HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

Berger, Emily; Yörükoğlu, Deniz; Peng, Jian; Berger, Bonnie

doi:10.1007/978-3-319-05269-4_2

Cited by 23 publications

(38 citation statements)

References 16 publications

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“…We use both real data and simulated data to compare the performance of our algorithms H-PoP, H-PoPG and three recent single individual polyplotyping algorithms HapCompass (Aguiar and Istrail, 2013), HapTree (Berger et al, 2014) and SDhaP (Das and Vikalo, 2015). Besides aligned SNP reads, all algorithms except H-PoP and SDhaP require genotype information as an additional input.…”

Section: Resultsmentioning

confidence: 99%

“…When the genotype of the reconstructed haplotypes equals to the original genotype, another measure vector error rate (Rv) (Berger et al, 2014) is used too. Let the set of k haplotypes reconstructed by an algorithm be H = {H 1 , H 2 , ..., H k } and the set of true haplotypes be …”

Section: Results On Simulated Datamentioning

confidence: 99%

“…The vector error measure is a generalization of the switch error measure for diploid haplotype assembly to polyploid phasing. The vector errors in k reconstructed haplotypes are defined in (Berger et al, 2014) as the minimum number of segments on all chromosomes for which a switch must occur. To make it easy to understand, we give another equivalent definition of the measure here.…”

Section: Results On Simulated Datamentioning

confidence: 99%

“…The input aligned reads are denoted by an m × n SNP matrix M as in previous work (Xie et al, 2008(Xie et al, , 2012Aguiar and Istrail, 2013;Berger et al, 2014), where m is the number of reads and n the number of heterozygous SNP loci. M [i, j], the entry of M at the ith row and jth column, encodes the allele of the ith read at the jth heterozygous SNP loci.…”

Section: Formulation and Problemmentioning

confidence: 99%

“…Recently, three polyploid haplotyping algorithms HapCompass (Aguiar and Istrail, 2013), HapTree (Berger et al, 2014) and SDhaP (Das and Vikalo, 2015) have been introduced in the literature. The HapCompass algorithm converts a haplotype phasing as a spanning tree of the graph built from DNA reads, where the nodes represent single nucleotide polymorphisms (SNPs) and the edges indicate the evidence of co-occurring SNP alleles in a haplotype as supported by the reads.…”

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confidence: 99%

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H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

et al. 2016

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Motivation: Some economically important plants including wheat and cotton have more than two copies of each chromosome. With the decreasing cost and increasing read length of next-generation sequencing technologies, reconstructing the multiple haplotypes of a polyploid genome from its sequence reads becomes practical. However, the computational challenge in polyploid haplotyping is much greater than that in diploid haplotyping, and there are few related methods. Results: This paper models the polyploid haplotyping problem as an optimal poly-partition problem of the reads, called the Polyploid Balanced Optimal Partition (PBOP) model. For the reads sequenced from a k -ploid genome, the model tries to divide the reads into k groups such that the difference between the reads of the same group is minimized while the difference between the reads of different groups is maximized. When the genotype information is available, the model is extended to the Polyploid Balanced Optimal Partition with Genotype constraint (PBOPG) problem. These models are all NP-hard. We propose two heuristic algorithms, H-PoP and H-PoPG, based on dynamic programming and a strategy of limiting the number of intermediate solutions at each iteration, to solve the two models, respectively. Extensive experimental results on simulated and real data show that our algorithms can solve the models effectively, and are much faster and more accurate than the recent state-of-the-art polyploid haplotyping algorithms. The experiments also show that our algorithms can deal with long reads and deep read coverage effectively and accurately. Furthermore, H-PoP might be applied to help determine the ploidy of an organism. Availability: https://github.com/MinzhuXie/H-PoPG Contact:

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Section: Resultsmentioning

confidence: 99%

Section: Results On Simulated Datamentioning

confidence: 99%

Section: Results On Simulated Datamentioning

confidence: 99%

Section: Formulation and Problemmentioning

confidence: 99%

mentioning

confidence: 99%

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H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

et al. 2016

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Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

et al. 2020

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Haplotype reconstruction of distant genetic variants remains an unsolved problem due to the short-read length of common sequencing data. Here, we introduce HapTree-X, a probabilistic framework that utilizes latent long-range information to reconstruct unspecified haplotypes in diploid and polyploid organisms. It introduces the observation that differential allele-specific expression can link genetic variants from the same physical chromosome, thus even enabling using reads that cover only individual variants. We demonstrate HapTree-X’s feasibility on in-house sequenced Genome in a Bottle RNA-seq and various whole exome, genome, and 10X Genomics datasets. HapTree-X produces more complete phases (up to 25%), even in clinically important genes, and phases more variants than other methods while maintaining similar or higher accuracy and being up to 10× faster than other tools. The advantage of HapTree-X’s ability to use multiple lines of evidence, as well as to phase polyploid genomes in a single integrative framework, substantially grows as the amount of diverse data increases.

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Long-read sequence and assembly of segmental duplications

et al. 2018

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We developed a computational method based on polyploid phasing of long sequence reads to resolve collapsed regions of segmental duplications within genome assemblies. The approach, Segmental Duplication Assembler (SDA), constructs graphs where paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges allowing us to partition and assemble long reads corresponding to distinct paralogs. We apply it to single-molecule, real-time sequence data from three human genomes and recover 33–79 Mbp of duplications where approximately half of the loci are diverged (<99.8%) when compared to the reference genome. We show that the corresponding sequence is highly accurate (>99.9%) and that the diverged sequence corresponds to copy number variable paralogs that are absent from the human reference. Our method can be applied to other complex genomes to resolve the last gene-rich gaps, improve duplicate gene annotation, and better understand copy number variant genetic diversity at the base-pair level.

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HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

Cited by 23 publications

References 16 publications

H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

Long-read sequence and assembly of segmental duplications

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