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237 results for “allele specificity”

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zenodo48/100

Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models.

Precise values obtained during the research that led to the publishing of scientific paper entitled 'Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models'.

opencc-by-4.0Jan 2023View details →

zenodo44/100

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"

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 DAT of patient S1 with the following format: <ol> <li>DAT.raw_read_counts.bed.gz 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>DAT.phased_snps_counts.pos.gz 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> All the files have been compressed using standard gzip.

opencc-by-4.0May 2020View details →

zenodo44/100

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"

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 DAT of patient S0 with the following format: <ol> <li>DAT.raw_read_counts.bed.gz 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>DAT.phased_snps_counts.pos.gz 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> All the files have been compressed using standard gzip.

opencc-by-4.0May 2020View details →

zenodo44/100

Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences

This repository consists of minisatellite VNTR genotypes for 2,800 samples (2,770 individuals). The raw VCF files were produced using <a href="https://github.com/yzhernand/VNTRseek">VNTRseek</a> on xxx data sources: <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/">30 high coverage WGS datasets</a> from the 1000 Genomes Project phase 3, <a href="https://www.internationalgenome.org/data-portal/data-collection/30x-grch38">2,504 unrelated genomes</a> from New York Genome Center (NYGC), <a href="https://www.internationalgenome.org/data-portal/data-collection/sgdp">253 genomes from Simons Diversity Genome Project</a> (SGDP), <a href="https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/tumor-normal.html">two tumor-normal breast cancer samples</a> from Illumina Basespace, haploid genomes <a href="https://www.ncbi.nlm.nih.gov/sra/SRX652547">CHM1 </a>and <a href="https://www.ncbi.nlm.nih.gov/sra/SRX1009644">CHM13</a>, and seven genomes from the Personal Genome Project from the Genome In A Bottle Consortium (GIAB). Raw VCF files are provided for each data source separately. The raw VCF files were preprocessed (preprocess.sh) to extract genotypes and provided in VNTRseek_preprocessed_data.tar.gz (uncompressed size 10G). The R Markdown code to analyze the preprocessed data and produce figures and tables is also provided (tables_and_figures.Rmd). For more information see the ReadMe file. This work was supported in part by NSF grants IIS-1423022 and DBI-1559829.

opencc-by-4.0Nov 2020View details →

dryad36/100

Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections

Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. Borrelia burgdorferi, a bacterium that causes Lyme disease, is typically transmitted among wildlife by Ixodes ticks. Despite the existence of many alleles of B. burgdorferi's sensu stricto outer surface protein C (ospC) gene, most human infections are caused by a small number of ospC alleles ["human infectious alleles" (HIAs)], suggesting variation in host specificity associated with ospC. To characterize the wildlife host association of B. burgdorferi's ospC alleles, we used metagenomics to sequence ospC alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele ("mixed") infections were common. HIAs were most common in mice (Peromyscus spp.) and only one HIA was detected at a site where mice were rarely captured. OspC allele U was exclusively found in chipmunks (Tamias striatus), and although a significant number of different alleles were observed in chipmunks, including HIAs, allele U never co-occurred with other alleles in mixed infections. Our results suggest that allele U may be excluding other alleles, thereby reducing the capacity of chipmunks to act as reservoirs for HIAs.

opencc-zeroDec 2023View details →

dryad36/100

Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression

Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the Major Histocompatibility Complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi-locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ datasets of three-spined stickleback gDNA, cDNA, and "artificial" plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, gDNA-optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template-specific pipeline optimization for reliable genotyping of multi-locus gene families. Through accurate paired gDNA-cDNA typing and MHC-II haplotype inference, we show that MHC-II allele-specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship-assisted cDNA-typing of MHC-I revealed novel variants linked in haplotype blocks and a higher-than-previously-reported individual MHC-I allelic diversity. In conclusion, we provide novel genotyping protocols for the three-spined stickleback MHC-I and -II genes and evaluate the performance of popular NGS-genotyping pipelines. We also show that fine-tuned genotyping of paired gDNA-cDNA samples facilitates amplification bias-corrected MHC allele expression analysis.

opencc-zeroJan 2024View details →

zenodo36/100

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> Texasv3_vs_Texasv2_GeneID.txt -- gene ID conversion between Texasv3 and Texasv2 (https://www.rosaceae.org/analysis/295) pdulcis26_to_F1_liftoff_polished.gff3 -- Texasv2 gene annotation liftoff on Phase-1 assembly (Phase-1 coordinates) <h3># Phase-1</h3> Texas_F1_K80_chr.fasta  -- genome asssembly, phase-1  Texas_F1_gene_models.gff3 --  phase-1  gene annotation (de novo annotation) Functional_annotation_TexasF1.csv --  phase-1 gene functions   Texas_F1_ref_SV.vcf --- Structural variations relative to phase-0 (This file uses Phase-1 as reference) <h3># Phase-0</h3> Texas_F0_K80_chr.fasta -- genome asssembly, phase-0  Texas_F0_gene_models.gff3 --  phase-0  gene annotation (liftoff from Phase-1) Functional_annotation_TexasF0.csv --  phase-0  gene functions   Texas_F0_ref_SV.vcf --- Structural variations relative to phase-1 (This file uses Phase-0 as reference) <h3># Transposable element annotation</h3> Texas_F0_HiConf_TE_v3.gff3 --- TE annotation in Phase-0 Texas_F1_HiConf_TE_v3.gff3 --- TE annotation in Phase-1 Texasv3_TElib.fa --- TE library of TexasV3 (non-redundant repeat consensuses taking the account the two genome phases) <h3># Gene sequences in fasta</h3> Transcript, CDS and protein sequences in fasta format for phase-0 (F0) and phase-1 (F1)

opencc-by-4.0Mar 2024View details →

dryad36/100

Figure e-1.- Effect of APOE alleles on cognitive domain-specific composite measures.

Supplemental Figure of our original article "Association of APOE Genotype with Heterogeneity of Cognitive Decline Rate in Alzheimer's Disease" published in Neurology showing model 1-based trajectories of cognitive domain-specific composite measures by APOE genotype, as well as the difference of the APOEe2 and APOEe4 groups with respect to the APOEe3/e3 reference group.

opencc-zeroFeb 2022View details →

zenodo36/100

Computational models from: Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer

Computational models, compressed molecular dynamics (MD) simulation trajectories, and sample input files for "Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer". An early version of this manuscript is available as a preprint here: https://www.biorxiv.org/content/10.1101/2022.03.16.484661v1

opencc-by-4.0May 2022View details →

dryad36/100

PAM-altering SNP-based allele-specific CRISPR-Cas9 therapeutic strategies for Huntington's disease

Huntington's disease (HD) is caused by an expanded CAG repeat in huntingtin (HTT). Since HD is dominant, and loss of HTT leads to neurological abnormalities, safe therapeutic strategies require selective inactivation of mutant HTT. Previously, we proposed a concept of CRISPR-Cas9 using mutant-specific PAM sites generated by SNPs to selectively inactivate mutant HTT. Aiming at revealing suitable targets for clinical development, we analyzed the largest HD genotype dataset to reveal target PAM-altering SNPs (PAS) and subsequently evaluated their allele specificities. The gRNAs based on the PAM sites generated by rs2857935, rs16843804, and rs16843836 showed high levels of allele specificity in patient-derived cells. Simultaneous use of two gRNAs based on rs2857935-rs16843804 or rs2857935-rs16843836 produced selective genomic deletions in mutant HTT and prevented the transcription of mutant HTT mRNA without impacting the expression of normal counterpart or re-integration of the excised fragment elsewhere in the genome. RNAseq and off-target analysis confirmed high levels of allele specificity and the lack of recurrent off-targeting. Approximately 60% of HD subjects are eligible for mutant-specific CRISPR-Cas9 strategies of targeting one of these 3 PAS in conjunction with one non-allele-specific site, supporting high applicability of PAS-based allele-specific CRISPR approaches in the HD patient population.

opencc-zeroAug 2022View details →

dryad36/100

Complete allele-specific silencing of the gain-of-function mutation of Huntington's disease

Dominant gain-of-function mechanism in Huntington's disease (HD) suggests selective inactivation of mutant HTT produces the biggest therapeutic benefit. Here, we developed a complete allele-specific CRISPR/Cas9 strategy to permanently silence mutant HTT through nonsense-mediated decay (NMD), capitalizing on an exonic PAM (protospacer adjacent motif)-Altering SNP (PAS). Comprehensive sequence/haplotype analysis identified PAS-generated NGG PAM sites on exons of common HTT haplotypes in HD patients, revealing a single clinically meaningful PAS-based mutant-specific NMD-CRISPR/Cas9 strategy. The alternative allele of rs363099 eliminates NGG PAM site on the most frequent normal HTT haplotype in HD, permitting mutant HTT-specific CRISPR/Cas9 therapeutics in ~20% of HD patients with European ancestry. Our rs363099-based CRISPR/Cas9 showed perfect allele specificity and good targeting efficiencies in cells derived from HD patients. Dramatically reduced mutant HTT mRNA and complete loss of mutant HTT protein indicate that our allele-specific CRISPR/Cas9 strategy completely inactivates mutant HTT through NMD. RNAseq analysis also supported high levels of on-target gene specificity because no other genes except HTT were altered in clonal lines developed through our NMD-CRISPR/Cas9 strategy. Together, our data demonstrating significant target population, selective inactivation of mutant HTT, good targeting efficiency, and lack of recurrent off-targeting establish its therapeutic value of novel rs363099-based mutant HTT-specific NMD-CRISPR/Cas9 strategy in HD.

opencc-zeroAug 2022View details →

dryad36/100

Borrelia infection in bank voles Myodes glareolus is associated with specific DQB haplotypes which affect allelic divergence within individuals

The high polymorphism of Major Histocompatibility Complex (MHC) genes is generally considered to be a result of pathogen-mediated balancing selection. Such selection may operate in the form of heterozygote advantage, and/or through specific MHC allele–pathogen interactions. Specific MHC allele–pathogen interactions may promote polymorphism via negative frequency-dependent selection (NFDS), or selection that varies in time and/or space because of variability in the composition of the pathogen community (fluctuating selection; FS). In addition, divergent allele advantage (DAA) may act on top of these forms of balancing selection, explaining the high sequence divergence between MHC alleles. DAA has primarily been thought of as an extension of heterozygote advantage. However, DAA could also work in concert with NFDS though this is yet to be tested explicitly. To evaluate the importance of DAA in pathogen-mediated balancing selection, we surveyed allelic polymorphism of MHC class II DQB genes in wild bank voles (Myodes glareolus) and tested for associations between DQB haplotypes and infection by Borrelia afzelii, a tick-transmitted bacterium causing Lyme disease in humans. We found two significant associations between DQB haplotypes and infection status: one haplotype was associated with lower risk of infection (resistance), while another was associated with higher risk of infection (susceptibility). Interestingly, allelic divergence within individuals was higher for voles with the resistance haplotype compared to other voles. In contrast, allelic divergence was lower for voles with the susceptibility haplotype than other voles. The pattern of higher allelic divergence in individuals with the resistance haplotype is consistent with NFDS favouring divergent alleles in a natural population, hence selection where DAA works in concert with NFDS.

opencc-zeroJul 2021View details →

dryad36/100

Allele‐specific cis‐regulatory methylation of the gene for vasoactive intestinal peptide in white‐throated sparrows

White-throated sparrows (Zonotrichia albicollis) offer a unique opportunity to connect genotype with behavioral phenotype. In this species, a rearrangement of the second chromosome is linked with territorial aggression; birds with a copy of this "supergene" rearrangement are more aggressive than those without it. The supergene has captured the gene VIP, which encodes vasoactive intestinal peptide, a neuromodulator that causes aggression in other songbirds. In white-throated sparrows, VIP expression is higher in the anterior hypothalamus of birds with the supergene than those without it, and expression of VIP in this region predicts the level of territorial aggression regardless of genotype. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of VIP both in breeding adults, which exhibit morph differences in territorial aggression, and in nestlings, before territorial behavior develops. We extracted and bisulfite-converted DNA from samples of the hypothalamus in wild-caught adults and nestlings and used high-throughput sequencing to measure DNA methylation of a region upstream of the VIP start site. We found that the allele inside the supergene was less methylated than the alternative allele in both adults and nestlings. The differential methylation was attributed primarily to CpG sites that were shared between the alleles, not to polymorphic sites, which suggests that epigenetic regulation is occurring independently of the genetic differentiation within the supergene. This work represents an initial step toward understanding how epigenetic differentiation inside chromosomal inversions leads to the development of alternative behavioral phenotypes.

opencc-zeroOct 2022View details →

dryad36/100

Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone-resistance evolution

Collateral sensitivity (CS), which arises when resistance to one antibiotic increases sensitivity towards other antibiotics, offers novel treatment opportunities to constrain or reverse the evolution of antibiotic resistance. The applicability of CS-informed treatments remains uncertain, in part because we lack an understanding of the generality of CS effects for different resistance mutations, singly or in combination. Here we address this issue in the Gram-positive pathogen Streptococcus pneumoniae by measuring collateral and fitness effects of clinically relevant gyrA and parC alleles, and their combinations, that confer resistance to fluoroquinolones. We integrated these results in a mathematical model which allowed us to evaluate how different in silico combination treatments impact the dynamics of resistance evolution. We identified common and conserved CS effects of different gyrA and parC alleles; however, the spectrum of collateral effects was unique for each allele or allelic pair. This indicated that allelic identity can impact the evolutionary dynamics of resistance evolution during monotreatment and combination treatment. Our model simulations, which included the experimentally derived antibiotic susceptibilities and fitness effects, and antibiotic-specific pharmacodynamics, revealed that both collateral and fitness effects impact the population dynamics of resistance evolution. Overall, we provide evidence that allelic identity and interactions can have a pronounced impact on collateral effects of different antibiotics and suggest that these need to be considered in models examining CS-based therapies.

opencc-zeroNov 2022View details →

dryad36/100