Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Taudien, Stefan ^a   Galgoczy, Petra ^a   Huse, Klaus ^a   Reichwald, Kathrin ^a   Schilhabel, Markus ^a   Szafranski, Karol ^a   Shimizu, Atsushi ^b   Asakawa, Shuichi ^b   Frankish, Adam ^c   Loncarevic, Ivan F ^d   Shimizu, Nobuyoshi ^b   Siddiqui, Roman ^a   Platzer, Matthias ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

^b KEIO UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DEFENSIN; PROTEIN;

APE; ARTICLE; CHIMPANZEE; CHROMOSOME 8P; CHROMOSOME DUPLICATION; CHROMOSOME POLYMORPHISM; CHROMOSOME STRUCTURE; DISEASE PREDISPOSITION; EUCHROMATIN; GENE CLUSTER; GENE LOCUS; GENE SEQUENCE; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN CHROMOSOME; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN STRUCTURE; PSEUDOGENE; SINGLE NUCLEOTIDE POLYMORPHISM;

BACTERIA (MICROORGANISMS); PAN TROGLODYTES;

EID: 25444457773     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-5-92     Document Type: Article

References (53)

1. Eichler EE, Clark RA, She X: An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet 2004, 5:345-354.
2. Tilford CA, Kuroda-Kawaguchi T, Skaletsky H, Rozen S, Brown LG, Rosenberg M, McPherson JD, Wylie K, Sekhon M, Kucaba TA, Waterston RH, Page DC: A physical map of the human Y chromosome. Nature 2001, 409:943-945.
3. Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE: BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J Med Genet 2004, 41:175-182.
4. Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, et al: The DNA sequence of human chromosome 7. Nature 2003, 424:157-164.
5. Sebire NJ, Fisher RA, Rees HC: Histopathological diagnosis of partial and complete hydatidiform mole in the first trimester of pregnancy. Pediatr Dev Pathol 2003, 6:69-77.
6. Fredman D, White SJ, Potter S, Eichler EE, Dunnen JT, Brookes AJ: Complex SNP-related sequence variation in segmental genome duplications. Nat Genet 2004, 36:861-866.
7. Benham F, Hart K, Crolla J, Bobrow M, Francavilla M, Goodfellow PN: A method for generating hybrids containing nonselected fragments of human chromosomes. Genomics 1989, 4:509-517.
8. Bailey JA, Baertsch R, Kent WJ, Haussler D, Eichler EE: Hotspots of mammalian chromosomal evolution. Genome Biol 2004, 5:R23.
9. Schmutz J, Wheeler J, Grimwood J, Dickson M, Yang J, Caoile C, Bajorek E, Black S, Chan YM, Denys M, Escobar J, Flowers D, Fotopulos D, Garcia C, Gomez M, Gonzales E, Haydu L, Lopez F, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salazar A, Tsai M, Myers RM: Quality assessment of the human genome sequence. Nature 2004, 429:365-368.
10. University of California Santa Cruz (UCSC) Genome Browser [http://genome.ucsc.edu/cgi-bin/hgGateway]
11. Ganz T: Defensins: antimicrobial peptides of innate immunity. Nat Rev Immunol 2003, 3:710-720.
12. Schullerus D, von Knobloch R, Chudek J, Herbers J, Kovacs G: Microsatellite analysis reveals deletion of a large region at chromosome 8p in conventional renal cell carcinoma. Int J Cancer 1999, 80:22-24.
13. Young AN, de Oliveira Salles PG, Lim SD, Cohen C, Petros JA, Marshall FF, Neish AS, Amin MB: Beta defensin-1, parvalbumin, and vimentin: a panel of diagnostic immunohistochemical markers for renal tumors derived from gene expression profiling studies using cDNA microarrays. Am J Surg Pathol 2003, 27:199-205.
14. Donald CD, Sun CQ, Lim SD, Macoska J, Cohen C, Amin MB, Young AN, Ganz TA, Marshall FF, Petros JA: Cancer-specific loss of betadefensin 1 in renal and prostatic carcinomas. Lab Invest 2003, 83:501-505.
15. Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM: Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res 2003, 63:2872-2880.
16. Giglio S, Broman KW, Matsumoto N, Calvari V, Gimelli G, Neumann T, Ohashi H, Voullaire L, Larizza D, Giorda R, Weber JL, Ledbetter DH, Zuffardi O: Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. Am J Hum Genet 2001, 68:874-883.
17. Shimokawa O, Kurosawa K, Ida T, Harada N, Kondoh T, Miyake N, Yoshiura K, Kishino T, Ohta T, Niikawa N, Matsumoto N: Molecular characterization of inv dup del(8p): analysis of five cases. Am J Med Genet 2004, 128A:133-137.
18. Sugawara H, Harada N, Ida T, Ishida T, Ledbetter DH, Yoshiura K, Ohta T, Kishino T, Niikawa N, Matsumoto N: Complex low-copy repeats associated with a common polymorphic inversion at human chromosome 8p23. Genomics 2003, 82:238-244.
19. Mars WM, Patmasiriwat P, Maity T, Huff V, Weil MM, Saunders GF: Inheritance of unequal numbers of the genes encoding the human neutrophil defensins HP-1 and HP-3. J Biol Chem 1995, 270:30371-30376.
20. Hollox EJ, Armour JA, Barber JC: Extensive normal copy number variation of a beta-defensin antimicrobial-gene cluster. Am J Hum Genet 2003, 73:591-600.
21. Human and vertebrate analysis and annotation initiative [http://www.sanger.ac.uk/HGP/havana/]
22. Vertebrate Genome Annotation Database [http://vega.sanger.ac.uk/]
23. University of California Santa Cruz (UCSC) Home page [http://genome.ucsc.edu/]
24. Trace archive at NCBI [http://www.ncbi.nlm.nih.gov/Traces]
25. Jurevic RJ, Chrisman P, Mancl L, Livingston R, Dale BA: Single-nucleotide polymorphisms and haplotype analysis in beta-defensin genes in different ethnic populations. Genet Test 2002, 6:261-269.
26. 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:R25.
27. Jeffreys AJ, May CA: Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat Genet 2004, 36:151-156.
28. 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, 423:873-876.
29. SNP database at NCBI [http://www.ncbi.nlm.nih.gov/SNP/]
30. Wu Z, Hoover DM, Yang D, Boulegue C, Santamaria F, Oppenheim JJ, Lubkowski J, Lu W: Engineering disulfide bridges to dissect antimicrobial and chemotactic activities of human betadefensin 3. Proc Natl Acad Sci U S A 2003, 100:8880-8885.
31. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, et al: The sequence of the human genome. Science 2001, 291:1304-1351.
32. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, et al: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
33. Townson JR, Barcellos LF, Nibbs RJ: Gene copy number regulates the production of the human chemokine CCL3-L1. Eur J Immunol 2002, 32:3016-3026.
34. Prince JA, Feuk L, Howell WM, Jobs M, Emahazion T, Blennow K, Brookes AJ: Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. Genome Res 2001, 11:152-162.
35. Utting M, Hampe J, Platzer M, Huse K: Locking of 3′ ends of singlestranded DNA templates for improving Pyrosequencing(TM). BioTechniques 2004, 37:66-73.
36. White SJ, Vink GR, Kriek M, Wuyts W, Schouten J, Bakker B, Breuning MH, den Dunnen JT: Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses. Hum Mutat 2004, 24:86-92.
37. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002, 30:e57.
38. Lucito R, Healy J, Alexander J, Reiner A, Esposito D, Chi M, Rodgers L, Brady A, Sebat J, Troge J, West JA, Rostan S, Nguyen KC, Powers S, Ye KQ, Olshen A, Venkatraman E, Norton L, Wigler M: Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res 2003, 13:2291-2305.
39. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M: Large-scale copy number polymorphism in the human genome. Science 2004, 305:525-528.
40. Bonfield JK, Smith K, Staden R: A new DNA sequence assembly program. Nucleic Acids Res 1995, 23:4992-4999.
41. Miropeats program [http://genome.wustl.edu/groups/informatics/ software/miropeats/]
42. Chao KM, Zhang J, Ostell J, Miller W: A local alignment tool for very long DNA sequences. Comput Appl Biosci 1995, 11:147-153.
43. WU-Blast [http://blast.wustl.edu]
44. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
45. Repeatmasker program [http://www.repeatmasker.org/cgi-bin/ WEBRepeatMasker]
46. Kent WJ: BLAT-the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
47. RIKEN chimpanzee BAC end sequence database [http://hgp.gsc.riken.go.jp]
48. Finishing Standards for the Human Genome Project [http://genome.wustl.edu/Overview/g16stand.php]
49. Taudien S, Rump A, Platzer M, Drescher B, Schattevoy R, Gloeckner G, Dette M, Baumgart C, Weber J, Menzel U, Rosenthal A: RUMMAGE- a high-throughput sequence annotation system. Trends Genet 2000, 16:519-520.
50. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project. Nucleic Acids Res 2002, 30:38-41.
51. Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580.
52. Verma RS, Babu A: Human Chromosomes 2nd edition. Pergamon Press Inc; 1989.
53. Nietzel A, Rocchi M, Starke H, Heller A, Fiedler W, Wlodarska I, Loncarevic IF, Beensen V, Claussen U, Liehr T: A new multicolor- FISH approach for the characterization of marker chromosomes: centromere-specific multicolor-FISH (cenM-FISH). Hum Genet 2001, 108:199-204.