Systematic biases in DNA copy number originate from isolation procedures

被引：36

作者：

van Heesch, Sebastiaan ^{[1
,2
]}

Mokry, Michal ^{[1
,2
]}

Boskova, Veronika ^{[1
,2
]}

Junker, Wade ^{[3
]}

Mehon, Rajdeep

Toonen, Pim ^{[1
,2
]}

de Bruijn, Ewart ^{[1
,2
]}

Shull, James D. ^{[3
]}

Aitman, Timothy J. ^{[4
]}

Cuppen, Edwin ^{[1
,2
,5
]}

Guryev, Victor ^{[1
,2
]}

机构：

[1] Hubrecht Inst, NL-3584 CT Utrecht, Netherlands

[2] Univ Med Ctr Utrecht, NL-3584 CT Utrecht, Netherlands

[3] 985805 Univ Nebraska Med Ctr, Dept Genet Cell Biol & Anat, Omaha, NE 68198 USA

[4] Univ London Imperial Coll Sci Technol & Med, Med Res Council Clin Sci Ctr, London W12 0NN, England

[5] UMC Utrecht, Dept Med Genet, NL-3584 GG Utrecht, Netherlands

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 04期

关键词：

Copy number variation; DNA isolation; Technological bias; Tissue specificity; DETECTABLE CLONAL MOSAICISM; GENOME; WAVES; PROFILES; TISSUES; CANCER; MOUSE; AGE;

D O I：

10.1186/gb-2013-14-4-r33

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal. Results: While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing. Conclusion: These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.

引用

页数：9

共 21 条

[1] Somatic retrotransposition alters the genetic landscape of the human brain [J].

Baillie, J. Kenneth ;

Barnett, Mark W. ;

Upton, Kyle R. ;

Gerhardt, Daniel J. ;

Richmond, Todd A. ;

De Sapio, Fioravante ;

Brennan, Paul ;

Rizzu, Patrizia ;

Smith, Sarah ;

Fell, Mark ;

Talbot, Richard T. ;

Gustincich, Stefano ;

Freeman, Thomas C. ;

Mattick, John S. ;

Hume, David A. ;

Heutink, Peter ;

Carninci, Piero ;

Jeddeloh, Jeffrey A. ;

Faulkner, Geoffrey J. .

NATURE, 2011, 479 (7374) :534-537

[2] Summarizing and correcting the GC content bias in high-throughput sequencing [J].

Benjamini, Yuval ;

Speed, Terence P. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (10) :e72

[3]

Ceulemans S, 2012, METHODS MOL BIOL, V838, P311, DOI 10.1007/978-1-61779-507-7_15

[4]

Chen YW, 2012, NAT METHODS, V9, P609, DOI [10.1038/NMETH.1985, 10.1038/nmeth.1985]

[5] Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms [J].

Diskin, Sharon J. ;

Li, Mingyao ;

Hou, Cuiping ;

Yang, Shuzhang ;

Glessner, Joseph ;

Hakonarson, Hakon ;

Bucan, Maja ;

Maris, John M. ;

Wang, Kai .

NUCLEIC ACIDS RESEARCH, 2008, 36 (19)

[6] Ensembl 2012 [J].

Flicek, Paul ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Gordon, Leo ;

Hendrix, Maurice ;

Hourlier, Thibaut ;

Johnson, Nathan ;

Kaehaeri, Andreas K. ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Komorowska, Monika ;

Koscielny, Gautier ;

Kulesha, Eugene ;

Larsson, Pontus ;

Longden, Ian ;

McLaren, William ;

Muffato, Matthieu ;

Overduin, Bert ;

Pignatelli, Miguel ;

Pritchard, Bethan ;

Riat, Harpreet Singh ;

Ritchie, Graham R. S. ;

Ruffier, Magali ;

Schuster, Michael ;

Sobral, Daniel ;

Tang, Y. Amy ;

Taylor, Kieron ;

Trevanion, Stephen ;

Vandrovcova, Jana ;

White, Simon ;

Wilson, Mark ;

Wilder, Steven P. ;

Aken, Bronwen L. ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard ;

Fernandez-Suarez, Xose M. ;

Harrow, Jennifer ;

Herrero, Javier ;

Hubbard, Tim J. P. .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D84-D90

[7] Detectable clonal mosaicism and its relationship to aging and cancer [J].

Jacobs, Kevin B. ;

Yeager, Meredith ;

Zhou, Weiyin ;

Wacholder, Sholom ;

Wang, Zhaoming ;

Rodriguez-Santiago, Benjamin ;

Hutchinson, Amy ;

Deng, Xiang ;

Liu, Chenwei ;

Horner, Marie-Josephe ;

Cullen, Michael ;

Epstein, Caroline G. ;

Burdett, Laurie ;

Dean, Michael C. ;

Chatterjee, Nilanjan ;

Sampson, Joshua ;

Chung, Charles C. ;

Kovaks, Joseph ;

Gapstur, Susan M. ;

Stevens, Victoria L. ;

Teras, Lauren T. ;

Gaudet, Mia M. ;

Albanes, Demetrius ;

Weinstein, Stephanie J. ;

Virtamo, Jarmo ;

Taylor, Philip R. ;

Freedman, Neal D. ;

Abnet, Christian C. ;

Goldstein, Alisa M. ;

Hu, Nan ;

Yu, Kai ;

Yuan, Jian-Min ;

Liao, Linda ;

Ding, Ti ;

Qiao, You-Lin ;

Gao, Yu-Tang ;

Koh, Woon-Puay ;

Xiang, Yong-Bing ;

Tang, Ze-Zhong ;

Fan, Jin-Hu ;

Aldrich, Melinda C. ;

Amos, Christopher ;

Blot, William J. ;

Bock, Cathryn H. ;

Gillanders, Elizabeth M. ;

Harris, Curtis C. ;

Haiman, Christopher A. ;

Henderson, Brian E. ;

Kolonel, Laurence N. ;

Le Marchand, Loic .

NATURE GENETICS, 2012, 44 (06) :651-U68

[8] Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays [J].

Komura, Daisuke ;

Shen, Fan ;

Ishikawa, Shumpei ;

Fitch, Karen R. ;

Chen, Wenwei ;

Zhang, Jane ;

Liu, Guoying ;

Ihara, Sigeo ;

Nakamura, Hiroshi ;

Hurles, Matthew E. ;

Lee, Charles ;

Scherer, Stephen W. ;

Jones, Keith W. ;

Shapero, Michael H. ;

Huang, Jing ;

Aburatani, Hiroyuki .

GENOME RESEARCH, 2006, 16 (12) :1575-1584

[9] Initial sequencing and analysis of the human genome [J].

Lander, ES ;

Int Human Genome Sequencing Consortium ;

Linton, LM ;

Birren, B ;

Nusbaum, C ;

Zody, MC ;

Baldwin, J ;

Devon, K ;

Dewar, K ;

Doyle, M ;

FitzHugh, W ;

Funke, R ;

Gage, D ;

Harris, K ;

Heaford, A ;

Howland, J ;

Kann, L ;

Lehoczky, J ;

LeVine, R ;

McEwan, P ;

McKernan, K ;

Meldrim, J ;

Mesirov, JP ;

Miranda, C ;

Morris, W ;

Naylor, J ;

Raymond, C ;

Rosetti, M ;

Santos, R ;

Sheridan, A ;

Sougnez, C ;

Stange-Thomann, N ;

Stojanovic, N ;

Subramanian, A ;

Wyman, D ;

Rogers, J ;

Sulston, J ;

Ainscough, R ;

Beck, S ;

Bentley, D ;

Burton, J ;

Clee, C ;

Carter, N ;

Coulson, A ;

Deadman, R ;

Deloukas, P ;

Dunham, A ;

Dunham, I ;

Durbin, R ;

French, L .

NATURE, 2001, 409 (6822) :860-921

[10] Detectable clonal mosaicism from birth to old age and its relationship to cancer [J].

Laurie, Cathy C. ;

Laurie, Cecelia A. ;

Rice, Kenneth ;

Doheny, Kimberly F. ;

Zelnick, Leila R. ;

McHugh, Caitlin P. ;

Ling, Hua ;

Hetrick, Kurt N. ;

Pugh, Elizabeth W. ;

Amos, Chris ;

Wei, Qingyi ;

Wang, Li-E ;

Lee, Jeffrey E. ;

Barnes, Kathleen C. ;

Hansel, Nadia N. ;

Mathias, Rasika ;

Daley, Denise ;

Beaty, Terri H. ;

Scott, Alan F. ;

Ruczinski, Ingo ;

Scharpf, Rob B. ;

Bierut, Laura J. ;

Hartz, Sarah M. ;

Landi, Maria Teresa ;

Freedman, Neal D. ;

Goldin, Lynn R. ;

Ginsburg, David ;

Li, Jun ;

Desch, Karl C. ;

Strom, Sara S. ;

Blot, William J. ;

Signorello, Lisa B. ;

Ingles, Sue A. ;

Chanock, Stephen J. ;

Berndt, Sonja I. ;

Le Marchand, Loic ;

Henderson, Brian E. ;

Monroe, Kristine R. ;

Heit, John A. ;

de Andrade, Mariza ;

Armasu, Sebastian M. ;

Regnier, Cynthia ;

Lowe, William L. ;

Hayes, M. Geoffrey ;

Marazita, Mary L. ;

Feingold, Eleanor ;

Murray, Jeffrey C. ;

Melbye, Mads ;

Feenstra, Bjarke ;

Kang, Jae H. .

NATURE GENETICS, 2012, 44 (06) :642-U58

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