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Series GSE9598 Query DataSets for GSE9598
Status Public on Sep 16, 2008
Title Somatic mosaicism for copy number variation in differentiated human tissues
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Genetic variation is responsible for the generation of phenotypic diversity, including susceptibility to disease. Two major types of variation are known: single nucleotide polymorphisms (SNPs) and a more recently discovered structural variation, involving changes in copy number (CNVs) of kilobase- to megabase-sized chromosomal segments. Variation caused by CNVs has exceeded the amount of SNP-based differences expected to exist between two unrelated humans. Furthermore, many CNVs have been associated with disease predisposition. It is unknown whether CNVs arise in somatic cells, but it is, however, generally assumed that normal cells are genetically identical. Here we show that CNVs are frequent in healthy somatic cells of adult humans. We tested 34 tissue samples from three subjects and, having analyzed for each tissue <10-6 of all cells expected in an adult human, we observed at least six CNVs, affecting a single organ or one or more tissues of the same subject. The CNVs ranged from 82-176 kb, often encompassing known genes, potentially affecting gene function. Our results point to a paradigm shift in the genetics of somatic cells and indicate that humans are commonly affected by somatic mosaicism for stochastic CNVs, which occur in a substantial fraction of cells. A considerable number of phenotypes and diseases affecting humans are a consequence of a somatic process. Thus, our conclusions will be important for the delineation of genetic factors behind these phenotypes. Consequently, biobanks should consider sampling multiple tissues in order to better address mosaicism in the studies of somatic disorders. Furthermore, forensic medicine laboratories should be sensitized to the issue of underestimated frequency of somatic CNV mosaicism.
Keywords: copy number variation (CNV), phenotype diversity, somatic cells
 
Overall design 31 experiments; each experiment consists of two hybridizations, i.e. regular and dye-swap (62 hybridizations in total); cerebellum from corresponding subject was used as a reference; additionally 12 control self-self hybridizations are included (cerrebellum vs self)
 
Contributor(s) Dumanski JP, Piotrowski A, Bruder CE
Citation(s) 18570184
Submission date Nov 13, 2007
Last update date Mar 17, 2012
Contact name Jan Dumanski
E-mail(s) jdumanski@genetics.uab.edu
Phone 205 996 4045
Fax 205 996 4056
URL http://www.genetics.uab.edu/Faculty/
Organization name University of Alabama at Birmingham
Department Department of Genetics
Lab Howell and Elizabeth Heflin Center for Human Genetics
Street address 1530 3rd. Ave. S., Kaul 420
City Birmingham
State/province AL
ZIP/Postal code 35294
Country USA
 
Platforms (1)
GPL6088 UAB 32K v1
Samples (74)
GSM242734 Brain-cortex_subject1_regular
GSM242735 Brain-cortex_subject1_dye-swap
GSM242736 Brain-pons_subject1_regular
Relations
BioProject PRJNA103443

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9598_RAW.tar 262.3 Mb (http)(custom) TAR (of TAB)
Processed data included within Sample table

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