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Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array

de Ståhl, Teresita Díaz, Sandgren, Johanna, Piotrowski, Arkadiusz, Nord, Helena, Andersson, Robin, Menzel, Uwe, Bogdan, Adam, Thuresson, Ann-Charlotte, Poplawski, Andrzej, von Tell, Desiree, Hansson, Caisa M., Elshafie, Amir I., ElGhazali, Gehad, Imreh, Stephan, Nordenskjöld, Magnus, Upadhyaya, Meena, Komorowski, Jan, Bruder, Carl E.G. and Dumanski, Jan P. 2008. Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. Human Mutation 29 (3) , pp. 398-408. 10.1002/humu.20659

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Abstract

To further explore the extent of structural large-scale variation in the human genome, we assessed copy number variations (CNVs) in a series of 71 healthy subjects from three ethnic groups. CNVs were analyzed using comparative genomic hybridization (CGH) to a BAC array covering the human genome, using DNA extracted from peripheral blood, thus avoiding any culture-induced rearrangements. By applying a newly developed computational algorithm based on Hidden Markov modeling, we identified 1,078 autosomal CNVs, including at least two neighboring/overlapping BACs, which represent 315 distinct regions. The average size of the sequence polymorphisms was -350 kb and involved in total -117Mb or -3.5% of the genome. Gains were about four times more common than deletions, and segmental duplications (SDs) were overrepresented, especially in larger deletion variants. This strengthens the notion that SDs often define hotspots of chromosomal rearrangements. Over 60% of the identified autosomal rearrangements match previously reported CNVs, recognized with various platforms. However, results from chromosome X do not agree well with the previously annotated CNVs. Furthermore, data from single BACs deviating in copy number suggest that our above estimate of total variation is conservative. This report contributes to the establishment of the common baseline for CNV, which is an important resource in human genetics.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Subjects: Q Science > QH Natural history > QH426 Genetics
R Medicine > R Medicine (General)
Uncontrolled Keywords: genetic variation; array-CGH; genetics; population; polymorphism; human genome; gene dosage
Publisher: Wiley Blackwell
ISSN: 1059-7794
Last Modified: 04 Jun 2017 03:33
URI: http://orca.cf.ac.uk/id/eprint/22684

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