title: Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq.
abstract: Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration and utilizes already available gene expression profiles to determine chromosomal aberrations.
authors.affiliation: The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
authors.forename: Uri
authors.initials: U
authors.lastname: Weissbein
authors.affiliation: The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
authors.forename: Maya
authors.initials: M
authors.lastname: Schachter
authors.affiliation: The New York Stem Cell Foundation Research Institute, New York, New York 10032, USA.|Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA.|Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA.
authors.forename: Dieter
authors.initials: D
authors.lastname: Egli
authors.affiliation: The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel.
authors.forename: Nissim
authors.initials: N
authors.lastname: Benvenisty
mesh_terms: D000483:Alleles; D002460:Cell Line; D002869:Chromosome Aberrations; D005240:Feasibility Studies; D020869:Gene Expression Profiling / Q000379:methods*; D042822:Genomic Instability; D006801:Humans; D007621:Karyotyping / Q000379:methods*; D039904:Pluripotent Stem Cells / Q000378:metabolism; D012313:RNA / Q000235:genetics; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA