The reliability of haplotyping inference in nuclear families: Misassignment rates for SNPs and microsatellites

Human Heredity

Volumn 57, Issue 3, 2004, Pages 117-127

  Lindholm, Eva ^a,b,c   Zhang, Junying ^a   Hodge, Susan E ^a,b   Greenberg, David A ^a,b  

^a Department of Medicine   (United States)

^b NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

Allele frequencies; GENEHUNTER; Haplotype sizes; Microsatellites; Nuclear families; Polymorphisms; Sib pairs; SIMWALK; SNPs; Triads

Indexed keywords

MICROSATELLITE DNA;

ALGORITHM; ALLELE; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; EQUILIBRIUM CONSTANT; GENE FREQUENCY; GENE LOCUS; GENETIC ANALYSIS; GENETIC LINKAGE; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HUMAN; MAJOR CLINICAL STUDY; MATHEMATICAL COMPUTING; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; EVALUATION STUDIES; GENE FREQUENCY; HAPLOTYPES; HETEROZYGOTE; HUMANS; LINKAGE (GENETICS); MICROSATELLITE REPEATS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; RESEARCH DESIGN; SOFTWARE;

EID: 4344713454     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000079242     Document Type: Article

References (18)

1. Goddard KA, Wijsman EM: Characteristics of genetic markers and maps for cost-effective genome screens using diallelic markers. Genet Epidemiol 2002;22:205-220.
2. Matise TC, Sachidanandam R, Clark AG, Kruglyak L, Wijsman E, Kakol J, Buyske S, Chui B, Cohen P, de Toma C, Ehm M, Glanowski S, He C, Heil J, Markianos K, McMullen I, Pericak-Vance MA, Silbergleit A, Stein L, Wagner M, Wilson AF, Winick JD, Winn-Deen ES, Yamashiro CT, Cann HM, Lai E, Holden AL: A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. Am J Hum Genet 2003;73:271-284.
3. Hodge SE, Boehnke M, Spence MA: Loss of information due to ambiguous haplotyping of SNPs. Nat Genet 1999;21:360-361.
4. Michalatos-Beloin S, Tishkoff SA, Bentley KL, Kidd KK, Ruano G: Molecular haplotyping of genetic markers 10 kb apart by allele-specific long-range PCR. Nucleic Acids Res 1996;24:4841-4843.
5. Antonellis A, Rogus JJ, Canani LH, Makita Y, Pezzolesi MG, Nam M, Ng D, Moczulski D, Warram JH, Krolewski AS: A method for developing high-density SNP maps and its application at the type 1 angiotensin II receptor (AGTR1) locus. Genomics 2002;79:326-332.
6. Inbar E, Yakir B, Darvasi A: An efficient haplotyping method with DNA pools. Nucleic Acids Res 2002;30:e76.
7. McDonald OG, Krynetski EY, Evans WE: Molecular haplotyping of genomic DNA for multiple single-nucleotide polymorphisms located kilobases apart using long-range polymerase chain reaction and intramolecular ligation. Pharmacogenetics 2002;12:93-99.
8. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander EL: Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 1996;58:1347-1363.
9. Sobel E, Lange K: Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics. Am J Hum Genet 1996;58:1323-1337.
10. Clark AG: Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 1990;7:111-122.
11. Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995;12:921-927.
12. Hawley ME, Kidd KK: HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 1995;86:409-411.
13. Excoffier L, Slatkin M: Incorporating genotypes of relatives into a test of linkage disequilibrium. Am J Hum Genet 1998;62:171-180.
14. Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001;68:978-989.
15. Zhou G, Zhao H: Haplotype frequency estimation in the presence of genotyping errors. Hum Hered 2003;56:131-138.
16. 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.
17. Schaid DJ, McDonnell SK, Wang L, Cunningham JM, Thibodeau SN: Caution on pedigree haplotype inference with software that assumes linkage equilibrium. Am J Hum Genet 2002;71:992-995.
18. Rohde K, Fuerst R: Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information. Hum Mutat 2001;17:289-295.