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Results 1 - 10
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343
Inferring demographic history from a spectrum of shared haplotype lengths
"... There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is t ..."
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Cited by 13 (1 self)
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events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a
Cross Haplotype Sharing Statistic: Haplotype length based method for whole genome association testing
"... We analyzed a dataset of 2,300 SNPs from a region of 10 Mb of chromosome 18q, which had shown linkage evidence for Rheumatoid Arthritis [1]. To test for disease association, a novel method, called the Cross-test, was used, which is based on differences between direct sharing of a patient and a contr ..."
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control haplotype and sharing of two patients or two control haplotypes. We found highly significant association at a position ~4,407 kb from the starting SNP and a second less significant one at position ~4,863 kb. These results are supported by a single marker chi-square test and the Haplotype Sharing
A fine-scale linkage-disequilibrium measure based on length of haplotype sharing
- American Journal of Human Genetics
, 2006
"... High-throughput genotyping technologies for SNPs have enabled the recent completion of the International HapMap Project (phase I), which has stimulated much interest in studying genomewide linkage-disequilibrium (LD) patterns. Conventional LD measures, such as and, are two-point measurements, and th ..."
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Cited by 3 (0 self)
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, and their relationship with physical ′ 2D r distance is highly noisy. We propose a new LD measure, D, defined in terms of the correlation coefficient for shared haplotype lengths around two loci, thereby borrowing information from multiple loci. A U-statistic–based estimator of D, which takes into consideration
RESEARCH Open Access On the design of clone-based haplotyping
"... Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable ..."
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heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically
Linear Reduction for Haplotype Inference
- Proc. Workshop on Algorithms in Bioinformatics, September 2004, Lecture Notes in Bioinformatics
, 2004
"... Abstract. Haplotype inference problem asks for a set of haplotypes explaining a given set of genotypes. Popular software tools for haplotype inference (e.g., PHASE, HAPLOTYPER) as well as new algorithms recently proposed for perfect phylogeny inference (DPPH) are often not well scalable. When the nu ..."
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Cited by 12 (4 self)
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, linear decoding allows to recover haplotypes of full length for given genotypes. Experiments show that our method significantly speeds up popular haplotype inference tools while finding almost the same solution practically in all cases thus not compromising the quality of the known haplotype inference
HAPLO: A Program Using the EM Algorithm to Estimate the Frequencies of Multi-site Haplotypes
, 1995
"... A DNA haplotype system combines information from two or more distinct polymorphic systems located within a small length of DNA in which there is little recombination. Each possible combination of alleles, one from each component system, constitutes a distinct haplotype that is treated as an allele o ..."
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Cited by 92 (3 self)
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A DNA haplotype system combines information from two or more distinct polymorphic systems located within a small length of DNA in which there is little recombination. Each possible combination of alleles, one from each component system, constitutes a distinct haplotype that is treated as an allele
High-Performance Haplotype Assembly
"... Abstract. The problem of Haplotype Assembly is an essential step in human genome analysis. It is typically formalised as the Minimum Error Correction (MEC) problem which is NP-hard. MEC has been approached using heuristics, integer linear programming, and fixed-parameter tractability (FPT), includin ..."
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Abstract. The problem of Haplotype Assembly is an essential step in human genome analysis. It is typically formalised as the Minimum Error Correction (MEC) problem which is NP-hard. MEC has been approached using heuristics, integer linear programming, and fixed-parameter tractability (FPT
REPRODUCTIVE TRAITS OF TWO HAPLOTYPES OF THE
, 2007
"... ABSTRACT- Four hundred and two pairs of hares belonging to the mountain and brown haplotypes of the European hare Lepus europaeus Pallas, 1778 were raised in a farm lo-cated in central Italy over 4 years (from 2003 to 2006). The birth date, total number of young born, and number of surviving and wea ..."
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(192 days vs 156 days) and a higher productivity. The most frequent gestation length was 37-41 days. The distribution of delivery intervals did not differ between the two haplotypes.
RESEARCH Open Access Strobe sequence design for haplotype assembly
"... Background: Humans are diploid, carrying two copies of each chromosome, one from each parent. Separating the paternal and maternal chromosomes is an important component of genetic analyses such as determining genetic association, inferring evolutionary scenarios, computing recombination rates, and d ..."
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and upcoming sequencing technologies, and study the impact of design choice on the length of the haplotype. Results: We show that a number of parameters influence haplotype length, with the most significant one being the advance length (distance between two fragments of a clone). Given technologies like strobe
Results 1 - 10
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343
