Biomedical subjects

Paul Eilers

Publications and source records attributed to Paul Eilers.

4 recordsLinked to original sources

PubMed2005

Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors.

Multiplex ligation-dependent probe amplification (MLPA) is a new assay for the detection of multiple chromosomal deletions in tumor tissue in a single experiment. Since genotyping of gliomas with oligodendroglial features by the detection of 1p/19q chromosomal deletions became essential for treatment decisions, we developed and validated an MLPA-based assay to determine these losses in formalin fixed and paraffin embedded oligodendroglial tumors (OG). Nineteen OGs, and 10 control samples were analyzed by MLPA and the results were correlated with those obtained by fluorescent in situ hybridization (FISH). The MLPA results were reproducible in all samples in which repeated experiments were performed. In 18 of 19 OGs, MLPA and FISH were concordant for presence or absence of 1p deletion. In 3 OGs, MLPA detected a 19q deletion not shown by FISH. For the other 15 OGs, MLPA and FISH were concordant. In one sample with 50% to 75% of tumor, MLPA failed to detect the 1p/19q deletions revealed by FISH (though with borderline values of significance). We conclude that MLPA is a valid and reproducible method for the detection of 1p/19q chromosomal deletions in OGs stored on formalin fixed, paraffin embedded tissue.

Brain Neoplasms↗

PubMed2004

Positioning of cervical carcinoma and Burkitt lymphoma translocation breakpoints with respect to the human papillomavirus integration cluster in FRA8C at 8q24.13.

Molecular cytogenetic analysis frequently shows human papillomavirus (HPV) integration near translocation breakpoints in cervical cancer cells. We have recently described a cluster of HPV18 integrations in the distal end of the common fragile site FRA8C at 8q24 in primary cervical carcinoma samples. Chromosome band 8q24 contains the MYC gene (alias c-MYC), FRA8C, and FRA8D. The MYC gene is frequently deregulated--usually by translocation or amplification--in various tumor types. In the present study, we performed a molecular cytogenetic analysis of HPV18 integration patterns and the 8q24 translocation in a primary cervical carcinoma and in HeLa cells using combined binary ratio-fluorescence in situ hybridization. Our aim was to determine how the chromosomal breaks involved in these events relate physically to the MYC gene; whether they map to the FRA8C site, the FRA8D site, or both; and how they correlate with the occurrence of DNA flexibility domains. The 8q24 translocation breakpoints mapped between stretches of integrated HPV18 sequences in the distal end of FRA8C. This region contained DNA helix flexibility clusters, several of which mapped in the vicinity of HPV integration sites and translocation breakpoints in cervical carcinomas. DNA helix flexibility clusters were also found near known MYC translocation breakpoints in Burkitt lymphomas (BL), but most BL breakpoints mapped clearly outside FRA8C. Our data revealed that FRA8C is involved in HPV integration and chromosomal translocations in cervical carcinoma; however, this fragile site is not involved in classical MYC translocations in most BLs. In the context of the familial nature of cervical cancer, FRA8C may be considered a candidate susceptibility region for cervical carcinoma.

Burkitt Lymphoma↗

PubMed2004

Modeling microarray data using a threshold mixture model.

An important goal of microarray studies is the detection of genes that show significant changes in expression when two classes of biological samples are being compared. We present an ANOVA-style mixed model with parameters for array normalization, overall level of gene expression, and change of expression between the classes. For the latter we assume a mixing distribution with a probability mass concentrated at zero, representing genes with no changes, and a normal distribution representing the level of change for the other genes. We estimate the parameters by optimizing the marginal likelihood. To make this practical, Laplace approximations and a backfitting algorithm are used. The performance of the model is studied by simulation and by application to publicly available data sets.

Animals↗

PubMed2004

Smooth random effects distribution in a linear mixed model.

A linear mixed model with a smooth random effects density is proposed. A similar approach to P-spline smoothing of Eilers and Marx (1996, Statistical Science 11, 89-121) is applied to yield a more flexible estimate of the random effects density. Our approach differs from theirs in that the B-spline basis functions are replaced by approximating Gaussian densities. Fitting the model involves maximizing a penalized marginal likelihood. The best penalty parameters minimize Akaike's Information Criterion employing Gray's (1992, Journal of the American Statistical Association 87, 942-951) results. Although our method is applicable to any dimensions of the random effects structure, in this article the two-dimensional case is explored. Our methodology is conceptually simple, and it is relatively easy to fit in practice and is applied to the cholesterol data first analyzed by Zhang and Davidian (2001, Biometrics 57, 795-802). A simulation study shows that our approach yields almost unbiased estimates of the regression and the smoothing parameters in small sample settings. Consistency of the estimates is shown in a particular case.

Biometry↗