Eichler EE: Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 2001, 17 (11): 661-669.
Article
CAS
PubMed
Google Scholar
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE: Recent segmental duplications in the human genome. Science. 2002, 297 (5583): 1003-1007.
Article
CAS
PubMed
Google Scholar
Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW: Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 2003, 4 (4): R25-
Article
PubMed Central
PubMed
Google Scholar
Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, et al: Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001, 409 (6822): 953-958.
Article
CAS
PubMed
Google Scholar
Nei M: Selectionism and neutralism in molecular evolution. Mol Biol Evol. 2005, 22: 2318-2342.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bailey JA, Eichler EE: Genome-wide detection and analysis of recent segmental duplications within mammalian organisms. Cold Spring Harb Symp Quant Biol. 2003, 68: 115-124.
Article
CAS
PubMed
Google Scholar
Horvath JE, Schwartz S, Eichler EE: The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome. Genome Res. 2000, 10 (6): 839-852.
Article
PubMed Central
CAS
PubMed
Google Scholar
She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, et al: The structure and evolution of centromeric transition regions within the human genome. Nature. 2004, 430: 857-864.
Article
CAS
PubMed
Google Scholar
Eichler EE, Budarf ML, Rocchi M, Deaven LL, Doggett NA, Baldini A, Nelson DL, Mohrenweiser HW: Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity. Hum Mol Genet. 1997, 6 (7): 991-1002.
Article
CAS
PubMed
Google Scholar
Horvath JE, Gulden CL, Vallente RU, Eichler MY, Ventura M, McPherson JD, Graves TA, Wilson RK, Schwartz S, Rocchi M, et al: Punctuated duplication seeding events during the evolution of human chromosome 2p11. Genome Res. 2005, 15 (7): 914-927.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bailey JA, Liu G, Eichler EE: An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet. 2003, 73 (4): 823-834.
Article
PubMed Central
CAS
PubMed
Google Scholar
Eichler EE, Archidiacono N, Rocchi M: CAGGG repeats and the pericentromeric duplication of the hominoid genome. Genome Res. 1999, 9 (11): 1048-1058.
Article
CAS
PubMed
Google Scholar
Horvath JE, Bailey JA, Locke DP, Eichler EE: Lessons from the human genome: transitions between euchromatin and heterochromatin. Hum Mol Genet. 2001, 10 (20): 2215-2223.
Article
CAS
PubMed
Google Scholar
Bailey JA, Eichler EE: Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet. 2006, 7 (7): 552-564.
Article
CAS
PubMed
Google Scholar
Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR: Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res. 2004, 14 (11): 2209-2220.
Article
PubMed Central
CAS
PubMed
Google Scholar
She X, Liu G, Ventura M, Zhao S, Misceo D, Roberto R, Cardone MF, Rocchi M, Green ED, Archidiacano N, et al: A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great ape expansion of intrachromosomal duplications. Genome Res. 2006, 16 (5): 576-583.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cheng Z, Ventura M, She X, Khaitovich P, Graves T, Osoegawa K, Church D, DeJong P, Wilson RK, Paabo S, et al: A genome-wide comparison of recent chimpanzee and human segmental duplications. Nature. 2005, 437 (7055): 88-93.
Article
CAS
PubMed
Google Scholar
Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, et al: Fine-scale structural variation of the human genome. Nat Genet. 2005, 37 (7): 727-732.
Article
CAS
PubMed
Google Scholar
Goidts V, Cooper DN, Armengol L, Schempp W, Conroy J, Estivill X, Nowak N, Hameister H, Kehrer-Sawatzki H: Complex patterns of copy number variation at sites of segmental duplications: an important category of structural variation in the human genome. Hum Genet. 2006, 120 (2): 270-284.
Article
CAS
PubMed
Google Scholar
Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, et al: Segmental duplications and copy-number variation in the human genome. Am J Hum Genet. 2005, 77 (1): 78-88.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kuroda-Kawaguchi T, Skaletsky H, Brown LG, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Silber S, Oates R, Rozen S, et al: The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nat Genet. 2001, 29 (3): 279-286.
Article
CAS
PubMed
Google Scholar
Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Page DC: Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature. 2003, 423 (6942): 873-876.
Article
CAS
PubMed
Google Scholar
Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, et al: The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003, 423 (6942): 825-837.
Article
CAS
PubMed
Google Scholar
Kirsch S, Weiss B, Miner TL, Waterston RH, Clark RA, Eichler EE, Münch C, Schempp W, Rappold G: Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome. Genome Res. 2005, 15 (2): 195-204.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kirsch S, Münch C, Jiang Z, Cheng Z, Chen L, Batz C, Eichler EE, Schempp W: Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions. Genome Res. 2008, 18 (7): 1030-1042.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jiang Z, Tang H, Ventura M, Cardone MF, Marques-Bonet T, She X, Pevzner PA, Eichler EE: Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution. Nat Genet. 2007, 39 (11): 1361-1368.
Article
CAS
PubMed
Google Scholar
Matsuoka S, Huang M, Elledge SJ: Linkage of ATM to cell cycle regulation by the Chk2 protein kinase. Science. 1998, 282 (5395): 1893-1897.
Article
CAS
PubMed
Google Scholar
Cybulski C, Gorski B, Huzarski T, Masojc B, Mierzejewski M, Debniak T, Teodorczyk U, Byrski T, Gronwald J, Matyjasik J, et al: CHEK2 is a multiorgan cancer susceptibility gene. Am J Hum Genet. 2004, 75 (6): 1131-1135.
Article
PubMed Central
CAS
PubMed
Google Scholar
Allen JB, Zhou Z, Siede W, Friedberg EC, Elledge SJ: The SAD1/RAD53 protein kinase controls multiple checkpoints and DNA damage-induced transcription in yeast. Genes Dev. 1994, 8 (20): 2401-2415.
Article
CAS
PubMed
Google Scholar
Guo Z, Dunphy WG: Response of Xenopus Cds1 in cell-free extracts to DNA templates with double-stranded ends. Mol Biol Cell. 2000, 11 (5): 1535-1546.
Article
PubMed Central
CAS
PubMed
Google Scholar
Higashitani A, Aoki H, Mori A, Sasagawa Y, Takanami T, Takahashi H: Caenorhabditis elegans Chk2-like gene is essential for meiosis but dispensable for DNA repair. FEBS Lett. 2000, 485 (1): 35-39.
Article
CAS
PubMed
Google Scholar
Murakami H, Okayama H: A kinase from fission yeast responsible for blocking mitosis in S phase. Nature. 1995, 374 (6525): 817-819.
Article
CAS
PubMed
Google Scholar
Oishi I, Sugiyama S, Otani H, Yamamura H, Nishida Y, Minami Y: A novel Drosophila nuclear protein serine/threonine kinase expressed in the germline during its establishment. Mech Dev. 1998, 71 (1–2): 49-63.
Article
CAS
PubMed
Google Scholar
Bartek J, Falck J, Lukas J: CHK2 kinase–a busy messenger. Nat Rev Mol Cell Biol. 2001, 2 (12): 877-886.
Article
CAS
PubMed
Google Scholar
Feinberg AP, Vogelstein B: A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983, 132 (1): 6-13.
Article
CAS
PubMed
Google Scholar
Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27 (2): 573-580.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ried T, Baldini A, Rand TC, Ward DC: Simultaneous visualization of seven different DNA probes by in situ hybridization using combinatorial fluorescence and digital imaging microscopy. Proc Natl Acad Sci USA. 1992, 89 (4): 1388-1392.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schempp W, Binkele A, Arnemann J, Glaser B, Ma K, Taylor K, Toder R, Wolfe J, Zeitler S, Chandley AC: Comparative mapping of YRRM- and TSPY-related cosmids in man and hominoid apes. Chromosome Res. 1995, 3 (4): 227-234.
Article
CAS
PubMed
Google Scholar
Jauch A, Wienberg J, Stanyon R, Arnold N, Tofanelli S, Ishida T, Cremer T: Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting. Proc Natl Acad Sci USA. 1992, 89 (18): 8611-8615.
Article
PubMed Central
CAS
PubMed
Google Scholar
Higgins DG, Thompson JD, Gibson TJ: Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 1996, 266: 383-402.
Article
CAS
PubMed
Google Scholar
Tamura K, Dudley J, Nei M, Kumar S: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007, 24 (8): 1596-1599.
Article
CAS
PubMed
Google Scholar
Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980, 16 (2): 111-120.
Article
CAS
PubMed
Google Scholar
Goodman M, Grossman LI, Wildman DE: Moving primate genomics beyond the chimpanzee genome. Trends Genet. 2005, 21 (9): 511-517.
Article
CAS
PubMed
Google Scholar
Li W: Molecular evolution. 1997, Associates, Sunderland, MA
Google Scholar
Rochette CF, Gilbert N, Simard LR: SMN gene duplication and the emergence of the SMN2 gene occurred in distinct hominids: SMN2 is unique to Homo sapiens. Hum Genet. 2001, 108 (3): 255-266.
Article
CAS
PubMed
Google Scholar
Bieche I, Olivi M, Champeme MH, Vidaud D, Lidereau R, Vidaud M: Novel approach to quantitative polymerase chain reaction using real-time detection: application to the detection of gene amplification in breast cancer. Int J Cancer. 1998, 78 (5): 661-666.
Article
CAS
PubMed
Google Scholar
Rogers J, Garcia R, Shelledy W, Kaplan J, Arya A, Johnson Z, Bergstrom M, Novakowski L, Nair P, Vinson A, et al: An initial genetic linkage map of the rhesus macaque (Macaca mulatta) genome using human microsatellite loci. Genomics. 2006, 87 (1): 30-38.
Article
CAS
PubMed
Google Scholar
Eichler EE, Lu F, Shen Y, Antonacci R, Jurecic V, Doggett NA, Moyzis RK, Baldini A, Gibbs RA, Nelson DL: Duplication of a gene-rich cluster between 16p11.1 and Xq28: a novel pericentromeric-directed mechanism for paralogous genome evolution. Hum Mol Genet. 1996, 5 (7): 899-912.
Article
CAS
PubMed
Google Scholar
She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun E, Church DM, Sutton G, Halpern AL, Eichler EE: Shotgun sequence assembly and recent segmental duplications within the human genome. Nature. 2004, 431 (7011): 927-930.
Article
CAS
PubMed
Google Scholar
Bosch E, Hurles ME, Navarro A, Jobling MA: Dynamics of a human interparalog gene conversion hotspot. Genome Res. 2004, 14 (5): 835-844.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hallast P, Nagirnaja L, Margus T, Laan M: Segmental duplications and gene conversion: Human luteinizing hormone/chorionic gonadotropin beta gene cluster. Genome Res. 2005, 15 (11): 1535-1546.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pavlicek A, House R, Gentles AJ, Jurka J, Morrow BE: Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. Genome Res. 2005, 15 (11): 1487-1495.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jackson MS, Oliver K, Loveland J, Humphray S, Dunham I, Rocchi M, Viggiano L, Park JP, Hurles ME, Santibanez-Koref M: Evidence for widespread reticulate evolution within human duplicons. Am J Hum Genet. 2005, 77 (5): 824-840.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science. 2000, 290 (5494): 1151-1155.
Article
CAS
PubMed
Google Scholar
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV: Selection in the evolution of gene duplications. Genome Biol. 2002, 3 (2): RESEARCH0008-
Article
PubMed Central
PubMed
Google Scholar
Jordan IK, Wolf YI, Koonin EV: Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol. 2004, 4: 22-
Article
PubMed Central
PubMed
Google Scholar
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C: Detection of large-scale variation in the human genome. Nat Genet. 2004, 36 (9): 949-951.
Article
CAS
PubMed
Google Scholar
Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ: Complex SNP-related sequence variation in segmental genome duplications. Nat Genet. 2004, 36 (8): 861-866.
Article
CAS
PubMed
Google Scholar
Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006, 7 (2): 85-97.
Article
CAS
PubMed
Google Scholar
de Stahl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, et al: Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. Hum Mutat. 2008, 29 (3): 398-408.
Article
Google Scholar
Dong X, Wang L, Taniguchi K, Wang X, Cunningham JM, McDonnell SK, Qian C, Marks AF, Slager SL, Peterson BJ, et al: Mutations in CHEK2 associated with prostate cancer risk. Am J Hum Genet. 2003, 72 (2): 270-280.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meijers-Heijboer H, Wijnen J, Vasen H, Wasielewski M, Wagner A, Hollestelle A, Elstrodt F, Bos van den R, de Snoo A, Fat GT, et al: The CHEK2 1100delC mutation identifies families with a hereditary breast and colorectal cancer phenotype. Am J Hum Genet. 2003, 72 (5): 1308-1314.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sodha N, Williams R, Mangion J, Bullock SL, Yuille MR, Eeles RA: Screening hCHK2 for mutations. Science. 2000, 289 (5478): 359-
Article
CAS
PubMed
Google Scholar
Bell DW, Varley JM, Szydlo TE, Kang DH, Wahrer DC, Shannon KE, Lubratovich M, Verselis SJ, Isselbacher KJ, Fraumeni JF, et al: Heterozygous germ line hCHK2 mutations in Li-Fraumeni syndrome. Science. 1999, 286 (5449): 2528-2531.
Article
CAS
PubMed
Google Scholar
McConkey EH: Orthologous numbering of great ape and human chromosomes is essential for comparative genomics. Cytogenet Genome Res. 2004, 105 (1): 157-158.
Article
CAS
PubMed
Google Scholar
Sherlock JK, Griffin DK, Delhanty JD, Parrington JM: Homologies between human and marmoset (Callithrix jacchus) chromosomes revealed by comparative chromosome painting. Genomics. 1996, 33 (2): 214-219.
Article
CAS
PubMed
Google Scholar
Roberto R, Capozzi O, Wilson RK, Mardis ER, Lomiento M, Tuzun E, Cheng Z, Mootnick AR, Archidiacono N, Rocchi M, et al: Molecular refinement of gibbon genome rearrangements. Genome Res. 2007, 17 (2): 249-257.
Article
PubMed Central
CAS
PubMed
Google Scholar