Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms

American Journal of Human Genetics

Volumn 70, Issue 1, 2002, Pages 157-169

  Niu, Tianhua ^a,b   Qin, Zhaohui S ^d   Xu, Xiping ^a,c   Liu, Jun S ^d  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b NORTHEASTERN UNIVERSITY   (United States)

^c CHANNING LABORATORY   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 ADRENERGIC RECEPTOR; TRANSMEMBRANE CONDUCTANCE REGULATOR;

ALGORITHM; ANALYTIC METHOD; ARTICLE; BAYES THEOREM; CHROMOSOME 5Q; GENE MAPPING; GENETIC LINKAGE; GENETIC RECOMBINATION; HAPLOTYPE; MAXIMUM LIKELIHOOD METHOD; PREDICTION; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

EID: 0036138183     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/338446     Document Type: Article

References (55)

1. Haplotypes vs single marker linkage disequilibrium tests: What do we gain?
2. Homogeneous assays for single-nucleotide polymorphism typing using AlphaScreen
3. A new vector for recombination-based cloning of large DNA fragments from yeast artificial chromosomes
4. Predictive updating methods with application to Bayesian classification
5. Fine genetic mapping using haplotype analysis and the missing data problem
6. Inference of haplotypes from PCR-amplified samples of diploid populations
7. Data mining: Efficiency of using sequence databases for polymorphism discovery
8. High-resolution haplotype structure in the human genome
9. Maximum likelihood from incomplete data via EM algorithm
10. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies
11. 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness
12. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
13. Genetic analysis of case/control data using estimated haplotype frequencies: Application to APOE locus variation and Alzheimer's disease
14. Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data
15. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays
16. Fine-mapping of an ancestral recombination breakpoint in DCP1
17. Characterizing a joint probability distribution by conditionals
18. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays
19. HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes
20. Cladistic analysis: Its applications in association studies of complex diseases
21. Loss of information due to ambiguous haplotyping of SNPs
22. Gene genealogies and the coalescent process
23. 2-adrenergic receptor on the response to regular use of albuterol in asthma
24. Notes from the SNP vs haplotype front
25. Identification of the cystic fibrosis gene: Genetic analysis
26. Homozygosity mapping: A way to map human recessive traits with the DNA of inbred children
27. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
28. The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem
29. Bayesian analysis of haplotypes for linkage disequilibrium mapping
30. Mutation detection and single-molecule counting using isothermal rolling-circle amplification
31. An E-M algorithm and testing strategy for multiple-locus haplotypes
32. 2-adrenoceptor and response to albuterol in children with and without a history of wheezing
33. Molecular haplotyping of genetic markers 10 kb apart by allele-specific long-range PCR
34. Angiotensin converting enzyme gene insertion/deletion polymorphism and cardiovascular disease: Therapeutic implications
35. Detection of novel ALAD gene polymorphisms using denaturing high-performance liquid chromatography
36. Are rare variants responsible for susceptibility to complex diseases?
37. High-throughput genotyping with single nucleotide polymorphisms
38. Linkage disequilibrium in the human genome
39. 2-adrenergic receptor in normal and asthmatic subjects
40. Sequence variation in the human angiotensin converting enzyme
41. Searching for genetic determinants in the new millennium
42. High-level multiplex genotyping by MALDI-TOF mass spectrometry
43. Haplotype of multiple polymorphisms resolved by enzymatic amplification of single DNA molecules
44. Protection against bronchial asthma by CFTR ΔF508 mutation: A heterozygote advantage in cystic fibrosis
45. Haplotype variation and linkage disequilibrium in 313 human genes
46. A new statistical method for haplotype reconstruction from population data
47. A cladistic analysis of phenotypic associatins with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/ control sampling designs: Alzheimer's disease and the apoprotein E locus
48. Kidd-KK (2000) The accuracy of statistical methods for estimation of haplotype frequencies: An example from the CD4 locus
49. Data mining applied to linkage disequilibrium mapping
50. Molecular beficons: Probes that fluoresce upon hybridization
51. Logistic regression model for analyzing extended haplotype data
52. Direct haplotyping of kilobase-size DNA using carbon nanotube probes
53. Comparisons of two methods for haplotype reconstruction and haplotype frequency estimation from population data
54. Transmission/disequilibrium tests using multiple tightly linked markers