Characterization of large structural genetic mosaicism in human autosomes

American Journal of Human Genetics

Volumn 96, Issue 3, 2015, Pages 487-497

  Machiela, Mitchell J ^a   Zhou, Weiyin ^a   Sampson, Joshua N ^a   Dean, Michael C ^b   Jacobs, Kevin B ^a,c   Black, Amanda ^a   Brinton, Louise A ^a   Chang, I Shou ^d   Chen, Chu ^e   Chen, Constance ^f   Chen, Kexin ^g   Cook, Linda S ^h   Crous Bou, Marta ^f,i   De Vivo, Immaculata ^f,i   Doherty, Jennifer ^j   Friedenreich, Christine M ^k   Gaudet, Mia M ^l   Haiman, Christopher A ^m   Hankinson, Susan E ^i,n   Hartge, Patricia ^a   Henderson, Brian E ^m   Hong, Yun Chul ^o   Hosgood, H Dean ^a,p   Hsiung, Chao A ^d   Hu, Wei ^a   Hunter, David J ^f,i,q   Jessop, Lea ^a   Kim, Hee Nam ^r   Kim, Yeul Hong ^s   Kim, Young Tae ^t   Klein, Robert ^u   Kraft, Peter ^f   Lan, Qing ^a   Lin, Dongxin ^v   Liu, Jianjun ^w,x   Le Marchand, Loic ^y   Liang, Xiaolin ^u   Lissowska, Jolanta ^z   Lu, Lingeng ^aa   Magliocco, Anthony M ^ab   Matsuo, Keitaro ^ac   Olson, Sara H ^u   Orlow, Irene ^u   Park, Jae Yong ^ad   Pooler, Loreall ^m   Prescott, Jennifer ^f,i   Rastogi, Radhai ^u   Risch, Harvey A ^aa   Schumacher, Fredrick ^m   Seow, Adeline ^ae   Setiawan, Veronica Wendy ^m   Shen, Hongbing ^af   Sheng, Xin ^m   Shin, Min Ho ^ag   Shu, Xiao Ou ^ah   Vanden Berg, David ^m   Wang, Jiu Cun ^ai,aj   Wentzensen, Nicolas ^a   Wong, Maria Pik ^ak   Wu, Chen ^v   Wu, Tangchun ^al   Wu, Yi Long ^am   Xia, Lucy ^m   Yang, Hannah P ^a   Yang, Pan Chyr ^an   Zheng, Wei ^g   Zhou, Baosen ^ao   Abnet, Christian C ^a   Albanes, Demetrius ^a   Aldrich, Melinda C ^g,ap   Amos, Christopher ^aq   Amundadottir, Laufey T ^a   Berndt, Sonja I ^a   Blot, William J ^g,ar   Bock, Cathryn H ^as   Bracci, Paige M ^at   Burdett, Laurie ^a   Buring, Julie E ^au   Butler, Mary A ^av   Carreón, Tania ^av   Chatterjee, Nilanjan ^a   Chung, Charles C ^a   Cook, Michael B ^a   Cullen, Michael ^a   Davis, Faith G ^aw   Ding, Ti ^ax   Duell, Eric J ^ay   Epstein, Caroline G ^a   Fan, Jin Hu ^az   Figueroa, Jonine D ^a   Fraumeni, Joseph F ^a   Freedman, Neal D ^a   Fuchs, Charles S ^i,ba   Gao, Yu Tang ^bb   Gapstur, Susan M ^l   Patiño Garcia, Ana ^bc   Garcia Closas, Montserrat ^bd   Gaziano, J Michael ^i,be   Giles, Graham G ^bf   Gillanders, Elizabeth M ^a   Giovannucci, Edward L ^f,i   Goldin, Lynn ^a   Goldstein, Alisa M ^a   Greene, Mark H ^a   Hallmans, Goran ^bg   Harris, Curtis C ^a   Henriksson, Roger ^bg   Holly, Elizabeth A ^at   Hoover, Robert N ^a   Hu, Nan ^a   Hutchinson, Amy ^a   Jenab, Mazda ^bh   Johansen, Christoffer ^bi,bj   Khaw, Kay Tee ^bk   Koh, Woon Puay ^ae,bl   Kolonel, Laurence N ^y   Kooperberg, Charles ^e   Krogh, Vittorio ^bm   Kurtz, Robert C ^u   Lacroix, Andrea ^e   Landgren, Annelie ^a   Landi, Maria Teresa ^a   Li, Donghui ^aq   Liao, Linda M ^a   Malats, Nuria ^bn   McGlynn, Katherine A ^a   McNeill, Lorna H ^aq,bo   McWilliams, Robert R ^bp   Melin, Beatrice S ^bg   Mirabello, Lisa ^a   Peplonska, Beata ^bq   Peters, Ulrike ^e   Petersen, Gloria M ^bp   Prokunina Olsson, Ludmila ^a   Purdue, Mark ^a   Qiao, You Lin ^br   Rabe, Kari G ^bp   Rajaraman, Preetha ^a   Real, Francisco X ^bn,bs   Riboli, Elio ^bt   Rodríguez Santiago, Benjamín ^bs,bu,bv   Rothman, Nathaniel ^a   Ruder, Avima M ^av   Savage, Sharon A ^a   Schwartz, Ann G ^as   Schwartz, Kendra L ^as   Sesso, Howard D ^au   Severi, Gianluca ^bf,bw   Silverman, Debra T ^a   Spitz, Margaret R ^bx   Stevens, Victoria L ^l   Stolzenberg Solomon, Rachael ^a   Stram, Daniel ^m   Tang, Ze Zhong ^ax   Taylor, Philip R ^a   Teras, Lauren R ^l   Tobias, Geoffrey S ^a   Viswanathan, Kala ^by   Wacholder, Sholom ^a   Wang, Zhaoming ^a   Weinstein, Stephanie J ^a   Wheeler, William ^bz   White, Emily ^e   Wiencke, John K ^ca   Wolpin, Brian M ^i,ba   Wu, Xifeng ^aq   Wunder, Jay S ^cb   Yu, Kai ^a   Zanetti, Krista A ^a   Zeleniuch Jacquotte, Anne ^cc,cd   Ziegler, Regina G ^a   De Andrade, Mariza ^bp   Barnes, Kathleen C ^ce   Beaty, Terri H ^by   Bierut, Laura J ^cb   Desch, Karl C ^cf   Doheny, Kimberly F ^ce   Feenstra, Bjarke ^cg   Ginsburg, David ^ch   Heit, John A ^bp   Kang, Jae H ⁱ   Laurie, Cecilia A ^ci   Li, Jun Z ^ch   Lowe, William L ^cj   Marazita, Mary L ^ck,cl   Melbye, Mads ^cg,cm   Mirel, Daniel B ^q   Murray, Jeffrey C ^cn   Nelson, Sarah C ^ci   Pasquale, Louis R ^i,cn   Rice, Kenneth ^ci   Wiggs, Janey L ^cn   Wise, Anastasia ^cn   Tucker, Margaret ^a   Pérez Jurado, Luis A ^bs,bu,cn   Laurie, Cathy C ^ci   Caporaso, Neil E ^a   Yeager, Meredith ^a   Chanock, Stephen J ^a   more..

^a NATIONAL CANCER INSTITUTE   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c BioInformed LLC   (United States)

^d NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

^e Fred Hutchinson Cancer Research Center   (United States)

^f HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^g TIANJIN MEDICAL UNIVERSITY   (China)

^h UNIVERSITY OF NEW MEXICO   (United States)

ⁱ HARVARD MEDICAL SCHOOL   (United States)

^j DARTMOUTH MEDICAL SCHOOL   (United States)

^k ALBERTA HEALTH SERVICES   (Canada)

^l AMERICAN CANCER SOCIETY   (United States)

^m UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

ⁿ UNIVERSITY OF MASSACHUSETTS   (United States)

^o Seoul National University College of Medicine   (South Korea)

^p ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^q BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^r Chonnam National University   (South Korea)

^s College of Medicine   (South Korea)

^t Seoul National University Graduate School   (South Korea)

^u MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^v CANCER HOSPITAL   (China)

^w GENOME INSTITUTE OF SINGAPORE   (Singapore)

^x ANHUI MEDICAL UNIVERSITY   (China)

^y UNIVERSITY OF HAWAII CANCER CENTER   (United States)

^z INSTITUTE OF ONCOLOGY   (Poland)

^aa YALE UNIVERSITY   (United States)

^ab H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^ac KYUSHU UNIVERSITY   (Japan)

^ad Kyungpook National University School of Medicine   (South Korea)

^ae NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^af NANJING MEDICAL UNIVERSITY   (China)

^ag Chonnam National University Medical School   (South Korea)

^ah VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^ai FUDAN UNIVERSITY   (China)

^aj FUDAN UNIVERSITY   (China)

^ak UNIVERSITY OF HONG KONG   (Hong Kong)

^al HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^am GUANGDONG PROVINCIAL PEOPLE'S HOSPITAL   (China)

^an NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^ao CHINA MEDICAL UNIVERSITY   (China)

^ap VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^aq UNIVERSITY OF TEXAS   (United States)

^ar INTERNATIONAL EPIDEMIOLOGY INSTITUTE   (United States)

^as WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^at UNIVERSITY OF CALIFORNIA   (United States)

^au BRIGHAM AND WOMEN S HOSPITAL   (United States)

^av NATIONAL INSTITUTE FOR OCCUPATIONAL SAFETY AND HEALTH   (United States)

^aw UNIVERSITY OF ALBERTA   (Canada)

^ax SHANXI CANCER HOSPITAL   (China)

^ay CATALAN INSTITUTE OF ONCOLOGY   (Spain)

^az SHANGHAI CANCER INSTITUTE   (China)

^ba DANA FARBER CANCER INSTITUTE   (United States)

^bb SHANGHAI JIAO TONG UNIVERSITY   (China)

^bc UNIVERSITY CLINIC OF NAVARRA   (Spain)

^bd INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^be VETERANS AFFAIRS MEDICAL CENTER   (United States)

^bf UNIVERSITY OF MELBOURNE   (Australia)

^bg UMEÅ UNIVERSITY   (Sweden)

^bh INTERNATIONAL AGENCY FOR RESEARCH ON CANCER   (France)

^bi FINSEN LABORATORY   (Denmark)

^bj DANISH CANCER SOCIETY RESEARCH CENTER   (Denmark)

^bk UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^bl DUKE NUS MEDICAL SCHOOL   (Singapore)

^bm NATIONAL CANCER INSTITUTE   (Italy)

^bn Structural Biology and Biocomputing Programme   (Spain)

^bo UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^bp MAYO CLINIC   (United States)

^bq NOFER INSTITUTE OF OCCUPATIONAL MEDICINE   (Poland)

^br PEKING UNION MEDICAL COLLEGE   (China)

^bs UNIVERSITAT POMPEU FABRA   (Spain)

^bt IMPERIAL COLLEGE LONDON   (United Kingdom)

^bu CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^bv SL   (Spain)

^bw Human Genetics Foundation   (Italy)

^bx BAYLOR COLLEGE OF MEDICINE   (United States)

^by JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^bz INFORMATION MANAGEMENT SERVICES INC   (United States)

^ca UNIVERSITY OF CALIFORNIA   (United States)

^cb WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^cc NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^cd NEW YORK UNIVERSITY   (United States)

^ce JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^cf UNIVERSITY OF MICHIGAN   (United States)

^cg STATENS SERUM INSTITUT   (Denmark)

^ch UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^ci UNIVERSITY OF WASHINGTON   (United States)

^cj NORTHWESTERN UNIVERSITY   (United States)

^ck UNIVERSITY OF PITTSBURGH   (United States)

^cl UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

^cm STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^cn NONE

more..

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AFRICAN; AGING; ANCESTRY GROUP; ARTICLE; AUTOSOME; AUTOSOME MOSAICISM; CONTROLLED STUDY; ENVIRONMENT; GENETIC ASSOCIATION; GENOME; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MOSAICISM; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; AGED; CHROMOSOME ABERRATION; FEMALE; GENETICS; HUMAN GENOME; MALE; META ANALYSIS; MIDDLE AGED; NEOPLASM;

AGED; CHROMOSOME ABERRATIONS; FEMALE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; MIDDLE AGED; MOSAICISM; NEOPLASMS;

EID: 84924140975     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.01.011     Document Type: Article

References (35)

1. T. Strachan, and A. Read Human Molecular Genetics 1999 Wiley-Liss New York
2. J.G. Hall Review and hypotheses: somatic mosaicism: observations related to clinical genetics Am. J. Hum. Genet. 43 1988 355 363
3. M.J. Machiela, and S.J. Chanock Detectable clonal mosaicism in the human genome Semin. Hematol. 50 2013 348 359
4. H. Youssoufian, and R.E. Pyeritz Mechanisms and consequences of somatic mosaicism in humans Nat. Rev. Genet. 3 2002 748 758
5. L.G. Biesecker, and N.B. Spinner A genomic view of mosaicism and human disease Nat. Rev. Genet. 14 2013 307 320
6. P.J. Ainsworth, P.K. Chakraborty, and R. Weksberg Example of somatic mosaicism in a series of de novo neurofibromatosis type 1 cases due to a maternally derived deletion Hum. Mutat. 9 1997 452 457
7. P. Papavassiliou, T.P. York, N. Gursoy, G. Hill, L.V. Nicely, U. Sundaram, A. McClain, S.H. Aggen, L. Eaves, B. Riley, and C. Jackson-Cook The phenotype of persons having mosaicism for trisomy 21/Down syndrome reflects the percentage of trisomic cells present in different tissues Am. J. Med. Genet. A. 149A 2009 573 583
8. B. Gottlieb, L.K. Beitel, and M.A. Trifiro Somatic mosaicism and variable expressivity Trends Genet. 17 2001 79 82
9. M.F. Amary, S. Damato, D. Halai, M. Eskandarpour, F. Berisha, F. Bonar, S. McCarthy, V.R. Fantin, K.S. Straley, and S. Lobo Ollier disease and Maffucci syndrome are caused by somatic mosaic mutations of IDH1 and IDH2 Nat. Genet. 43 2011 1262 1265
10. T.C. Pansuriya, R. van Eijk, P. d'Adamo, M.A. van Ruler, M.L. Kuijjer, J. Oosting, A.M. Cleton-Jansen, J.G. van Oosterwijk, S.L. Verbeke, and D. Meijer Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell hemangioma in Ollier disease and Maffucci syndrome Nat. Genet. 43 2011 1256 1261
11. W.F. Schwindinger, C.A. Francomano, and M.A. Levine Identification of a mutation in the gene encoding the alpha subunit of the stimulatory G protein of adenylyl cyclase in McCune-Albright syndrome Proc. Natl. Acad. Sci. USA 89 1992 5152 5156
12. L. Groesser, E. Herschberger, A. Ruetten, C. Ruivenkamp, E. Lopriore, M. Zutt, T. Langmann, S. Singer, L. Klingseisen, and W. Schneider-Brachert Postzygotic HRAS and KRAS mutations cause nevus sebaceous and Schimmelpenning syndrome Nat. Genet. 44 2012 783 787
13. M.J. Lindhurst, J.C. Sapp, J.K. Teer, J.J. Johnston, E.M. Finn, K. Peters, J. Turner, J.L. Cannons, D. Bick, and L. Blakemore A mosaic activating mutation in AKT1 associated with the Proteus syndrome N. Engl. J. Med. 365 2011 611 619
14. C. Hafner, and L. Groesser Mosaic RASopathies Cell Cycle 12 2013 43 50
15. S. Heim, and F. Mitelman Nonrandom chromosome abnormailities in cancer-an overview S. Heim, F. Mitelman, Cancer Cytogenetics 2009 John Wiley & Sons Hoboken 25 44
16. C.E. Bruder, A. Piotrowski, A.A. Gijsbers, R. Andersson, S. Erickson, T. Diaz de Ståhl, U. Menzel, J. Sandgren, D. von Tell, and A. Poplawski Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles Am. J. Hum. Genet. 82 2008 763 771
17. A. Piotrowski, C.E.G. Bruder, R. Andersson, T. Diaz de Ståhl, U. Menzel, J. Sandgren, A. Poplawski, D. von Tell, C. Crasto, and A. Bogdan Somatic mosaicism for copy number variation in differentiated human tissues Hum. Mutat. 29 2008 1118 1124
18. B. Rodríguez-Santiago, N. Malats, N. Rothman, L. Armengol, M. Garcia-Closas, M. Kogevinas, O. Villa, A. Hutchinson, J. Earl, and G. Marenne Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome Am. J. Hum. Genet. 87 2010 129 138
19. J.R. González, B. Rodríguez-Santiago, A. Cáceres, R. Pique-Regi, N. Rothman, S.J. Chanock, L. Armengol, and L.A. Pérez-Jurado A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data BMC Bioinformatics 12 2011 166
20. K.B. Jacobs, M. Yeager, W. Zhou, S. Wacholder, Z. Wang, B. Rodriguez-Santiago, A. Hutchinson, X. Deng, C. Liu, and M.-J. Horner Detectable clonal mosaicism and its relationship to aging and cancer Nat. Genet. 44 2012 651 658
21. C.C. Laurie, C.A. Laurie, K. Rice, K.F. Doheny, L.R. Zelnick, C.P. McHugh, H. Ling, K.N. Hetrick, E.W. Pugh, and C. Amos Detectable clonal mosaicism from birth to old age and its relationship to cancer Nat. Genet. 44 2012 642 650
22. L.A. Forsberg, C. Rasi, H.R. Razzaghian, G. Pakalapati, L. Waite, K.S. Thilbeault, A. Ronowicz, N.E. Wineinger, H.K. Tiwari, and D. Boomsma Age-related somatic structural changes in the nuclear genome of human blood cells Am. J. Hum. Genet. 90 2012 217 228
23. U.M. Schick, A. McDavid, P.K. Crane, N. Weston, K. Ehrlich, K.M. Newton, R. Wallace, E. Bookman, T. Harrison, and A. Aragaki Confirmation of the reported association of clonal chromosomal mosaicism with an increased risk of incident hematologic cancer PLoS ONE 8 2013 e59823
24. A. Bonnefond, B. Skrobek, S. Lobbens, E. Eury, D. Thuillier, S. Cauchi, O. Lantieri, B. Balkau, E. Riboli, and M. Marre Association between large detectable clonal mosaicism and type 2 diabetes with vascular complications Nat. Genet. 45 2013 1040 1043
25. L.A. Forsberg, C. Rasi, N. Malmqvist, H. Davies, S. Pasupulati, G. Pakalapati, J. Sandgren, T. Diaz de Ståhl, A. Zaghlool, and V. Giedraitis Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer Nat. Genet. 46 2014 624 628
26. I.M. Campbell, B. Yuan, C. Robberecht, R. Pfundt, P. Szafranski, M.E. McEntagart, S.C.S. Nagamani, A. Erez, M. Bartnik, and B. Wis̈niowiecka-Kowalnik Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders Am. J. Hum. Genet. 95 2014 173 182
27. J. Staaf, J. Vallon-Christersson, D. Lindgren, G. Juliusson, R. Rosenquist, M. Höglund, A. Borg, and M. Ringnér Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios BMC Bioinformatics 9 2008 409
28. S.J. Diskin, M. Li, C. Hou, S. Yang, J. Glessner, H. Hakonarson, M. Bucan, J.M. Maris, and K. Wang Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms Nucleic Acids Res. 36 2008 e126
29. R. Pique-Regi, A. Cáceres, and J.R. González R-Gada: a fast and flexible pipeline for copy number analysis in association studies BMC Bioinformatics 11 2010 380
30. M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S.J. Jones, and M.A. Marra Circos: an information aesthetic for comparative genomics Genome Res. 19 2009 1639 1645
31. P.J. Kurtin, G.W. Dewald, D.J. Shields, and C.A. Hanson Hematologic disorders associated with deletions of chromosome 20q: a clinicopathologic study of 107 patients Am. J. Clin. Pathol. 106 1996 680 688
32. H. Döhner, S. Stilgenbauer, A. Benner, E. Leupolt, A. Kröber, L. Bullinger, K. Döhner, M. Bentz, and P. Lichter Genomic aberrations and survival in chronic lymphocytic leukemia N. Engl. J. Med. 343 2000 1910 1916
33. L.I. Shlush, S. Zandi, A. Mitchell, W.C. Chen, J.M. Brandwein, V. Gupta, J.A. Kennedy, A.D. Schimmer, A.C. Schuh, K.W. Yee HALT Pan-Leukemia Gene Panel Consortium Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia Nature 506 2014 328 333
34. K.A. Frazer, D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 449 2007 851 861
35. R Development Core Team R: A Language and Environment for Statistical Computing 2013 R Foundation for Statistical Computing Vienna, Austria