Expansion of a 12-kb VNTR containing the REXO1L1 gene cluster underlies the microscopically visible euchromatic variant of 8q21.2

European Journal of Human Genetics

Volumn 22, Issue 4, 2014, Pages 458-463

  Tyson, Christine ^a   Sharp, Andrew J ^b   Hrynchak, Monica ^a   Yong, Siu L ^c   Hollox, Edward J ^d   Warburton, Peter ^b   Barber, John C K ^e  

^a ROYAL COLUMBIAN HOSPITAL   (Canada)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d UNIVERSITY OF LEICESTER   (United Kingdom)

^e UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

8q21.2; Copy number variant; DNA array; Euchromatic variant; Hepatitis C; NanoString technology; REXO1L1

Indexed keywords

EXONUCLEASE;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME 8Q; CHROMOSOME ANALYSIS; CHROMOSOME VARIANT; CLINICAL ARTICLE; DIPLOIDY; FEMALE; GENE; GENE CLUSTER; HUMAN; KARYOTYPING; MALE; MICROARRAY ANALYSIS; PHENOTYPE; PRIORITY JOURNAL; REXO1L1 GENE; SACCHAROMYCES CEREVISIAE; SEGMENTAL DUPLICATION; TANDEM REPEAT; VARIABLE NUMBER OF TANDEM REPEAT;

ADULT; CARRIER PROTEINS; CHILD, PRESCHOOL; CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, HUMAN, PAIR 8; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOME, HUMAN; HEPACIVIRUS; HEPATITIS C; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INFANT, NEWBORN; KARYOTYPING; MALE; MULTIGENE FAMILY; NUCLEAR PROTEINS; PHENOTYPE; SEGMENTAL DUPLICATIONS, GENOMIC;

EID: 84896549711     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2013.185     Document Type: Article

References (49)

1. Itsara A, Cooper GM, Baker C et al: Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 2009; 84: 148-161
2. Barber JCK: Directly transmitted unbalanced chromosome abnormalities and euchromatic variants. J Med Genet 2005; 42: 609-629
3. Balikova I, Martens K, Melotte C et al: Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16. Am J Hum Genet 2008; 82: 181-187
4. Harada N, Takano J, Kondoh T et al: Duplication of 8p23.2: A benign cytogenetic variant?. Am J Med Genet 2002; 111: 285-288
5. Hollox EJ, Huffmeier U, Zeeuwen PL et al: Psoriasis is associated with increased betadefensin genomic copy number. Nat Genet 2008; 40: 23-25
6. Stuart PE, Hüffmeier U, Nair RP et al: Association of b-defensin copy number and psoriasis in three cohorts of European origin. J Invest Dermatol 2012; 132: 2407-2413
7. Hardwick RJ, Amogne W, Mugusi S et al: B-defensin genomic copy number is associated with HIV load and immune reconstitution in sub-saharan Africans. J Infect Dis 2012; 206: 1012-1019
8. Hardwick RJ, Machado LR, Zuccherato LW et al: A worldwide analysis of beta-defensin copy number variation suggests recent selection of a high-expressing DEFB103 gene copy in East Asia. Hum Mutat 2011; 32: 743-750
9. Manvelyan M, Cremer FW, Lance J et al: New cytogenetically visible copy number variant in region 8q21.2. Mol Cytogenet 2011; 4: 1
10. Lecce R, Murdolo M, Gelli G et al: The euchromatic 9p+ polymorphism is a locus-specific amplification caused by repeated copies of a small DNA segment mapping within 9p12. Hum Genet 2006; 118: 760-766
11. Di Giacomo MC, Cesarano C, Bukvic N et al: Duplication of 9 p11.2-p13.1: A benign cytogenetic variant. Prenat Diagn 2004; 24: 619-622
12. Kosyakova N, Grigorian A, Liehr T et al: Heteromorphic variants of chromosome 9. Mol Cytogenet 2013; 6: 14
13. Wojiski SA, Rhodes CH, Brodhurst CA et al: The G positive band of the rare euchromatic 9qh variant is derived from 9p12. Appl Cytogenet 1997; 23: 125-129
14. Willatt LR, Barber JCK, Clarkson A et al: Novel deletion variants of 9q13-q21.12 and classical euchromatic variants of 9q12/qh involve deletion, duplication and triplication of large tracts of segmentally duplicated pericentromeric euchromatin. Eur J Hum Genet 2007; 15: 45-52
15. Joseph-George AM, He Y, Marshall CR et al: Euchromatic 9q13-q21 duplication variants are tandem segmental amplifications of sequence reciprocal to 9q13-q21 deletions. J Med Genet 2011; 48: 317-322
16. Barber JC, Rodrigues R, Maloney VK et al: Another family with a euchromatic duplication variant of 9q13-q21.1 derived from segmentally duplicated pericentromeric euchromatin. Cytogenet Genome Res 2013; 141: 64-69
17. Starke H, Seidel J, Henn W et al: Homologous sequences at human chromosome 9 bands p12 and q13-21.1 are involved in different patterns of pericentric rearrangements. Eur J Hum Genet 2002; 10: 790-800
18. Goumy C, Mihaescu M, Tchirkov A et al: An unusual familial chromosome 9 'variant' with variable phenotype: Characterization by CGH analysis. Morphologie 2005; 89: 71-75
19. Barber JC, Cross IE, Douglas F et al: Neurofibromatosis pseudogene amplification underlies euchromatic cytogenetic duplications and triplications of proximal 15q. Hum Genet 1998; 103: 600-607
20. Fantes JA, Mewborn SK, Lese CM et al: Organisation of the pericentromeric region of chromosome 15: At least four partial gene copies are amplified in patients with a proximal duplication of 15q. J Med Genet 2002; 39: 170-177
21. Carelle-Calmels N, Girard-Lemaire F, Gué rin E et al: Proximal 15q familial euchromatic variant and PWS/AS critical region duplication in the same patient: A cytogenetic pitfall. Eur J Med Genet 2008; 51: 547-557
22. Barber JC, Reed CJ, Dahoun SP, Joyce CA: Amplification of a pseudogene cassette underlies euchromatic variation of 16p at the cytogenetic level. Hum Genet 1999; 104: 211-218
23. López Pajares I, Villa O, Salido M et al: Euchromatic variant 16p+. Implications in prenatal diagnosis. Prenat Diagn 2006; 26: 535-538
24. Barber JCK, Hall V, Maloney VK et al: 16p11.2-p21.2 duplication syndrome; a genomic condition differentiated from euchromatic variation of 16p11.2. Eur J Hum Genet 2013; 21: 182-189
25. Barber JCK, Brasch-Andersen C, Maloney VK et al: A novel pseudo-dicentric variant of 16p11.2-q11.2 contains euchromatin from 16p11.2-p11.1 and resembles pathogenic duplications of proximal 16q. Cytogenet Genome Res 2013; 39: 59-64
26. Geiss GK, Bumgarner RE, Birditt B et al: Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008; 26: 317-325
27. Warburton PE, Hasson D, Guillem F et al: Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 2008; 9: 533
28. Furey TS, Haussler D: Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet 2003; 12: 1037-1044
29. Francke U: Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenet Cell Genet 1994; 65: 206-218
30. Morton NE: Parameters of the human genome. Proc Natl Acad Sci USA 1991; 88: 7474-7476
31. 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
32. Sudmant PH, Kitzman JO, Antonacci F et al: Diversity of human copy number variation and multicopy genes. Science 2010; 330: 641-646
33. Alkan C, Kidd JM, Marques-Bonet T et al: Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 2009; 41: 1061-1067
34. Whitby H, Tsalenko A, Aston E et al: Benign copy number changes in clinical cytogenetic diagnostics by array CGH. Cytogenet Genome Res 2008; 123: 94-101
35. Iafrate AJ, Feuk L, Rivera MN et al: Detection of large-scale variation in the human genome. Nat Genet 2004; 36: 949-951
36. Barber JCK: Reply to Dundar et al: Why a causal association between classical euchromatic variants of chromosome 9 and multiple miscarriages is unlikely. Genet Couns 2010; 21: 469-471
37. Matsuzaki H, Wang PH, Hu J et al: High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. Genome Biol 2009; 10: R125
38. Perry GH, Ben-Dor A, Tsalenko A et al: The fine-scale and complex architecture of human copy-number variation. Am J Hum Genet 2008; 82: 685-695
39. Kidd JM, Cooper GM, Donahue WF et al: Mapping and sequencing of structural variation from eight human genomes. Nature 2008; 453: 56-64
40. Schuster SC, Miller W, Ratan A et al: Complete Khoisan and Bantu genomes from southern Africa. Nature 2010; 463: 943-947
41. Giglio S, Broman KW, Matsumoto N et al: Olfactory receptor-gene clusters, genomicinversion polymorphisms, and common chromosome rearrangements. Am J Hum Genet 2001; 68: 874-883
42. Hasson D, Alonso A, Cheung F et al: Formation of novel CENP-A domains on tandem repetitive DNA and across chromosome breakpoints on human chromosome 8q21 neocentromeres. Chromosoma 2011; 120: 621-632
43. Perry GH, Dominy NJ, Claw KG et al: Diet and the evolution of human amylase gene copy number variation. Nat Genet 2007; 39: 1256-1260
44. Carpenter D, Färnert A, Rooth I et al: CCL3L1 copy number and susceptibility to malaria. Infect Genet Evol 2012; 12: 1147-1154
45. Grünhage F, Nattermann J, Gressner OA et al: Lower copy numbers of the chemokine CCL3L1 gene in patients with chronic hepatitis C. J Hepatol 2010; 52: 153-159
46. Quiroga JA, Castillo I, Bartolome J, Carren V: Serum immunoglobulin G antibodies to the GOR autoepitope are present in patients with occult hepatitis C virus (HCV) infection despite lack of HCV-specific antibodies. Clin Vaccine Immunol 2007; 14: 1302-1306
47. Schaefer EA, Chung RT: The impact of human gene polymorphisms on HCV infection and disease outcome. Semin Liver Dis 2011; 31: 375-386
48. Byrne JA, Chen Y, Martin La Rotta N, Peters GB: Challenges in identifying candidate amplification targets in human cancers: Chromosome 8q21 as a case study. Genes Cancer 2012; 3: 87-101
49. Ramakrishna M, Williams LH, Boyle SE et al: Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis. PLoS One 2010; 5: E9983