Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics

被引：63

作者：

Le Scouarnec, S. ^{[1
]}

Gribble, S. M. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

HEREDITY | 2012年 / 108卷 / 01期

基金：

英国惠康基金;

关键词：

array-CGH; array painting; breakpoint mapping; copy-number variant; next-generation sequencing; structural variant; DNA COPY-NUMBER; COMPARATIVE GENOMIC HYBRIDIZATION; HIGH-RESOLUTION ANALYSIS; IN-SITU HYBRIDIZATION; WHOLE HUMAN GENOME; ARRAY-CGH ANALYSIS; STRUCTURAL VARIATION; OLIGONUCLEOTIDE MICROARRAYS; INSITU HYBRIDIZATION; ABERRANT CHROMOSOMES;

D O I：

10.1038/hdy.2011.100

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

Genomic rearrangements can result in losses, amplifications, translocations and inversions of DNA fragments thereby modifying genome architecture, and potentially having clinical consequences. Many genomic disorders caused by structural variation have initially been uncovered by early cytogenetic methods. The last decade has seen significant progression in molecular cytogenetic techniques, allowing rapid and precise detection of structural rearrangements on a whole-genome scale. The high resolution attainable with these recently developed techniques has also uncovered the role of structural variants in normal genetic variation alongside single-nucleotide polymorphisms (SNPs). We describe how array-based comparative genomic hybridisation, SNP arrays, array painting and next-generation sequencing analytical methods (read depth, read pair and split read) allow the extensive characterisation of chromosome rearrangements in human genomes. Heredity (2012) 108, 75-85; doi:10.1038/hdy.2011.100; published online 16 November 2011

引用

页码：75 / 85

页数：11

共 132 条

[1] SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data [J].

Abel, Haley J. ;

Duncavage, Eric J. ;

Becker, Nils ;

Armstrong, Jon R. ;

Magrini, Vincent J. ;

Pfeifer, John D. .

BIOINFORMATICS, 2010, 26 (21) :2684-2688

[2] AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision [J].

Abyzov, Alexej ;

Gerstein, Mark .

BIOINFORMATICS, 2011, 27 (05) :595-603

[3] 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

[4] Limitations of next-generation genome sequence assembly [J].

Alkan, Can ;

Sajjadian, Saba ;

Eichler, Evan E. .

NATURE METHODS, 2011, 8 (01) :61-65

[5] Personalized copy number and segmental duplication maps using next-generation sequencing [J].

Alkan, Can ;

Kidd, Jeffrey M. ;

Marques-Bonet, Tomas ;

Aksay, Gozde ;

Antonacci, Francesca ;

Hormozdiari, Fereydoun ;

Kitzman, Jacob O. ;

Baker, Carl ;

Malig, Maika ;

Mutlu, Onur ;

Sahinalp, S. Cenk ;

Gibbs, Richard A. ;

Eichler, Evan E. .

NATURE GENETICS, 2009, 41 (10) :1061-U29

[6] A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[7] A segmental maximum a posteriori approach to genome-wide copy number profiling [J].

Andersson, Robin ;

Bruder, Carl E. G. ;

Piotrowski, Arkadiusz ;

Menzel, Uwe ;

Nord, Helena ;

Sandgren, Johanna ;

Hvidsten, Torgeir R. ;

de Stahl, Teresita Diaz ;

Dumanski, Jan P. ;

Komorowski, Jan .

BIOINFORMATICS, 2008, 24 (06) :751-758

[8] Array painting using microdissected chromosomes to map chromosomal breakpoints [J].

Backx, L. ;

Van Esch, H. ;

Melotte, C. ;

Kosyakova, N. ;

Starke, H. ;

Frijns, J-P ;

Liehr, T. ;

Vermeesch, J. R. .

CYTOGENETIC AND GENOME RESEARCH, 2007, 116 (03) :158-166

[9] Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA [J].

Barrett, MT ;

Scheffer, A ;

Ben-Dor, A ;

Sampas, N ;

Lipson, D ;

Kincaid, R ;

Tsang, P ;

Curry, B ;

Baird, K ;

Meltzer, PS ;

Yakhini, Z ;

Bruhn, L ;

Laderman, S .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (51) :17765-17770

[10] A NEW METHOD FOR FLUORESCENCE MICROSCOPICAL LOCALIZATION OF SPECIFIC DNA-SEQUENCES BY INSITU HYBRIDIZATION OF FLUOROCHROME-LABELED RNA [J].

BAUMAN, JGJ ;

WIEGANT, J ;

BORST, P ;

VANDUIJN, P .

EXPERIMENTAL CELL RESEARCH, 1980, 128 (02) :485-490

← 1 2 3 4 5 6 7 8 9 10 →