References of "Genetic Epidemiology"
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See detailExome copy number variation detection: Use of a pool of unrelated healthy tissue as reference sample
Wenric, Stéphane ULg; Sticca, Tiberio ULg; CABERG, Jean-Hubert ULg et al

in Genetic Epidemiology (2017)

An increasing number of bioinformatic tools designed to detect CNVs (copy number variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been ... [more ▼]

An increasing number of bioinformatic tools designed to detect CNVs (copy number variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been published in the recent years. The idea of using a pool of unrelated healthy DNA as reference has previously been formulated but not thoroughly validated. As of today, the gold standard for CNV calling is still aCGH but there is an increasing interest in detecting CNVs by exome sequencing. We propose to design a metric allowing the comparison of two CNV profiles, independently of the technique used and assessed the validity of using a pool of unrelated healthy DNA instead of a matched healthy tissue as reference in exome-based CNV detection. We compared the CNV profiles obtained with three different approaches (aCGH, exome sequencing with a matched healthy tissue as reference, exome sequencing with a pool of eight unrelated healthy tissue as reference) on three multiple myeloma samples. We show that the usual analyses performed to compare CNV profiles (deletion/amplification ratios and CNV size distribution) lack in precision when confronted with low LRR values, as they only consider the binary status of each CNV. We show that the metric-based distance constitutes a more accurate comparison of two CNV profiles. Based on these analyses, we conclude that a reliable picture of CNV alterations in multiple myeloma samples can be obtained from whole-exome sequencing in the absence of a matched healthy sample. [less ▲]

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See detailClustering of Crohn’s disease patients: Identification of sub-phenotypes and population stratification
Maus, Bärbel ULg; Génin, Emmanuelle; Mahachie John, Jestinah ULg et al

in Genetic Epidemiology (2012), 36(7), 729

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See detailA Family-Based Association Test to Detect Gene-Gene Interactions in the Presence of Linkage
De Lobel, L.; De Meyer, H.; Thijs, L. et al

in Genetic Epidemiology (2009), 33(8), 77168

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See detailA Family-based Association Test for Quantitative Traits to Detect Gene-Gene Interactions
De Lobel, L.; De Meyer, H.; Thijs, L. et al

in Genetic Epidemiology (2008), 32(7), 686-686

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See detailGenomic screening in family-based association testing
Van Steen, Kristel ULg; McQueen, M.; Herbert, A. et al

in Genetic Epidemiology (2004), 27

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See detailUsing word frequencies for testing equivalence between two DNA sequences
Jansen, I.; Van Steen, Kristel ULg; Molenberghs, G. et al

in Genetic Epidemiology (2002), 23

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See detailMerits of the multivariate Dale model in genetic association studies
Van Steen, Kristel ULg; Molenberghs, G.; Tahri, N.

in Genetic Epidemiology (2002), 23

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