Index of papers in PLOS Comp. Biol. that mention
  • haplotypes
Noa Slater, Yoram Louzoun, Loren Gragert, Martin Maiers, Ansu Chatterjee, Mark Albrecht
Abstract
Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions.
Abstract
We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions.
Abstract
Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual.
Author Summary
The distribution of haplotypes and species tend to be heavy tailed.
Author Summary
Accurate measures of diversity are difficult to achieve given that a limited number of common hap-lotypes represent the majority of the population, whereas the major contributor to haplo-type diversity comes from unique haplotypes that are “rare” and present in only a fraction of the population.
Author Summary
We here use a power-law methodology that accommodates heavy-tails to estimate both the population coverage by ethnicity in the US and the genetic diversity of alleles and haplotypes .
haplotypes is mentioned in 127 sentences in this paper.
Topics mentioned in this paper:
Oren E. Livne, Lide Han, Gorka Alkorta-Aranburu, William Wentworth-Sheilds, Mark Abney, Carole Ober, Dan L. Nicolae
IBD Segment Identification
Therefore, we created a complete IBD dictionary by identifying IBD segments between each pair of the 2x1,415 = 2,830 haplotypes in the sample (81 Text).
IBD Segment Identification
Our HMM is the haplotype analogue of the genotype HMM used for phasing, and is similar to the HBD-HMM developed previously [18].
IBD Segment Identification
A total of 97,821,947 IBD segments were identified among the 1,415 Hutterites (~1.1 segment per haplotype pair on average, because there are 2830x2829/2 = 4,003,035 individual pairs and 22 chromosomes).
IBD Segment Indexing into Cliques
We organize IBD segments in an IBD segment index data structure, which consists of a set of IBD cliques at each SNV and allows a quick O(1)time queries of whether a pair of haplotypes is IBD at a certain SNV.
IBD Segment Indexing into Cliques
2) whose nodes are the 2,830 haplotypes of the 1,415 Hutterites, an edge indicates the two haplotypes are IBD, and the edge weight is the HMM posterior probability of IBD (81 Text, Eq.
IBD Segment Indexing into Cliques
Large weights are thus given to haplotype pairs that have a higher probability of being IBD.
Introduction
LD-based imputation methods require a reference panel of genotype training data, usually from unrelated individuals, to infer local haplotype structure, and sharing of hap-lotype stretches are used for filling in missing genotypes [8—11].
Introduction
We first phased the SNV genotypes using pedigree-based phasing algorithms [16,17] and determined IBD segments between each pair of haplotypes using a Hidden-Markov Model [18].
Introduction
To improve the call rate, the missing genotypes were imputed using the LD-based IMPUTE2 program [11], with the phased haplotypes of the 98 whole genome sequenced Hutterites as the reference panel.
Results
The first four require only the framework SNVs: (i) phasing; (ii) identifying IBD segments among all haplotype pairs; (iii) indexing IBD segments into a dictionary of IBD cliques; and (iV) assigning parental origin to haplotypes .
haplotypes is mentioned in 30 sentences in this paper.
Topics mentioned in this paper:
Gabriel R. A. Margarido, David Heckerman
Abstract
Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype.
Discussion
In the cancer framework, a single haplotype is usually expected to be present in multiple copies.
Introduction
insights about how haplotypes influence phenotype.
Introduction
Our goal is to identify the number of potentially collapsed haplotypes in any given contig, affording information for subsequent efforts aimed at properly separating distinct genomic segments.
Switchgrass Dataset
A closer look at the reads aligned against a region containing some of the variants in that contig provides a picture of how the alleles are organized in haplotypes (S7 Fig).
Switchgrass Dataset
Interestingly, in this case, most minor alleles are linked to each other in the same reads, forming a single haplotype .
Switchgrass Dataset
This haplotype is present in a roughly 1:5 ratio with regards to the underlying reference sequence.
haplotypes is mentioned in 7 sentences in this paper.
Topics mentioned in this paper: