Genomes and Genes
- Imputing missing genotypes with weighted k nearest neighborsHolger Schwender
Statistics, TU Dortmund University, Dortmund, Germany
J Toxicol Environ Health A 75:438-46. 2012..Moreover, KNNcatImpute can also be applied to data from genome-wide association studies, as an application to a subset of the HapMap data demonstrates...
- Rapid testing of SNPs and gene-environment interactions in case-parent trio data based on exact analytic parameter estimationHolger Schwender
TU Dortmund University, 44221 Dortmund, Germany
Biometrics 68:766-73. 2012....
- Identification of SNP interactions using logic regressionHolger Schwender
Department of Statistics, University of Dortmund, 44221 Dortmund, Germany
Biostatistics 9:187-98. 2008....
- Testing SNPs and sets of SNPs for importance in association studiesHolger Schwender
Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
Biostatistics 12:18-32. 2011..We show how the proposed procedure can be adapted for testing SNP sets, and how it can be applied to blocks of SNPs in linkage disequilibrium (LD) to overcome problems caused by LD...
- Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palateTerri H Beaty
School of Public Health, Johns Hopkins University, 615 N Wolfe St, Baltimore, Maryland, USA
Genet Epidemiol 35:469-78. 2011..8. These results emphasize the need to consider G × E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as nonsyndromic CP...
- Examining markers in 8q24 to explain differences in evidence for association with cleft lip with/without cleft palate between Asians and EuropeansTanda Murray
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
Genet Epidemiol 36:392-9. 2012....
- A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate riskSamuel G Younkin
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
BMC Genet 15:24. 2014..We compare de novo deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios...
- Fast detection of de novo copy number variants from SNP arrays for case-parent triosRobert B Scharpf
Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
BMC Bioinformatics 13:330. 2012..We evaluate these issues in a study of oral cleft case-parent trios...
- A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral cleftsSamuel G Younkin
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore
Birth Defects Res A Clin Mol Teratol 103:276-83. 2015..Individual patients with multiple birth defects (including oral clefts) have been shown to carry small and large chromosomal deletions...
- Efficient simulation of epistatic interactions in case-parent triosQing Li
Statistical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
Hum Hered 75:12-22. 2013....
- Logic regression and its extensionsHolger Schwender
Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
Adv Genet 72:25-45. 2010....
- Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactionsMargaret A Taub
Department of Biostatistics, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205 2179, USA
Genet Epidemiol 36:225-34. 2012..We find that by far the least biased results are obtained when family structure is taken into account and currently recommend this approach in spite of its intense computational requirements...
- Empirical Bayes analysis of single nucleotide polymorphismsHolger Schwender
Collaborative Research Center 475, Faculty of Statistics, Dortmund University of Technology, 44221 Dortmund, Germany
BMC Bioinformatics 9:144. 2008..However, the empirical Bayes analysis of microarrays has only been suggested for binary responses when considering expression values, i.e. continuous predictors...
- Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent triosYanzi Xiao
Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
Genet Epidemiol . 2016..8 × 10-8 ) in case-parent trios of European ancestry, which remained significant after correcting for multiple comparisons. However, no significant interaction was detected in trios of Asian ancestry...
- A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4Terri H Beaty
Johns Hopkins University, School of Public Health, Baltimore, Maryland, USA
Nat Genet 42:525-9. 2010..Expression studies support a role for MAFB in palatal development...
- Classification with high-dimensional genetic data: assigning patients and genetic features to known classesHolger Schwender
Technische Universitat Dortmund, Fakultat Statistik, Vogelpothsweg 87, Dortmund, Germany
Biom J 50:911-26. 2008..Finally, we show how the resulting statistical models can be validated...
- Analytic power and sample size calculation for the genotypic transmission/disequilibrium test in case-parent trio studiesChristoph Neumann
Faculty of Statistics, TU Dortmund University, 44221, Dortmund, Germany
Biom J 56:1076-92. 2014..This comparison reveals that these tests have almost the same power, with the score test being slightly more powerful. ..
- Genotyping NAT2 with only two SNPs (rs1041983 and rs1801280) outperforms the tagging SNP rs1495741 and is equivalent to the conventional 7-SNP NAT2 genotypeSilvia Selinski
Leibniz Research Centre for Working Environment and Human Factors IfADo, Dortmund, Germany
Pharmacogenet Genomics 21:673-8. 2011..This procedure represents a facilitation in individualized dosing of NAT2 substrates without losing sensitivity or specificity...
- A pilot study on the application of statistical classification procedures to molecular epidemiological dataHolger Schwender
Department of Statistics, Collaborative Research Centre 475, University of Dortmund, Dortmund, Germany
Toxicol Lett 151:291-9. 2004..The findings, nevertheless, suggest that SNP data might be useful for the classification of individuals into categories of high or low risk of diseases...
- Importance measures for epistatic interactions in case-parent triosHolger Schwender
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21218, USA
Ann Hum Genet 75:122-32. 2011..We illustrate the performance of the novel procedure in simulation studies and in a case study of 461 case-parent trios with autistic children...
- Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalitiesMartin Schafer
Collaborative Research Center 475, TU Dortmund University, Dortmund, Germany
Bioinformatics 25:3228-35. 2009..We employ this approach, based on a modified correlation coefficient and an explorative Wilcoxon test, to find DNA regions of such abnormalities in GE and CN (e.g. underexpressed genes accompanied by a loss of DNA material)...
- Detecting high-order interactions of single nucleotide polymorphisms using genetic programmingRobin Nunkesser
Collaborative Research Center 475, Department of Computer Science, University of Dortmund, Dortmund, Germany
Bioinformatics 23:3280-8. 2007..This method called GPAS cannot only be used for feature selection, but can also be employed for discrimination...
- Genetic variants in urinary bladder cancer: collective power of the "wimp SNPs"Klaus Golka
Leibniz Research Centre for Working Environment and Human Factors, Ardeystrasse 67, 44139, Dortmund, Germany
Arch Toxicol 85:539-54. 2011..In future, besides identifying novel disease-associated rare variants by deep sequencing, it will also be important to understand how the already identified variants interact...
- Statistical methods for detecting genetic interactions: a head and neck squamous-cell cancer studyKatja Ickstadt
Fakultat Statistik, Collaborative Research Centre 475, Technische Universitat Dortmund, Dortmund
J Toxicol Environ Health A 71:803-15. 2008....