy number phenotype and single nucleotide polymorphism (SNP) phenotype associations as part of the analytic strategy. However, genomewide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post hoc quality control procedures to exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of biallelic genotype calls from experimental data to estimate batch-specific and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in the quantile-normalized intensities, while the latter illustrates the robustness of our approach to a data set in which approximately 27% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package crlmm at Bioconductor (http:www.bioconductor.org).
doi:10.1093/biostatistics/kxq043
PMCID: PMC3006124  PMID: 20625178
Bioinformatics; Hierarchical models; DNA copy number variations; Single nucleotide polymorphism array
3.  Genetic Variations in NOS1AP are Associated with Sudden Cardiac Death in U.S. White Community Based Populations 
Circulation  2009;119(7):940-951.
Background
The electrocardiographic QT interval is associated with risk of sudden cardiac death (SCD). A previous genome-wide association study demonstrated that allelic variants (rs10494366 and rs4657139) in NOS1AP, which encodes a carboxy-terminal PDZ ligand of neuronal nitric oxide synthase, are associated with the QT interval in white adults. The present analysis was conducted to validate the association between NOS1AP variants and the QT interval and to examine the association with SCD in a combined population of 19,295 black and white adults from the Atherosclerosis Risk in Communities (ARIC) study and the Cardiovascular Health Study (CHS).
Methods and Results
We examined 19 tagging SNPs in the genomic blocks containing rs10494366 and rs4657139 in NOS1AP. SCD was defined as a sudden pulseless condition of cardiac origin in a previously stable individual. General linear models and Cox proportional hazards regression models were used. Multiple SNPs in NOS1AP, including rs10494366, rs4657139, and rs16847548 were significantly associated with adjusted QT interval in whites (P<0.0001). In whites, after adjusting for age, sex, and study, the relative hazard (RH) of SCD associated with each C allele at rs16847548 was 1.31 (95% CI: 1.10 to 1.56, P=0.002), assuming an additive model. In addition, a downstream neighboring SNP, rs12567209, not correlated with rs16847548 or QT interval, was also independently associated with SCD in whites (RH = 0.57, 95%CI: 0.39, 0.83; P = 0.003). Adjustment for QT interval and CHD risk factors attenuated, but did not eliminate, the association between rs16847548 and SCD, and such adjustment had no effect on the association between rs12567209 and SCD. No significant associations between tagging SNPs in NOS1AP and either QT interval or SCD were observed in blacks.
Conclusions
In a combined analysis of two population-based prospective cohort studies, sequence variations in NOS1AP were associated with baseline QT interval and the risk of SCD in white U.S. adults.
doi:10.1161/CIRCULATIONAHA.108.791723
PMCID: PMC2782762  PMID: 19204306
death; sudden; QT interval; genetics; epidemiology
4.  Normalization of microarray expression data using within-pedigree pool and its effect on linkage analysis 
BMC Proceedings  2007;1(Suppl 1):S152.
"Genetical genomics", the study of natural genetic variation combining data from genetic marker-based studies with gene expression analyses, has exploded with the recent development of advanced microarray technologies. To account for systematic variation known to exist in microarray data, it is critical to properly normalize gene expression traits before performing genetic linkage analyses. However, imposing equal means and variances across pedigrees can over-correct for the true biological variation by ignoring familial correlations in expression values. We applied the robust multiarray average (RMA) method to gene expression trait data from 14 Centre d'Etude du Polymorphisme Humain (CEPH) Utah pedigrees provided by GAW15 (Genetic Analysis Workshop 15). We compared the RMA normalization method using within-pedigree pools to RMA normalization using all individuals in a single pool, which ignores pedigree membership, and investigated the effects of these different methods on 18 gene expression traits previously found to be linked to regions containing the corresponding structural locus. Familial correlation coefficients of the expressed traits were stronger when traits were normalized within pedigrees. Surprisingly, the linkage plots for these traits were similar, suggesting that although heritability increases when traits are normalized within pedigrees, the strength of linkage evidence does not necessarily change substantially.
PMCID: PMC2367611  PMID: 18466497
5.  Application of the propensity score in a covariate-based linkage analysis of the Collaborative Study on the Genetics of Alcoholism 
BMC Genetics  2005;6(Suppl 1):S33.
Background
Covariate-based linkage analyses using a conditional logistic model as implemented in LODPAL can increase the power to detect linkage by minimizing disease heterogeneity. However, each additional covariate analyzed will increase the degrees of freedom for the linkage test, and therefore can also increase the type I error rate. Use of a propensity score (PS) has been shown to improve consistently the statistical power to detect linkage in simulation studies. Defined as the conditional probability of being affected given the observed covariate data, the PS collapses multiple covariates into a single variable. This study evaluates the performance of the PS to detect linkage evidence in a genome-wide linkage analysis of microsatellite marker data from the Collaborative Study on the Genetics of Alcoholism. Analytical methods included nonparametric linkage analysis without covariates, with one covariate at a time including multiple PS definitions, and with multiple covariates simultaneously that corresponded to the PS definitions. Several definitions of the PS were calculated, each with increasing number of covariates up to a maximum of five. To account for the potential inflation in the type I error rates, permutation based p-values were calculated.
Results
Results suggest that the use of individual covariates may not necessarily increase the power to detect linkage. However the use of a PS can lead to an increase when compared to using all covariates simultaneously. Specifically, PS3, which combines age at interview, sex, and smoking status, resulted in the greatest number of significant markers identified. All methods consistently identified several chromosomal regions as significant, including loci on chromosome 2, 6, 7, and 12.
Conclusion
These results suggest that the use of a propensity score can increase the power to detect linkage for a complex disease such as alcoholism, especially when multiple important covariates can be used to predict risk and thereby minimize linkage heterogeneity. However, because the PS is calculated as a conditional probability of being affected, it does require the presence of observed covariate data on both affected and unaffected individuals, which may not always be available in real data sets.
doi:10.1186/1471-2156-6-S1-S33
PMCID: PMC1866752  PMID: 16451643
6.  Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium 
BMC Genetics  2005;6(Suppl 1):S73.
We compared seven different tagging single-nucleotide polymorphism (SNP) programs in 10 regions with varied amounts of linkage disequilibrium (LD) and physical distance. We used the Collaborative Studies on the Genetics of Alcoholism dataset, part of the Genetic Analysis Workshop 14. We show that in regions with moderate to strong LD these programs are relatively consistent, despite different parameters and methods. In addition, we compared the selected SNPs in a multipoint linkage analysis for one region with strong LD. As the number of selected SNPs increased, the LOD score, mean information content, and type I error also increased.
doi:10.1186/1471-2156-6-S1-S73
PMCID: PMC1866708  PMID: 16451687
7.  Candidate high myopia loci on chromosomes 18p and 12q do not play a major role in susceptibility to common myopia 
BMC Medical Genetics  2004;5:20.
Background
To determine whether previously reported loci predisposing to nonsyndromic high myopia show linkage to common myopia in pedigrees from two ethnic groups: Ashkenazi Jewish and Amish. We hypothesized that these high myopia loci might exhibit allelic heterogeneity and be responsible for moderate /mild or common myopia.
Methods
Cycloplegic and manifest refraction were performed on 38 Jewish and 40 Amish families. Individuals with at least -1.00 D in each meridian of both eyes were classified as myopic. Genomic DNA was genotyped with 12 markers on chromosomes 12q21-23 and 18p11.3. Parametric and nonparametric linkage analyses were conducted to determine whether susceptibility alleles at these loci are important in families with less severe, clinical forms of myopia.
Results
There was no strong evidence of linkage of common myopia to these candidate regions: all two-point and multipoint heterogeneity LOD scores were < 1.0 and non-parametric linkage p-values were > 0.01. However, one Amish family showed slight evidence of linkage (LOD>1.0) on 12q; another 3 Amish families each gave LOD >1.0 on 18p; and 3 Jewish families each gave LOD >1.0 on 12q.
Conclusions
Significant evidence of linkage (LOD> 3) of myopia was not found on chromosome 18p or 12q loci in these families. These results suggest that these loci do not play a major role in the causation of common myopia in our families studied.
doi:10.1186/1471-2350-5-20
PMCID: PMC512288  PMID: 15291966
8.  Importance sampling method of correction for multiple testing in affected sib-pair linkage analysis 
BMC Genetics  2003;4(Suppl 1):S73.
Using the Genetic Analysis Workshop 13 simulated data set, we compared the technique of importance sampling to several other methods designed to adjust p-values for multiple testing: the Bonferroni correction, the method proposed by Feingold et al., and naïve Monte Carlo simulation. We performed affected sib-pair linkage analysis for each of the 100 replicates for each of five binary traits and adjusted the derived p-values using each of the correction methods. The type I error rates for each correction method and the ability of each of the methods to detect loci known to influence trait values were compared. All of the methods considered were conservative with respect to type I error, especially the Bonferroni method. The ability of these methods to detect trait loci was also low. However, this may be partially due to a limitation inherent in our binary trait definitions.
doi:10.1186/1471-2156-4-S1-S73
PMCID: PMC1866512  PMID: 14975141

Results 1-8 (8)