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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. / Díaz de Ståhl, Teresita; 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; Dumanski, Jan P.

In: Human Mutation, Vol. 29, No. 3, 03.2008, p. 398-408.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Díaz de Ståhl, T, Sandgren, J, Piotrowski, A, Nord, H, Andersson, R, Menzel, U, Bogdan, A, Thuresson, A-C, Poplawski, A, von Tell, D, Hansson, CM, Elshafie, AI, Elghazali, G, Imreh, S, Nordenskjöld, M, Upadhyaya, M, Komorowski, J, Bruder, CEG & Dumanski, JP 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, vol. 29, no. 3, pp. 398-408. https://doi.org/10.1002/humu.20659

APA

Díaz de Ståhl, T., Sandgren, J., Piotrowski, A., Nord, H., Andersson, R., Menzel, U., Bogdan, A., Thuresson, A-C., Poplawski, A., von Tell, D., Hansson, C. M., Elshafie, A. I., Elghazali, G., Imreh, S., Nordenskjöld, M., Upadhyaya, M., Komorowski, J., Bruder, C. E. G., & Dumanski, J. 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), 398-408. https://doi.org/10.1002/humu.20659

Vancouver

Díaz de Ståhl T, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U et al. 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. 2008 Mar;29(3):398-408. https://doi.org/10.1002/humu.20659

Author

Díaz de Ståhl, Teresita ; 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 ; Dumanski, Jan P. / Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. In: Human Mutation. 2008 ; Vol. 29, No. 3. pp. 398-408.

Bibtex

@article{df4321dbd5ce4a049f8ddbb804cba445,
title = "Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array",
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 approximately 350 kb and involved in total approximately 117 Mb or approximately 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.",
keywords = "African Continental Ancestry Group, Algorithms, Asian Continental Ancestry Group, Chromosomes, Artificial, Bacterial, Chromosomes, Human, X, Continental Population Groups, European Continental Ancestry Group, Female, Gene Dosage, Gene Duplication, Gene Rearrangement, Genetic Variation, Genome, Human, Humans, Male, Markov Chains, Oligonucleotide Array Sequence Analysis",
author = "{D{\'i}az de St{\aa}hl}, Teresita and Johanna Sandgren and Arkadiusz Piotrowski and Helena Nord and Robin Andersson and Uwe Menzel and Adam Bogdan and Ann-Charlotte Thuresson and Andrzej Poplawski and {von Tell}, Desiree and Hansson, {Caisa M} and Elshafie, {Amir I} and Gehad Elghazali and Stephan Imreh and Magnus Nordenskj{\"o}ld and Meena Upadhyaya and Jan Komorowski and Bruder, {Carl E G} and Dumanski, {Jan P}",
year = "2008",
month = mar,
doi = "10.1002/humu.20659",
language = "English",
volume = "29",
pages = "398--408",
journal = "Human Mutation",
issn = "1059-7794",
publisher = "JohnWiley & Sons, Inc.",
number = "3",

}

RIS

TY - JOUR

T1 - Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array

AU - Díaz de Ståhl, Teresita

AU - Sandgren, Johanna

AU - Piotrowski, Arkadiusz

AU - Nord, Helena

AU - Andersson, Robin

AU - Menzel, Uwe

AU - Bogdan, Adam

AU - Thuresson, Ann-Charlotte

AU - Poplawski, Andrzej

AU - von Tell, Desiree

AU - Hansson, Caisa M

AU - Elshafie, Amir I

AU - Elghazali, Gehad

AU - Imreh, Stephan

AU - Nordenskjöld, Magnus

AU - Upadhyaya, Meena

AU - Komorowski, Jan

AU - Bruder, Carl E G

AU - Dumanski, Jan P

PY - 2008/3

Y1 - 2008/3

N2 - 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 approximately 350 kb and involved in total approximately 117 Mb or approximately 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.

AB - 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 approximately 350 kb and involved in total approximately 117 Mb or approximately 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.

KW - African Continental Ancestry Group

KW - Algorithms

KW - Asian Continental Ancestry Group

KW - Chromosomes, Artificial, Bacterial

KW - Chromosomes, Human, X

KW - Continental Population Groups

KW - European Continental Ancestry Group

KW - Female

KW - Gene Dosage

KW - Gene Duplication

KW - Gene Rearrangement

KW - Genetic Variation

KW - Genome, Human

KW - Humans

KW - Male

KW - Markov Chains

KW - Oligonucleotide Array Sequence Analysis

U2 - 10.1002/humu.20659

DO - 10.1002/humu.20659

M3 - Journal article

C2 - 18058796

VL - 29

SP - 398

EP - 408

JO - Human Mutation

JF - Human Mutation

SN - 1059-7794

IS - 3

ER -

ID: 106776343