Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Levine, Adam P ^a   Connor, Thomas M ^a   Oygar, D Deren ^b   Neild, Guy H ^a   Segal, Anthony W ^a   Maxwell, Patrick H ^c   Gale, Daniel P ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b Nalbantoglu Lefkosa Devlet Hastanesi   (Cyprus)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Haplotype; Identical by descent; Linkage; Pedigree; Phenocopy

Indexed keywords

ACCESS TO INFORMATION; ALLELE; ARTICLE; CLINICAL ARTICLE; COMPUTER PROGRAM; CONFLICTING HOMOZYGOSITY; CONTROLLED STUDY; CYPRIOT; DOMINANT INHERITANCE; FAMILY STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ANALYSIS; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC TRAIT; GENOTYPE; HAPLOTYPE; HOMOZYGOSITY; HUMAN; INHERITANCE; INTERNET; KIDNEY DISEASE; PEDIGREE ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; DOMINANT GENE; GENETICS; GENOMICS; HOMOZYGOTE; PEDIGREE; PHENOTYPE; PROCEDURES;

ALGORITHMS; GENES, DOMINANT; GENETIC LINKAGE; GENOMICS; GENOTYPE; HOMOZYGOTE; HUMANS; KIDNEY DISEASES; LINKAGE DISEQUILIBRIUM; PEDIGREE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC;

EID: 84925092421     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1360-4     Document Type: Article

References (25)

1. Zielinski D, Gymrek M, Erlich Y. Back to the family: a renewed approach to rare variant studies. Genome Med. 2012;4:97.
2. Wijsman EM. The role of large pedigrees in an era of high-throughput sequencing. Hum Genet. 2012;131:1555-63.
3. Kirichenko AV, Belonogova NM, Aulchenko YS, Axenovich TI. PedStr software for cutting large pedigrees for haplotyping, IBD computation and multipoint linkage analysis. Ann Hum Genet. 2009;73(Pt 5):527-31.
4. Dyer TD, Blangero J, Williams JT, Göring HH, Mahaney MC. The effect of pedigree complexity on quantitative trait linkage analysis. Genet Epidemiol. 2001;21 Suppl 1:S236-43.
5. Tong L, Thompson E. Multilocus lod scores in large pedigrees: combination of exact and approximate calculations. Hum Hered. 2008;65:142-53.
6. Medlar A, Gowacka D, Stanescu H, Bryson K, Kleta R. SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU. Bioinformatics. 2013;29:413-9.
7. Clerget-Darpoux F, Bonaïti-Pellié C, Hochez J. Effects of misspecifying genetic parameters in lod score analysis. Biometrics. 1986;42:393-9.
8. Hodge SE, Elston RC. Lods, wrods, and mods: the interpretation of lod scores calculated under different models. Genet Epidemiol. 1994;11:329-42.
9. Macgregor S, Knott SA, Visscher PM. False disease region identification from identity-by-descent haplotype sharing in the presence of phenocopies. Twin Res Hum Genet. 2006;9:9-16.
10. Thomas A, Camp NJ, Farnham JM, Allen-Brady K, Cannon-Albright LA. Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays. Ann Hum Genet. 2008;72(Pt 2):279-87.
11. Leibon G, Rockmore DN, Pollak MR. A SNP streak model for the identification of genetic regions identical-by-descent. Stat Appl Genet Mol Biol. 2008;7:Article16.
12. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559-75.
13. Seelow D, Schuelke M. HomozygosityMapper2012--bridging the gap between homozygosity mapping and deep sequencing. Nucleic Acids Res. 2012;40(Web Server issue):W516-20.
14. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27:2156-8.
15. Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, et al. Integrating common and rare genetic variation in diverse human populations. Nat. 2010;467:52-8.
16. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207-10.
17. Anderson CA, Pettersson FH, Clarke GM, Cardon LR, Morris AP, Zondervan KT. Data quality control in genetic case-control association studies. Nat Protoc. 2010;5:1564-73.
18. Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE. Mega2: data-handling for facilitating genetic linkage and association analyses. Bioinformatics. 2005;21:2556-7.
19. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, et al. Linkage disequilibrium in the human genome. Nat. 2001;411:199-204.
20. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002;30:97-101.
21. Voskarides K, Damianou L, Neocleous V, Zouvani I, Christodoulidou S, Hadjiconstantinou V, et al. COL4A3/COL4A4 mutations producing focal segmental glomerulosclerosis and renal failure in thin basement membrane nephropathy. J Am Soc Nephrol. 2007;18:3004-16.
22. Gale DP, de Jorge EG, Cook HT, Martinez-Barricarte R, Hadjisavvas A, McLean AG, et al. Identification of a mutation in complement factor H-related protein 5 in patients of Cypriot origin with glomerulonephritis. Lancet. 2010;376:794-801.
23. Sobel E, Lange K. Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. Am J Hum Genet. 1996;58:1323-37.
24. Pierides A, Voskarides K, Athanasiou Y, Ioannou K, Damianou L, Arsali M, et al. Clinico-pathological correlations in 127 patients in 11 large pedigrees, segregating one of three heterozygous mutations in the COL4A3/ COL4A4 genes associated with familial haematuria and significant late progression to proteinuria and chronic kidney dis. Nephrol Dial Transplant. 2009;24:2721-9.
25. Chadban SJ, Briganti EM, Kerr PG, Dunstan DW, Welborn TA, Zimmet PZ, et al. Prevalence of kidney damage in Australian adults: the AusDiab kidney study. J Am Soc Nephrol. 2003;14(7 Suppl 2):S131-8.