Differential decay of parent-of-origin-specific genomic sharing in cystic fibrosis-affected sib pairs maps a paternally imprinted locus to 7q34

European Journal of Human Genetics

Volumn 18, Issue 5, 2010, Pages 553-559

  Stanke, Frauke ^a   Davenport, Colin ^a   Hedtfeld, Silke ^a   Tümmler, Burkhard ^a  

^a HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

Cystic fibrosis; Decay of genomic sharing; Gene mapping; Imprinting; Modifier gene

Indexed keywords

TRANSCRIPTION FACTOR CTCF; TRANSMEMBRANE CONDUCTANCE REGULATOR;

ARTICLE; BINDING SITE; CHROMOSOME 7Q; CONSENSUS SEQUENCE; CONTROLLED STUDY; CPG ISLAND; CYSTIC FIBROSIS; DISEASE SEVERITY; GENE CLUSTER; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENOME IMPRINTING; GENOTYPE; HOMOLOGOUS RECOMBINATION; HOMOZYGOSITY; HUMAN; MICROSATELLITE MARKER; PATERNALISM; PHENOTYPE; PRIORITY JOURNAL; SIBLING;

ALLELES; BASE PAIRING; CHROMOSOMES, HUMAN, PAIR 7; CLUSTER ANALYSIS; CONSENSUS SEQUENCE; CPG ISLANDS; CYSTIC FIBROSIS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; FATHERS; FEMALE; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOMIC IMPRINTING; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; PARENTS; PHENOTYPE; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRESSOR PROTEINS; SIBLINGS;

EID: 77951620080     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.229     Document Type: Article

References (43)

1. Reinhart B, Caillet JR: Genomic imprinting: cis-acting sequences and regional control. Int Rev Cytol 2005; 243: 173-213.
2. Wood AJ, Oakey RJ: Genomic imprinting in mammals: emerging themes and established theories. PLoS Genet 2006; 2: e147.
3. Robertson KD: DNA methylation and human disease. Nat Rev Genet 2005; 6: 597-610.
4. Knapp M, Strauch K: Affected-sib-pair test for linkage based on constraints for identical-by-descent distributions corresponding to disease models with imprinting. Genet Epidemiol 2005; 26: 273-285.
5. Wu CC, Shete S, Amos CI: Linkage analysis of affected sib pairs allowing for parent-of-origin effects. Ann Hum Genet 2005; 69: 113-126.
6. Shete S, Amos CI: Testing for genetic linkage in families by a variance-components approach in the presence of genomic imprinting. Am J Hum Genet 2002; 70: 751-757.
7. Bush A, Alton EWFW, Davies JC, Griesenbach U, Jaffe A: Cystic Fibrosis in the 21st Century. Basel: Karger, 2006.
8. Cutting GR: Modifier genetics: cystic fibrosis. Annu Rev Genomics Hum Genet 2005; 6: 237-260.
9. Stanke F, Becker T, Cuppens H et al: The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis. Hum Genet 2006; 119: 331-343.
10. Mekus F, Laabs U, Veeze H, Tümmler B: Genes in the vicinity of CFTR modulate the cystic fibrosis phenotype in highly concordant or discordant F508del homozygous sib pairs. Hum Genet 2003; 112: 1-11.
11. Mekus F, Ballmann M, Bronsveld I, Bijman J, Veeze H, Tümmler B: Categories of deltaF508 homozygous cystic fibrosis twin and sibling pairs with distinct phenotypic characteristics. Twin Res 2000; 3: 277-293.
12. Sham PC, Curtis D: Monte Carlo tests for associations between disease and alleles at highly polymorphic loci. Ann Hum Genet 1995; 59: 97-105.
13. Herold C, Becker T: Genetic association analysis with FAMHAP: a major program update. Bioinformatics 2009; 25: 134-136.
14. Knapp M, Becker T: Family-based association analysis with tightly linked markers. Hum Hered 2003; 56: 2-9.
15. Spielman RS, McGinnis RE, Ewens WJ: Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus IDDM. Am J Hum Genet 1993; 52: 506-516.
16. Wang Z, Fan H, Yang HH et al: Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures. Genomics 2004; 83: 395-401.
17. Ishihara K, Sasaki H: An evolutionarily conserved putative insulator element near the 3¢ boundary of the imprinted Igf2/H19 domain. Hum Mol Genet 2002; 11: 1627-1636.
18. Kurtz S, Phillippy A, Delcher AL et al: Versatile and open software for comparing large genomes. Genome Biol 2004; 5: R1.
19. Reva ON, Tümmler B: Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics 2005; 6: 251.
20. Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000; 16: 276-277.
21. Giardine B, Riemer C, Hardison RC et al: Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005; 15: 1451-1455.
22. R Development Core Team: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, 2008.
23. Scherer SW, Cheung J, MacDonald JR et al: Human chromosome 7: DNA sequence and biology. Science 2003; 300: 767-772.
24. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ: miRbase: microRNAs sequences, targets and gene nomenclature. Nucl Acids Res 2006; 34: D140-D144.
25. Griffiths-Jones S: The microRNA Registry. Nucl Acids Res 2004; 32: D109-D111.
26. Morison IM, Paton CJ, Cleverley SD: The imprinted gene and parent-of-origin effect database. Nucl Acids Res 2001; 29: 275-276.
27. Kobayashi S, Kohda T, Miyoshi N et al: Human PEG1/MEST, an imprinted gene on chromosome 7. Hum Molec Genet 1997; 6: 781-786.
28. Blagitko N, Schulz U, Schinzel AA, Ropers HH, Kalscheuer VM: Gamma-2-COP, a novel imprinted gene on chromosome 7q32, defines a new imprinting cluster in the human genome. Hum Molec Genet 1999; 8: 2387-2396.
29. Luedi PP, Hartemink AJ, Jirtle RL: Genome-wide prediction of imprinted murine genes. Genome Res 2005; 15: 875-884.
30. Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ: Computational and experimental identification of novel human imprinted genes. Genome Res 2007; 17: 1723-1730.
31. Pollard KS, Serre D, Wang X et al: A genome-wide approach to identifying novel-imprinted genes. Hum Genet 2008; 122: 625-634.
32. Hore TA, Deakin JE, Marshall Graves JA: The evolution of epigenetic regulators CTCF and BORIS/CTCFL in amniotes. PLoS Genet 2008; 4: e1000169.
33. Hutter B, Helms V, Paulsen M: Tandem repeats in the CpG islands of imprinted genes. Genomics 2006; 88: 323-332.
34. Walter J, Hutter B, Khare T, Paulsen M: Repetitive elements in imprinted genes. Cytogenet Genome Res 2006; 113: 109-115.
35. Daura-Oller E, Cabré M, Montero MA, Paternáin JL, Romeu A: A first-stage approximation to identify new imprinted genes through sequence analysis of its coding regions. Comp Funct Genomics 2009; 549387, e-pub ahead of print 8 April 2009. PMID: 19360135.
36. Khatib H, Zaitoun I, Kim ES: Comparative analysis of sequence characteristics of imprinted genes in human, mouse, and cattle. Mamm Genome 2007; 18: 538-547.
37. Mattick JS: The genetic signatures of noncoding RNAs. PLoS Genet 2009; 5: e1000459.
38. Royo H, Cavaillé J: Non-coding RNAs in imprinted gene clusters. Biol Cell 2008; 100: 149-166.
39. Hannuila K, Lipsanen-Nymawn M, Kontiokari T, Kere J: A narrow segment of maternal uniparental disomy of chromosome 7q31-qter in Silver-Russel Syndrome delimits a candidate gene region. Am J Hum Genet 2001; 68: 247-253.
40. Hirschhorn JN, Lindgren CM, Daly MJ et al: Genomewide linkage analysis of stature in multiple populations reveals several regions with evidence of linkage to adult height. Am J Hum Genet 2001; 69: 106-116.
41. Perola M, Ohman M, Hiekkalinna T et al: Quantitative-trait-locus analysis of body-mass index and of stature, by combined analysis of genome scans of five Finnish study groups. Am J Hum Genet 2001; 69: 117-123.
42. Rowntree R, Harris A: DNA polymorphisms in potential regulatory elements of the CFTR gene alter transcription factor binding. Hum Genet 2002; 111: 66-74.
43. Arking DE, Cutler DJ, Brune CW et al: A common genetic variant in the neurexin superfamily member CNTNAP2 increases familial risk of autism. Am J Hum Genet 2008; 82: 160-164.