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19 results for “allele phasing”
Raw read counts and phased SNP counts for every single cell in the sequencing datasets of the breast cancer patient S1 from "Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL"
<p>This dataset contains the raw read counts and phased SNP counts for every single cell in the sequencing datasets of breast cancer patient S1 from “Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL” [Zaccaria & Raphael, 2020]. These data enable the full reproduction of all the results in the related manuscript for breast cancer patient S1. Specifically, the data are provided in two files for every dataset <em>DAT</em> of patient S1 with the following format:</p> <ol> <li><em>DAT.raw</em>_<em>read</em>_<em>counts.bed.gz </em>is a multi-cell BED file containing the raw read counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>START: the starting genomic position of a genomic bin in the chromosome</li> <li>END: the ending genomic position of the genomic bin in the chromosome</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>NORMAL: the raw read count for the specified bin from a matched-normal sample</li> <li>COUNT: the raw read count for the specified bin in the specified cell</li> <li>RDR: the estimated read-depth ratio for the specified bin in the specified cell</li> </ul> </li> <li><em>DAT.phased</em>_<em>snps</em>_<em>counts.pos.gz </em>is a multi-cell POS file containing the phased SNP counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>POS: the genomic position in the chromosome of a germline SNP</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>COUNT_HAPLOTYPE_A: the count of reads that cover the SNP and that belong to haplotype A in the specified cell</li> <li>COUNT_HAPLOTYPE_B: the count of reads that cover the SNP and that belong to haplotype B in the specified cell</li> </ul> </li> </ol> <p>All the files have been compressed using standard <em>gzip</em>.</p>
Raw read counts and phased SNP counts for every single cell in the sequencing datasets of the breast cancer patient S0 from "Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL"
<p>This dataset contains the raw read counts and phased SNP counts for every single cell in the sequencing datasets of breast cancer patient S0 from “Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL” [Zaccaria & Raphael, 2020]. These data enable the full reproduction of all the results in the related manuscript for breast cancer patient S0. Specifically, the data are provided in two files for every dataset <em>DAT</em> of patient S0 with the following format:</p> <ol> <li><em>DAT.raw</em>_<em>read</em>_<em>counts.bed.gz </em>is a multi-cell BED file containing the raw read counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>START: the starting genomic position of a genomic bin in the chromosome</li> <li>END: the ending genomic position of the genomic bin in the chromosome</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>NORMAL: the raw read count for the specified bin from a matched-normal sample</li> <li>COUNT: the raw read count for the specified bin in the specified cell</li> <li>RDR: the estimated read-depth ratio for the specified bin in the specified cell</li> </ul> </li> <li><em>DAT.phased</em>_<em>snps</em>_<em>counts.pos.gz </em>is a multi-cell POS file containing the phased SNP counts in the following fields: <ul> <li>CHROMOSOME: the name of a human chromosome</li> <li>POS: the genomic position in the chromosome of a germline SNP</li> <li>CELL: the cell barcode that uniquely identifies a cell</li> <li>COUNT_HAPLOTYPE_A: the count of reads that cover the SNP and that belong to haplotype A in the specified cell</li> <li>COUNT_HAPLOTYPE_B: the count of reads that cover the SNP and that belong to haplotype B in the specified cell</li> </ul> </li> </ol> <p>All the files have been compressed using standard <em>gzip</em>.</p>
Benefits and limits of phasing alleles for network inference of allopolyploid complexes
<p>Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared to haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American <em>Dryopteris </em>fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared to using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical non-identifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.</p>
Benefits and limits of phasing alleles for network inference of allopolyploid complexes
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Data from: Spatial patterns and rarity of the white-phased 'Spirit Bear' allele reveals gaps in habitat protection
<p>Preserving genetic and phenotypic diversity can help safeguard not only biodiversity but also cultural and economic values.</p> <p>Here, we present data that emerged from Indigenous-led research at the intersection of evolution and ecology to support conservation planning of a culturally salient, economically valuable, and rare phenotypic variant. We addressed three conservation objectives for the white-phased 'Spirit bear' polymorphism, a rare and endemic white-coated phenotype of black bear (Ursus americanus) in Kitasoo/Xai'xais and Gitga'at Territories and beyond in coastal British Columbia, Canada. First, we used non-invasively collected hair samples (n = 385 bears over ~18,000 km<sup>2</sup>) to assess the spatial variation in the frequency of the allele that controls the white-coloured morph (mc1r). Second, we compared our observed allele frequencies at mc1r with those expected under Hardy-Weinberg equilibrium. Finally, we examined how well current protected areas in the region aligned with spatial hotspots of Spirit bear alleles.</p> <p>We found that landscape-level allele frequency was lower than previously reported. For example, our systematic sampling estimated a frequency of 0.25 (95% CI 0.13-0.41) on Gribbell Island compared with the previously reported estimate of 0.56. Also, in contrast with previous reports, we failed to detect a statistically significant departure from Hardy-Weinberg equilibrium at mc1r, which calls into question the previously-posited role of homozygote gene flow, heterozygote disadvantage, and positive assortative mating in the maintenance of this polymorphism. Finally, we found a discrepancy between the placement of protected areas and the 90th percentile hotspots (upper 10% of all estimated values) of Spirit bear alleles, with ~50% of hotspots falling outside of protected areas.</p> <p>These results provide new insight into hypotheses related to the maintenance of this rare polymorphism, and directly relevant information to support evidence-based opportunities for Indigenous Nations of the area to attend to gaps in conservation planning.</p>
A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants
<h2># Genomic datasets associated to the publication: </h2> <h3># Gene-ID conversion with previous genome version</h3> <p>Texasv3_vs_Texasv2_GeneID.txt -- gene ID conversion between Texasv3 and Texasv2 (https://www.rosaceae.org/analysis/295)</p> <p>pdulcis26_to_F1_liftoff_polished.gff3 -- Texasv2 gene annotation liftoff on Phase-1 assembly (Phase-1 coordinates)</p> <h3># Phase-1</h3> <p>Texas_F1_K80_chr.fasta -- genome asssembly, phase-1 <br>Texas_F1_gene_models.gff3 -- phase-1 gene annotation (de novo annotation)<br>Functional_annotation_TexasF1.csv -- phase-1 gene functions <br>Texas_F1_ref_SV.vcf --- Structural variations relative to phase-0 (This file uses Phase-1 as reference)</p> <h3># Phase-0</h3> <p>Texas_F0_K80_chr.fasta -- genome asssembly, phase-0 <br>Texas_F0_gene_models.gff3 -- phase-0 gene annotation (liftoff from Phase-1)<br>Functional_annotation_TexasF0.csv -- phase-0 gene functions <br>Texas_F0_ref_SV.vcf --- Structural variations relative to phase-1 (This file uses Phase-0 as reference)</p> <h3># Transposable element annotation</h3> <p>Texas_F0_HiConf_TE_v3.gff3 --- TE annotation in Phase-0<br>Texas_F1_HiConf_TE_v3.gff3 --- TE annotation in Phase-1<br>Texasv3_TElib.fa --- TE library of TexasV3 (non-redundant repeat consensuses taking the account the two genome phases)</p> <h3># Gene sequences in fasta</h3> <p>Transcript, CDS and protein sequences in fasta format for phase-0 (F0) and phase-1 (F1) </p>
Data from: Spatial patterns and rarity of the white-phased ‘Spirit Bear’ allele reveals gaps in habitat protection
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Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
Premise of the study: Untapped information about allelic diversity within populations and individuals (i.e. heterozygosity) could improve phylogenetic resolution and accuracy. Many phylogenetic reconstructions ignore heterozygosity because it is difficult to assemble allele sequences and combine allelic data across unlinked loci and it is unclear how reconstruction methods accommodate variable sequences. We review the common methods of including heterozygosity in phylogenetic studies and present a novel method for assembling allele sequences from target enriched Illumina sequencing libraries. Methods: We perform supermatrix phylogeny reconstruction and species tree estimation of Artocarpus based on three methods of accounting for heterozygous sequences: a consensus method based on de novo sequence assembly, the use of ambiguity characters, and a novel method for phasing alleles. We characterize the extent to which highly heterozygous sequences impeded phylogeny reconstruction and determine whether the use of allele sequences improves resolution or decreases topological uncertainty. Key Results: We show that it is possible to infer phased alleles from target enriched Illumina libraries. We find that highly heterozygous sequences do not contribute disproportionately to poor phylogenetic resolution and that the use of allele sequences for phylogeny reconstruction does not have a clear effect on phylogenetic resolution or topological consistency. Conclusions: We provide a framework for inferring phased alleles from target enrichment data and for assessing the contribution of allelic diversity to phylogenetic reconstruction. In our dataset, the impact of allele phasing on phylogeny is minimal compared to the impact of using phylogenetic reconstruction methods that account for gene tree incongruence.
Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
Background: Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M. strasseri) have an allopolyploid origin - a question that has remained unsolved despite substantial previous research. We sequenced and analyzed ten low-copy nuclear genes from these and related species, phasing all alleles. To test the efficacy of allele phasing on the ability to recover the evolutionary origin of polyploids, we compared these results to analyses using unphased sequences. Results: In eight of the gene trees the alleles inferred from the tetraploids formed two clades, in a non-sister relationship. Each of these clades was more closely related to alleles sampled from other species of Medicago, a pattern typical of allopolyploids. However, we also observed that alleles from one of the remaining genes formed two clades that were sister to one another, as is expected for autopolyploids. Trees inferred from unphased sequences were very different, with the tetraploids often placed in poorly supported and different positions compared to results obtained using phased alleles. Conclusions: The complex phylogenetic history of M. arborea and M. strasseri is explained predominantly by shared allotetraploidy. We also observed that an increase in woodiness is correlated with polyploidy in this group of species and present a new possibility that woodiness could be a transgressive phenotype. Correctly phased homoeologues are likely to be critical for inferring the hybrid origin of allopolyploid species, when most genes retain more than one homoeologue. Ignoring homoeologous variation by merging the homoeologues can obscure the signal of hybrid polyploid origins and produce inaccurate results.
Data from: Allele phasing greatly improves the phylogenetic utility of ultraconserved elements
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Data from: Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus
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Data from: Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
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Data from: RPASE: individual based allele-specific expression detection without prior knowledge of haplotype phase
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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
GEO Series GSE183760. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing.
A Phase 2 Study to Evaluate the Safety, Tolerability, PK and PD of ELX-02 in Cystic Fibrosis Patients With G542X Allele
ClinicalTrials.gov study NCT04135495. IPD Sharing: Not stated. Countries: 2. Publications: 0.
A Phase 2 Study to Evaluate the Safety, Tolerability, PK and PD in Cystic Fibrosis Patients With at Least 1 G542X Allele
ClinicalTrials.gov study NCT04126473. IPD Sharing: Not stated. Countries: 3. Publications: 0.
Data from: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
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A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous transposon insertions
GEO Series GSE254853. Prunus dulcis; Prunus persica. 12 samples. Type: Expression profiling by high throughput sequencing.
Quantitative analysis of Escherichia coli sigma factor alleles wildtype rpoS, rpoS819 and rpoS92 transcriptomes in stationary-phase (16 hours)
GEO Series GSE119046. Escherichia coli. 6 samples. Type: Expression profiling by high throughput sequencing.
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