Associating multiple longitudinal traits with high-dimensional single-nucleotide polymorphism data: application to the Framingham Heart Study

Cardiovascular diseases are associated with combinations of phenotypic traits, which are in turn caused by a combination of environmental and genetic factors. Because of the diversity of pathways that may lead to cardiovascular diseases, we examined the so-called intermediate phenotypes, which are often repeatedly measured. We developed a penalized nonlinear canonical correlation analysis to associate multiple repeatedly measured traits with high-dimensional single-nucleotide polymorphism data

Association of repeatedly measured intermediate risk factors for complex diseases with high dimensional SNP data

BACKGROUND: The causes of complex diseases are difficult to grasp since many different factors play a role in their onset. To find a common genetic background, many of the existing studies divide their population into controls and cases; a classification that is likely to cause heterogeneity within the two groups. Rather than dividing the study population into cases and controls, it is better to identify the phenotype of a complex disease by a set of intermediate risk factors. But these risk factors often vary over time and are therefore repeatedly measured. RESULTS: We introduce a method to associate multiple repeatedly measured intermediate risk factors with a high dimensional set of single nucleotide polymorphisms (SNPs). Via a two-step approach, we summarized the time courses of each individual and, secondly apply these to penalized nonlinear canonical correlation analysis to obtain sparse results. CONCLUSIONS: Application of this method to two datasets which study the genetic background of cardiovascular diseases, show that compared to progression over time, mainly the constant levels in time are associated with sets of SNPs

Modeling Sage data with a truncated gamma-Poisson model

BACKGROUND: Serial Analysis of Gene Expressions (SAGE) produces gene expression measurements on a discrete scale, due to the finite number of molecules in the sample. This means that part of the variance in SAGE data should be understood as the sampling error in a binomial or Poisson distribution, whereas other variance sources, in particular biological variance, should be modeled using a continuous distribution function, i.e. a prior on the intensity of the Poisson distribution. One challenge is that such a model predicts a large number of genes with zero counts, which cannot be observed. RESULTS: We present a hierarchical Poisson model with a gamma prior and three different algorithms for estimating the parameters in the model. It turns out that the rate parameter in the gamma distribution can be estimated on the basis of a single SAGE library, whereas the estimate of the shape parameter becomes unstable. This means that the number of zero counts cannot be estimated reliably. When a bivariate model is applied to two SAGE libraries, however, the number of predicted zero counts becomes more stable and in approximate agreement with the number of transcripts observed across a large number of experiments. In all the libraries we analyzed there was a small population of very highly expressed tags, typically 1% of the tags, that could not be accounted for by the model. To handle those tags we chose to augment our model with a non-parametric component. We also show some results based on a log-normal distribution instead of the gamma distribution. CONCLUSION: By modeling SAGE data with a hierarchical Poisson model it is possible to separate the sampling variance from the variance in gene expression. If expression levels are reported at the gene level rather than at the tag level, genes mapped to multiple tags must be kept separate, since their expression levels show a different statistical behavior. A log-normal prior provided a better fit to our data than the gamma prior, but except for a small subpopulation of tags with very high counts, the two priors are similar

Comparing transformation methods for DNA microarray data

BACKGROUND: When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order to improve comparability and signal/noise ratio. These steps may include subtraction of an estimated background signal, subtracting the reference signal, smoothing (to account for nonlinear measurement effects), and more. Different authors use different approaches, and it is generally not clear to users which method they should prefer. RESULTS: We used the ratio between biological variance and measurement variance (which is an F-like statistic) as a quality measure for transformation methods, and we demonstrate a method for maximizing that variance ratio on real data. We explore a number of transformations issues, including Box-Cox transformation, baseline shift, partial subtraction of the log-reference signal and smoothing. It appears that the optimal choice of parameters for the transformation methods depends on the data. Further, the behavior of the variance ratio, under the null hypothesis of zero biological variance, appears to depend on the choice of parameters. CONCLUSIONS: The use of replicates in microarray experiments is important. Adjustment for the null-hypothesis behavior of the variance ratio is critical to the selection of transformation method

Responsiveness: a reinvention of the wheel?

BACKGROUND: Since the mid eighties, responsiveness is considered to be a separate property of health status questionnaires distinct from reliability and validity. The aim of the study was to assess the strength of the relationship between internal consistency reliability, referring to an instrument's sensitivity to differences in health status among subjects at one point in time, and responsiveness referring to sensitivity to health status changes over time. METHODS: We used three different datasets comprising the scores of patients on the Barthel, the SIP and the GO-QoL instruments at two points in time. The internal consistency was reduced stepwise by removing the item that contributed most to a scale's reliability. We calculated the responsiveness expressed by the Standardized Response Mean (SRM) on each set of remaining items. The strength of the relationship between the thus obtained internal consistency coefficients and SRMs was quantified by Spearman rank correlation coefficients. RESULTS: Strong to perfect correlations (0.90 – 1.00) was found between internal consistency coefficients and SRMs for all instruments indicating, that the two can be used interchangeably. CONCLUSION: The results contradict the conviction that responsiveness is a separate psychometric property. The internal consistency coefficient adequately reflects an instrument's potential sensitivity to changes over time

Cardiovascular research: data dispersion issues

Biological processes are full of variations and so are responses to therapy as measured in clinical research. Estimators of clinical efficacy are, therefore, usually reported with a measure of uncertainty, otherwise called dispersion. This study aimed to review both the flaws of data reports without measure of dispersion and those with over-dispersion

Practical methods for dealing with 'not applicable' item responses in the AMC Linear Disability Score project

Background:\ud Whenever questionnaires are used to collect data on constructs, such as functional status or health related quality of life, it is unlikely that all respondents will respond to all items. This paper examines ways of dealing with responses in a 'not applicable' category to items included in the AMC Linear Disability Score (ALDS) project item bank. \ud \ud Methods:\ud The data examined in this paper come from the responses of 392 respondents to 32 items and form part of the calibration sample for the ALDS item bank. The data are analysed using the one-parameter logistic item response theory model. The four practical strategies for dealing with this type of response are: cold deck imputation; hot deck imputation; treating the missing responses as if these items had never been offered to those individual patients; and using a model which takes account of the 'tendency to respond to items'. \ud \ud Results:\ud The item and respondent population parameter estimates were very similar for the strategies involving hot deck imputation; treating the missing responses as if these items had never been offered to those individual patients; and using a model which takes account of the 'tendency to respond to items'. The estimates obtained using the cold deck imputation method were substantially different. \ud \ud Conclusions:\ud The cold deck imputation method was not considered suitable for use in the ALDS item bank. The other three methods described can be usefully implemented in the ALDS item bank, depending on the purpose of the data analysis to be carried out. These three methods may be useful for other data sets examining similar constructs, when item response theory based methods are used