Single-molecule analysis reveals widespread structural variation in multiple myeloma

被引：44

作者：

Gupta, Aditya ^{[1
,2
,3
,4
]}

Place, Michael ^{[2
,3
,4
]}

Goldstein, Steven ^{[2
,3
,4
]}

Sarkar, Deepayan ^{[5
]}

Zhou, Shiguo ^{[2
,3
,4
]}

Potamousis, Konstantinos ^{[2
,3
,4
]}

Kim, Jaehyup ^{[4
,6
]}

Flanagan, Claire ^{[4
,6
]}

Li, Yang ^{[7
]}

Newton, Michael A. ^{[4
,8
]}

Callander, Natalie S. ^{[4
,6
]}

Hematti, Peiman ^{[4
,6
]}

Bresnick, Emery H. ^{[4
,9
]}

Ma, Jian ^{[7
]}

Asimakopoulos, Fotis ^{[4
,6
]}

Schwartz, David C. ^{[1
,2
,3
,4
]}

机构：

[1] Univ Wisconsin, Biophys Grad Program, Madison, WI 53706 USA

[2] Univ Wisconsin, Dept Chem, Genet Lab, Lab Mol & Computat Genom, Madison, WI 53706 USA

[3] Univ Wisconsin, Ctr Biotechnol, Madison, WI 53706 USA

[4] Univ Wisconsin, Carbone Canc Ctr, Madison, WI 53705 USA

[5] Indian Stat Inst, New Delhi 110016, India

[6] Univ Wisconsin, Sch Med & Publ Hlth, Dept Med, Madison, WI 53705 USA

[7] Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA

[8] Univ Wisconsin, Dept Stat, Madison, WI 53706 USA

[9] Univ Wisconsin, Madison Blood Res Program, Dept Cell & Regenerat Biol, Madison, WI 53705 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2015年 / 112卷 / 25期

关键词：

structural variation; copy number; multiple myeloma; optical mapping; DNA sequencing; COPY NUMBER; DISEASE; POLYMORPHISM; MUTATIONS; ALGORITHM; DIAGNOSIS; DELETIONS;

D O I：

10.1073/pnas.1418577112

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Multiple myeloma (MM), a malignancy of plasma cells, is characterized by widespread genomic heterogeneity and, consequently, differences in disease progression and drug response. Although recent large-scale sequencing studies have greatly improved our understanding of MM genomes, our knowledge about genomic structural variation in MM is attenuated due to the limitations of commonly used sequencing approaches. In this study, we present the application of optical mapping, a single-molecule, whole-genome analysis system, to discover new structural variants in a primary MM genome. Through our analysis, we have identified and characterized widespread structural variation in this tumor genome. Additionally, we describe our efforts toward comprehensive characterization of genome structure and variation by integrating our findings from optical mapping with those from DNA sequencing-based genomic analysis. Finally, by studying this MM genome at two time points during tumor progression, we have demonstrated an increase in mutational burden with tumor progression at all length scales of variation.

引用

页码：7689 / 7694

页数：6

共 40 条

[1] CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing [J].

Abyzov, Alexej ;

Urban, Alexander E. ;

Snyder, Michael ;

Gerstein, Mark .

GENOME RESEARCH, 2011, 21 (06) :974-984

[2] APPLICATIONS OF NEXT-GENERATION SEQUENCING Genome structural variation discovery and genotyping [J].

Alkan, Can ;

Coe, Bradley P. ;

Eichler, Evan E. .

NATURE REVIEWS GENETICS, 2011, 12 (05) :363-375

[3] A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk [J].

Antonacci, Francesca ;

Kidd, Jeffrey M. ;

Marques-Bonet, Tomas ;

Teague, Brian ;

Ventura, Mario ;

Girirajan, Santhosh ;

Alkan, Can ;

Campbell, Catarina D. ;

Vives, Laura ;

Malig, Maika ;

Rosenfeld, Jill A. ;

Ballif, Blake C. ;

Shaffer, Lisa G. ;

Graves, Tina A. ;

Wilson, Richard K. ;

Schwartz, David C. ;

Eichler, Evan E. .

NATURE GENETICS, 2010, 42 (09) :745-U29

[4] Perillyl alcohol inhibits a calcium-dependent constitutive nuclear factor-κB pathway [J].

Berchtold, CM ;

Chen, KS ;

Miyamoto, S ;

Gould, MN .

CANCER RESEARCH, 2005, 65 (18) :8558-8566

[5] Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data [J].

Boeva, Valentina ;

Popova, Tatiana ;

Bleakley, Kevin ;

Chiche, Pierre ;

Cappo, Julie ;

Schleiermacher, Gudrun ;

Janoueix-Lerosey, Isabelle ;

Delattre, Olivier ;

Barillot, Emmanuel .

BIOINFORMATICS, 2012, 28 (03) :423-425

[6] Heterogeneity of genomic evolution and mutational profiles in multiple myeloma [J].

Bolli, Niccolo ;

Avet-Loiseau, Herve ;

Wedge, David C. ;

Van Loo, Peter ;

Alexandrov, Ludmil B. ;

Martincorena, Inigo ;

Dawson, Kevin J. ;

Iorio, Francesco ;

Nik-Zainal, Serena ;

Bignell, Graham R. ;

Hinton, Jonathan W. ;

Li, Yilong ;

Tubio, Jose M. C. ;

McLaren, Stuart ;

Meara, Sarah O' ;

Butler, Adam P. ;

Teague, Jon W. ;

Mudie, Laura ;

Anderson, Elizabeth ;

Rashid, Naim ;

Tai, Yu-Tzu ;

Shammas, Masood A. ;

Sperling, Adam S. ;

Fulciniti, Mariateresa ;

Richardson, Paul G. ;

Parmigiani, Giovanni ;

Magrangeas, Florence ;

Minvielle, Stephane ;

Moreau, Philippe ;

Attal, Michel ;

Facon, Thierry ;

Futreal, P. Andrew ;

Anderson, Kenneth C. ;

Campbell, Peter J. ;

Munshi, Nikhil C. .

NATURE COMMUNICATIONS, 2014, 5

[7] Common variation at 3p22.1 and 7p15.3 influences multiple myeloma risk [J].

Broderick, Peter ;

Chubb, Daniel ;

Johnson, David C. ;

Weinhold, Niels ;

Foersti, Asta ;

Lloyd, Amy ;

Olver, Bianca ;

Ma, Yussanne P. ;

Dobbins, Sara E. ;

Walker, Brian A. ;

Davies, Faith E. ;

Gregory, Walter A. ;

Child, J. Anthony ;

Ross, Fiona M. ;

Jackson, Graham H. ;

Neben, Kai ;

Jauch, Anna ;

Hoffmann, Per ;

Muehleisen, Thomas W. ;

Noethen, Markus M. ;

Moebus, Susanne ;

Tomlinson, Ian P. ;

Goldschmidt, Hartmut ;

Hemminki, Kari ;

Morgan, Gareth J. ;

Houlston, Richard S. .

NATURE GENETICS, 2012, 44 (01) :58-U83

[8] Initial genome sequencing and analysis of multiple myeloma [J].

Chapman, Michael A. ;

Lawrence, Michael S. ;

Keats, Jonathan J. ;

Cibulskis, Kristian ;

Sougnez, Carrie ;

Schinzel, Anna C. ;

Harview, Christina L. ;

Brunet, Jean-Philippe ;

Ahmann, Gregory J. ;

Adli, Mazhar ;

Anderson, Kenneth C. ;

Ardlie, Kristin G. ;

Auclair, Daniel ;

Baker, Angela ;

Bergsagel, P. Leif ;

Bernstein, Bradley E. ;

Drier, Yotam ;

Fonseca, Rafael ;

Gabriel, Stacey B. ;

Hofmeister, Craig C. ;

Jagannath, Sundar ;

Jakubowiak, Andrzej J. ;

Krishnan, Amrita ;

Levy, Joan ;

Liefeld, Ted ;

Lonial, Sagar ;

Mahan, Scott ;

Mfuko, Bunmi ;

Monti, Stefano ;

Perkins, Louise M. ;

Onofrio, Robb ;

Pugh, Trevor J. ;

Rajkumar, S. Vincent ;

Ramos, Alex H. ;

Siegel, David S. ;

Sivachenko, Andrey ;

Stewart, A. Keith ;

Trudel, Suzanne ;

Vij, Ravi ;

Voet, Douglas ;

Winckler, Wendy ;

Zimmerman, Todd ;

Carpten, John ;

Trent, Jeff ;

Hahn, William C. ;

Garraway, Levi A. ;

Meyerson, Matthew ;

Lander, Eric S. ;

Getz, Gad ;

Golub, Todd R. .

NATURE, 2011, 471 (7339) :467-472

[9]

Chen K, 2009, NAT METHODS, V6, P677, DOI [10.1038/NMETH.1363, 10.1038/nmeth.1363]

[10] Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk [J].

Chubb, Daniel ;

Weinhold, Niels ;

Broderick, Peter ;

Chen, Bowang ;

Johnson, David C. ;

Foersti, Asta ;

Vijayakrishnan, Jayaram ;

Migliorini, Gabriele ;

Dobbins, Sara E. ;

Holroyd, Amy ;

Hose, Dirk ;

Walker, Brian A. ;

Davies, Faith E. ;

Gregory, Walter A. ;

Jackson, Graham H. ;

Irving, Julie A. ;

Pratt, Guy ;

Fegan, Chris ;

Fenton, James A. L. ;

Neben, Kai ;

Hoffmann, Per ;

Noethen, Markus M. ;

Muehleisen, Thomas W. ;

Eisele, Lewin ;

Ross, Fiona M. ;

Straka, Christian ;

Einsele, Hermann ;

Langer, Christian ;

Doerner, Elisabeth ;

Allan, James M. ;

Jauch, Anna ;

Morgan, Gareth J. ;

Hemminki, Kari ;

Houlston, Richard S. ;

Goldschmidt, Hartmut .

NATURE GENETICS, 2013, 45 (10) :1221-U366

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