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Haplotyping and Estimation of Haplotype Frequencies for Closely Linked Biallelic ... under HWE assumption and random mating(Weir, 1990; Xie and Ott, 1993;etc. and ...

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Each person has two copies of his chromosomes ... Equivalent definition: The four gamete test. No = forbidden submatrix. 12. Perfect Phylogeny ...

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N. Patil et al., (2001), Blocks of Limited Haplotype Diversity Revealed by High ... two copies of chromosome 21 using a rodent-human somatic cell hybrid technique ...

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Title: No Slide Title Author: Matthew Gordon Last modified by: Paul Selvin Created Date: 11/9/2004 7:02:01 PM Document presentation format: On-screen Show

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but given only genotype data, consistent with Am/aM as ... Visualising data and testing for association in Haploview. Detecting haplotpe association using whap ...

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L6: Haplotype phasing. Genotypes and Haplotypes. Each ... At each site, each chromosome has one of two alleles ... Input: A ternary matrix (0,1,2) M with N rows ...

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Haplotype. The genetic constitution of an individual chromosome ... cold spots'= haplotype blocks. Thus, alleles of a particular haplotype tend to be ...

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Haplotyping with Pedigree information. Haplotyping via sequencing ... With pedigree information. Relationships between at least some of the individuals are known ...

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Discovering Patterns in Haplotype Data

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We have a genome's worth of data on genetic variation ... Intensely punctate meiotic recombination in the class II region of the major ...

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Used the 'EM model' with Dirichlet prior, ... SNPHAP is a EM-based algorithm developed by David Clayton. ... is quite accurate using EM or Clark's algorithm. ...

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Human Haplotype Map. General Idea: Characterize the ... 10% Beijing/Shanghai/Hong Kong (Yang, Zeng, Huang, Tsui) 9% Whitehead Institute (Altshuler) ...

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Applying haplotype models to association study design. Natalie Castellana. June 7, 2005 ... Haplotype block method ... Haplotype motif method ...

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The tri-allele cases are usually considered to be the effect of genotyping errors. ... But we don't know the connection of alleles at different SNP loci. ...

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4 Gamete Test. Format the haplotypes in a matrix, two rows for each individual. ... 4 Gamete condition violated! 31. Combinatorial Algorithm. Consider all ...

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Single Nucleotide Polymorphisms (SNPs), Haplotypes, Linkage Disequilibrium, and the Human Genome Manish Anand Nihar Sheth Jim Costello Univ. of Indiana

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Complexity and Approximation of the Minimum Recombinant Haplotype Configuration Problem Authors: Lan Liu, Xi Chen, Jing Xiao & Tao Jiang

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the code for the creation of the cells is packed in a molecule called DNA. ... a minimum size set of haplotypes which conflate to produce the given genotypes ...

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If a recovered haplotype is identified, individual is resolved. ... Maximum likelihood method for population haplotype frequency estimation. ...

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Genotype Error Detection using Hidden Markov Models of Haplotype Diversity Ion Mandoiu CSE Department, University of Connecticut Joint work with Justin Kennedy and ...

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Human genetic variations are related to diseases (cancers, diabetes, ... The human genome project produces genotype sequences of humans ...

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Constrained Hidden Markov Models for Population-based Haplotyping ... constrained HMMs ... Constrained HMM for modeling genotypes. Apriori-style structure ...

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Pattern Identification in a Haplotype Block Kun-Mao Chao ( ) Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University, Taiwan

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ANALYSIS OF THE haplotype associated mutation in fanca Pau Castillo FA is a rare autosomal recessive genetic syndrome There are at least 13 complementation groups ...

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Introduction to DNA and protein microarray technology and their applications Mary ... Wirtenberger, M. et al. Hum Genet (2005) 117:389-397 ...

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Haplotype Inference (HI) Genetic variability between individuals ... Biological Basis for Population HI ... EM for HI ...

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It is possible when there no 4-gamete rule violations: ... Known programs for general data (with possible 4-gamete rule violations) ...

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Biostat 830 Winter 2006. Haplotype blocks ... Biostat 830 Winter 2006. Reich et al. 2001. Extended LD observed in part of the genome. ...

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Haplotypes, hidden SNPs, and hidden 'blocks' How dense is dense enough? ... Some correction for imputation scheme is necessary; plugging in 'best guess' can ...

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Super-charging Clark's method of 1990 - Two ideas: Min haps ... Generic Clark Method. Given a known haplotype H (original ... Method. How? ...

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Create an accurate base-wise multiple alignment of these sequences. ... samples with the following (longish) command line, piping several programs together: ...

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Combinatorial Algorithms for Maximum Likelihood Tag SNP Selection and Haplotype Inference ... Diploid organisms: cells have two homologous sets of chromosomes ...

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Outward, physical manifestation of the organism. Disease status, survival times, quantitative ... Huntington disease, cystic fibrosis. Method: Linkage analysis ...

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Haplotype Inference by Entropy Minimization Ion Mandoiu and Bogdan Pasaniuc, CSE Department, University of Connecticut Haplotype Inference by Entropy Minimization Ion ...

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Single Nucleotide Polymorphisms (SNPs), Haplotypes, Linkage Disequilibrium, and the Human Genome Manish Anand Nihar Sheth Jim Costello 24th November, 2003

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... Pedigrees.' Fishelson M., Dovgolevsky N. and Geiger D. Human Heredity, 2005 ... Gene basic unit of genetic information. They determine the inherited ...

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Much of common human genetic variation can be arranged on relatively few ... in HapMap that have not been typed in the association study (i.e. IMPUTATION) ...

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It can happen that the forced expansion of cells ... Find all the forced phase relationships by considering columns in pairs. ...

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paternal. maternal. Notations and Recombinant. 1122. 2222. Genotype. 1222. 2122 ... the paternal haplotype vector of a member j. ...

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Evaluation of the Haplotype Motif Model using the Principle of Minimum Description ... Extract haplotype patterns (motifs) from the model ...

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20 SNP can choose one man from 1 billion. 1 million SNP/ genome ... Softwares for pattern-analysis. Cluster analysis. Recent genomics ' ...

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A Single Nucleotide Polymorphism (SNP) is a single DNA base variation observed ... Cystic fibrosis. 18. National Taiwan University ...

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Do the data make sense, based on the known biology? Fungus that disperses through basidiospores ... RAPD DATA W/O COSEGREGATING MARKERS. PCA. AFLP. Amplified ...

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This is also the HW heterozygosity, which is expected since the subpopulation is ... What is the expected heterozygosity, under HW in the entire population? ...

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Haplotype Blocks: or how I learned to stop worrying and love the recombination hotspot Benjamin Neale, David Evans, Pak Sham Boulder, Colorado March 2005

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On Intractability of Haplotype Inferring via Galledtree Networks

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Block-based (Gerbil 2004,2005) Variable-length MC (HaploRec 2004,2006) Founder-based (HIT 2005) ... unlike PHASE, Gerbil. PMSB-06, Tuusula, Finland. Results: ...

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... and SNP haplotype map for disease association studies in the extended ... e.g., Celiac disease, Systemic Lupus Erythematosus (SLE), and organ transplant ...

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Liability genes = genes containing variants increasing ... Location of liability allele = (hot spot, blocky, very blocky) Draw 200 cases and 200 controls ...

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Genotype Error Detection using Hidden Markov Models of Haplotype Diversity Justin Kennedy, Ion Mandoiu, Bogdan Pasaniuc CSE Department, University of Connecticut

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Mesolithic man began sheep domestication 8000 9000 years ago (Ryder 1984), on ... oY1 only SNP that is polymorphic within species (A /G in O. aries) ...

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... manner of defining or disclosing a single nucleotide allele of a SNP site ... of an asserted association between alleles containing SNPs and disease X. ...

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Uses of Molecular Markers. Genetic characterization of plants and animals ... Molecular Markers in Strawberry. Randomly ... Complex Molecular Marker to ...

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Problem 2: Longest Haplotype Reconstruction. Problem 3: Pure Parsimony Haplotyping ... there exist two haplotypes such that every row of M has no conflicts with (at ...

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PCR-amplified from octoploid cultivated strawberry Festival, as well as diploids ... GPH markers will help define strawberry and the Rosaceae gene space and will ...

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