-
1
-
-
31144469134
-
Structural variation in the human genome
-
Feuk, L., Carson, A. R. & Scherer, S. W. Structural variation in the human genome. Nat. Rev. Genet. 7, 85-97 (2006).
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 85-97
-
-
Feuk, L.1
Carson, A.R.2
Scherer, S.W.3
-
2
-
-
33750368085
-
Structural variation of the human genome
-
Sharp, A. J., Cheng, Z. & Eichler, E. E. Structural variation of the human genome. Annu. Rev. Genomics Hum. Genet. 7, 407-442 (2006).
-
(2006)
Annu. Rev. Genomics Hum. Genet.
, vol.7
, pp. 407-442
-
-
Sharp, A.J.1
Cheng, Z.2
Eichler, E.E.3
-
3
-
-
77950461601
-
Origins and functional impact of copy number variation in the human genome
-
Conrad, D. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2009).
-
(2009)
Nature
, vol.464
, pp. 704-712
-
-
Conrad, D.1
-
4
-
-
77949831756
-
Structural variation in the human genome and its role in disease
-
Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437-455 (2010).
-
(2010)
Annu. Rev. Med.
, vol.61
, pp. 437-455
-
-
Stankiewicz, P.1
Lupski, J.R.2
-
5
-
-
68649123353
-
Duplication hotspots, rare genomic disorders, and common disease
-
Mefford, H. C. & Eichler, E. E. Duplication hotspots, rare genomic disorders, and common disease. Curr. Opin. Genet. Dev. 19, 196-204 (2009).
-
(2009)
Curr. Opin. Genet. Dev.
, vol.19
, pp. 196-204
-
-
Mefford, H.C.1
Eichler, E.E.2
-
6
-
-
77954657070
-
Functional impact of global rare copy number variation in autism spectrum disorders
-
Pinto, D. et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368-372 (2010).
-
(2010)
Nature
, vol.466
, pp. 368-372
-
-
Pinto, D.1
-
7
-
-
34247481814
-
Strong association of de novo copy number mutations with autism
-
Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007).
-
(2007)
Science
, vol.316
, pp. 445-449
-
-
Sebat, J.1
-
8
-
-
70350626873
-
Microduplications of 16p11.2 are associated with schizophrenia
-
McCarthy, S. E. et al. Microduplications of 16p11.2 are associated with schizophrenia. Nat. Genet. 41, 1223-1227 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 1223-1227
-
-
McCarthy, S.E.1
-
9
-
-
77950405093
-
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
-
Wellcome Trust Case Control Consortium et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464, 713-720 (2010).
-
(2010)
Nature
, vol.464
, pp. 713-720
-
-
Wellcome Trust Case Control Consortium et al.1
-
10
-
-
50449091647
-
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease
-
McCarroll, S. A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet. 40, 1107-1112 (2008).
-
(2008)
Nat. Genet.
, vol.40
, pp. 1107-1112
-
-
McCarroll, S.A.1
-
11
-
-
34547664096
-
Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes
-
Lupski, J. R. & Stankiewicz, P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 1, e49 (2005).
-
(2005)
PLoS Genet.
, vol.1
, pp. e49
-
-
Lupski, J.R.1
Stankiewicz, P.2
-
12
-
-
37349109667
-
A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
-
Lee, J. A., Carvalho, C. M. B. & Lupski, J. R. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235-1247 (2007).
-
(2007)
Cell
, vol.131
, pp. 1235-1247
-
-
Lee, J.A.1
Carvalho, C.M.B.2
Lupski, J.R.3
-
13
-
-
67649878596
-
The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans
-
Zhang, F. et al. The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat. Genet. 41, 849-853 (2009).
-
(2009)
Nat. Genet.
, vol.41
, pp. 849-853
-
-
Zhang, F.1
-
14
-
-
74049093136
-
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
-
Lam, H. Y. K. et al. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat. Biotechnol. 28, 47-55 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 47-55
-
-
Lam, H.Y.K.1
-
15
-
-
79251493015
-
A human genome structural variation sequencing resource reveals insights into mutational mechanisms
-
Kidd, J. M. et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143, 837-847 (2010).
-
(2010)
Cell
, vol.143
, pp. 837-847
-
-
Kidd, J.M.1
-
16
-
-
77951700086
-
Mutation spectrum revealed by breakpoint sequencing of human germline CNVs
-
Conrad, D. F. et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat. Genet. 42, 385-391 (2010).
-
(2010)
Nat. Genet.
, vol.42
, pp. 385-391
-
-
Conrad, D.F.1
-
17
-
-
84975804424
-
Mapping copy number variation by population-scale genome sequencing
-
Mills, R. E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65 (2011).
-
(2011)
Nature
, vol.470
, pp. 59-65
-
-
Mills, R.E.1
-
18
-
-
79960914208
-
Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
-
Ju, Y. S. et al. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat. Genet. 43, 745-752 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 745-752
-
-
Ju, Y.S.1
-
19
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
ENCODE Project Consortium et al.1
-
20
-
-
84862263248
-
The NIH Roadmap Epigenomics Program data resource
-
Chadwick, L. H. The NIH Roadmap Epigenomics Program data resource. Epigenomics 4, 317-324 (2012).
-
(2012)
Epigenomics
, vol.4
, pp. 317-324
-
-
Chadwick, L.H.1
-
21
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
Genomes Project Consortium et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 (2012).
-
(2012)
Nature
, vol.491
, pp. 56-65
-
-
1000 Genomes Project Consortium et al.1
-
22
-
-
84893695366
-
TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
-
Chen, K. et al. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 24, 310-317 (2014).
-
(2014)
Genome Res.
, vol.24
, pp. 310-317
-
-
Chen, K.1
-
23
-
-
79951961326
-
AGE: Defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
-
Abyzov, A. & Gerstein, M. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics 27, 595-603 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 595-603
-
-
Abyzov, A.1
Gerstein, M.2
-
24
-
-
84873081003
-
Mechanisms of formation of structural variation in a fully sequenced human genome
-
Pang, A. W. C., Migita, O., MacDonald, J. R., Feuk, L. & Scherer, S. W. Mechanisms of formation of structural variation in a fully sequenced human genome. Hum. Mutat. 34, 345-354 (2013).
-
(2013)
Hum. Mutat.
, vol.34
, pp. 345-354
-
-
Pang, A.W.C.1
Migita, O.2
Macdonald, J.R.3
Feuk, L.4
Scherer, S.W.5
-
25
-
-
77952296952
-
Towards a comprehensive structural variation map of an individual human genome
-
Pang, A. W. et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 11, R52 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R52
-
-
Pang, A.W.1
-
26
-
-
17444413395
-
Alu retrotransposition-mediated deletion
-
Callinan, P. A. et al. Alu retrotransposition-mediated deletion. J. Mol. Biol. 348, 791-800 (2005).
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 791-800
-
-
Callinan, P.A.1
-
27
-
-
0024403721
-
Restriction fragment length polymorphism caused by a deletion involving Alu sequences within the human alpha 2-plasmin inhibitor gene
-
Miura, O., Sugahara, Y., Nakamura, Y., Hirosawa, S. & Aoki, N. Restriction fragment length polymorphism caused by a deletion involving Alu sequences within the human alpha 2-plasmin inhibitor gene. Biochemistry 28, 4934-4938 (1989).
-
(1989)
Biochemistry
, vol.28
, pp. 4934-4938
-
-
Miura, O.1
Sugahara, Y.2
Nakamura, Y.3
Hirosawa, S.4
Aoki, N.5
-
28
-
-
84857956783
-
Detecting and annotating genetic variations using the HugeSeq pipeline
-
Lam, H. Y. K. et al. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat. Biotechnol. 30, 226-229 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 226-229
-
-
Lam, H.Y.K.1
-
29
-
-
84931271931
-
VarSim: A high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
-
Mu, J. C. et al. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics 31, 1469-1471 (2014).
-
(2014)
Bioinformatics
, vol.31
, pp. 1469-1471
-
-
Mu, J.C.1
-
30
-
-
84858433310
-
Personal omics profiling reveals dynamic molecular and medical phenotypes
-
Chen, R. et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148, 1293-1307 (2012).
-
(2012)
Cell
, vol.148
, pp. 1293-1307
-
-
Chen, R.1
-
31
-
-
63849094762
-
HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination
-
Sigurdsson, M. I., Smith, A. V., Bjornsson, H. T. & Jonsson, J. J. HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. Genome Res. 19, 581-589 (2009).
-
(2009)
Genome Res.
, vol.19
, pp. 581-589
-
-
Sigurdsson, M.I.1
Smith, A.V.2
Bjornsson, H.T.3
Jonsson, J.J.4
-
32
-
-
1842717957
-
Comparative recombination rates in the rat, mouse, and human genomes
-
Jensen-Seaman, M. I. et al. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 14, 528-538 (2004).
-
(2004)
Genome Res.
, vol.14
, pp. 528-538
-
-
Jensen-Seaman, M.I.1
-
33
-
-
80052937538
-
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
-
Molaro, A. et al. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146, 1029-1041 (2011).
-
(2011)
Cell
, vol.146
, pp. 1029-1041
-
-
Molaro, A.1
-
34
-
-
0028575909
-
Alu repeated DNAs are differentially methylated in primate germ cells
-
Rubin, C. M., VandeVoort, C. A., Teplitz, R. L. & Schmid, C. W. Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res. 22, 5121-5127 (1994).
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 5121-5127
-
-
Rubin, C.M.1
Vandevoort, C.A.2
Teplitz, R.L.3
Schmid, C.W.4
-
35
-
-
84865285978
-
Landscape of somatic retrotransposition in human cancers
-
Lee, E. et al. Landscape of somatic retrotransposition in human cancers. Science 337, 967-971 (2012).
-
(2012)
Science
, vol.337
, pp. 967-971
-
-
Lee, E.1
-
36
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
-
37
-
-
85027936863
-
Replicative mechanisms for CNV formation are error prone
-
Carvalho, C. M. B. et al. Replicative mechanisms for CNV formation are error prone. Nat. Genet. 45, 1319-1326 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1319-1326
-
-
Carvalho, C.M.B.1
-
38
-
-
84870955253
-
Differential relationship of DNA replication timing to different forms of human mutation and variation
-
Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033-1040 (2012).
-
(2012)
Am. J. Hum. Genet.
, vol.91
, pp. 1033-1040
-
-
Koren, A.1
-
39
-
-
84888018217
-
Organization of the mitotic chromosome
-
Naumova, N. et al. Organization of the mitotic chromosome. Science 342, 948-953 (2013).
-
(2013)
Science
, vol.342
, pp. 948-953
-
-
Naumova, N.1
-
40
-
-
84865681429
-
TrxG and PcG proteins but not methylated histones remain associated with DNA through replication
-
Petruk, S. et al. TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 150, 922-933 (2012).
-
(2012)
Cell
, vol.150
, pp. 922-933
-
-
Petruk, S.1
-
41
-
-
84863661788
-
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome
-
Li, J. et al. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet. 8, e1002692 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Li, J.1
-
42
-
-
84874765261
-
Comment on "genomic hypomethylation in the human germline associates with selective structural mutability in the human genome"
-
Watson, C. T., Garg, P. & Sharp, A. J. Comment on "genomic hypomethylation in the human germline associates with selective structural mutability in the human genome". PLoS Genet. 9, e1003332 (2013).
-
(2013)
PLoS Genet.
, vol.9
-
-
Watson, C.T.1
Garg, P.2
Sharp, A.J.3
-
43
-
-
67849121611
-
Extrachromosomal circular DNA in eukaryotes: Possible involvement in the plasticity of tandem repeats
-
Cohen, S. & Segal, D. Extrachromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats. Cytogenet. Genome Res. 124, 327-338 (2009).
-
(2009)
Cytogenet. Genome Res.
, vol.124
, pp. 327-338
-
-
Cohen, S.1
Segal, D.2
-
44
-
-
37549018501
-
Germline rates of de novo meiotic deletions and duplications causing several genomic disorders
-
Turner, D. J. et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat. Genet. 40, 90-95 (2008).
-
(2008)
Nat. Genet.
, vol.40
, pp. 90-95
-
-
Turner, D.J.1
-
45
-
-
84859516414
-
Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues
-
Shibata, Y. et al. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 336, 82-86 (2012).
-
(2012)
Science
, vol.336
, pp. 82-86
-
-
Shibata, Y.1
-
46
-
-
84866997011
-
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
-
Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999-1003 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 999-1003
-
-
Imakaev, M.1
-
47
-
-
0035863793
-
Target DNA chromatinization modulates nicking by L1 endonuclease
-
Cost, G. J., Golding, A., Schlissel, M. S. & Boeke, J. D. Target DNA chromatinization modulates nicking by L1 endonuclease. Nucleic Acids Res. 29, 573-577 (2001).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 573-577
-
-
Cost, G.J.1
Golding, A.2
Schlissel, M.S.3
Boeke, J.D.4
-
48
-
-
79951970227
-
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
-
Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 974-984
-
-
Abyzov, A.1
Urban, A.E.2
Snyder, M.3
Gerstein, M.4
-
49
-
-
84866440781
-
DELLY: Structural variant discovery by integrated paired-end and split-read analysis
-
Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. i333-i339
-
-
Rausch, T.1
-
50
-
-
79952194317
-
Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
-
Handsaker, R. E., Korn, J. M., Nemesh, J. & McCarroll, S. A. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat. Genet. 43, 269-276 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 269-276
-
-
Handsaker, R.E.1
Korn, J.M.2
Nemesh, J.3
McCarroll, S.A.4
-
51
-
-
70350694443
-
Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
-
Ye, K., Schulz, M., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2865-2871
-
-
Ye, K.1
Schulz, M.2
Long, Q.3
Apweiler, R.4
Ning, Z.5
-
52
-
-
69549116107
-
BreakDancer: An algorithm for high-resolution mapping of genomic structural variation
-
Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677-681 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 677-681
-
-
Chen, K.1
-
53
-
-
4944262040
-
Glocal alignment: Finding rearrangements during alignment
-
Brudno, M. et al. Glocal alignment: finding rearrangements during alignment. Bioinformatics 19(Suppl 1): i54-i62 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. i54-i62
-
-
Brudno, M.1
-
54
-
-
84864143346
-
BreakFusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
-
Chen, K. et al. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics 28, 1923-1924 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1923-1924
-
-
Chen, K.1
-
55
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
56
-
-
77949587649
-
Fast and accurate long read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate long read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
57
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent, W. J. BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
|