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Copy number variations

Tìm thấy 15+ kết quả cho từ khóa "Copy number variations"

Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing

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Genome-wide patterns of copy number variation in the Chinese yak genome. Multi-ethnic cytochrome-P450 copy number profiling: novel pharmacogenetic alleles and mechanism of copy number variation formation. Gene copy number variations: it is important to determine which allele is affected. Differential quantification of CYP2D6 gene copy number by four different. Consequences of CYP2D6 copy-number variation for pharmacogenomics in psychiatry.

Evaluation of tools for identifying large copy number variations from ultra-lowcoverage whole-genome sequencing data

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The average sensi- tivity, FDR and F1 score of the six CNV algorithms were Table 1 Summary of features for the algorithms. 1 Flowchart showing the main steps of our comparison, including preprocessing of the data, detection of copy number variations (CNVs) with six different algorithms (BIC-seq2, Canvas, CNVnator, FREEC, HMMcopy, and QDNAseq) and evaluation and validation of the results.

Comparative analyses of copy number variations between Bos taurus and Bos indicus

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Comparative analyses of copy number variations between Bos taurus and Bos indicus. Background: Bos taurus and Bos indicus are two main sub-species of cattle. Results: Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus.

Concordance rate between copy number variants detected using either high- or medium-density single nucleotide polymorphism genotype panels and the potential of imputing copy number variants from flanking high density single nucleotide polymorphism haplotypes in cattle

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Genomic population structure and prevalence of copy number variations in south African Nguni catle. A genome- wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle. A large interactive visual database of copy number variants discovered in taurine cattle. Large multiallelic copy number variations in humans. A whole-genome assembly of the domestic cow, Bos Taurus

Copy number variation in human genomes from three major ethno-linguistic groups in Africa

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Population-genetic nature of copy number variations in the human genome. Population structure in copy number variation and SNPs in the CCL4L chemokine gene. Evolutionary genetics of the human Rh blood group system. Origins and functional impact of copy number variation in the human genome..

Functional and population genetic features of copy number variations in two dairy cattle populations

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CNV: Copy number variation. performed data collection and was involved in preparation of the manuscript. MG is a member of the editorial board (Associate Editor) of BMC Genomics journal. Structural variation in the human genome.. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, et al.. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al.

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

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Genome- wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array. Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p. Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep. Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins.

Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds

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S7 Summary of the structural variations (SVs) and copy number variations (CNVs) in all 110 chicken genomes gen- erated in this study.. Annotation of the hybrid status of SNPs in each chicken genome sequenced in this study.. Annotation of structural variations in the chicken genomes sequenced in this study.. Annotation of copy number variations in the chicken genomes sequenced in this study.. The top 1% genomic windows in the selection scan by LSBL test..

Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication

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A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.. Global variation in copy number in the human genome. Copy number variations in the amylase gene (AMY2B) in Japanese native dog breeds. Multiple and ancient origins of the domestic dog. Molecular evolution of the dog family.

Genome-wide detection of CNVs and their association with performance traits in broilers

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An initial map of chromosomal segmental copy number variations in the chicken.

Structural variation of the malariaassociated human glycophorin A-B-E region

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Large multiallelic copy number variations in humans. A novel gene member of the human glycophorin a and B gene family.. Glycophorin variants and Plasmodium falciparum: protective effect of the Dantu phenotype in vitro. Red blood cell tension controls Plasmodium falciparum invasion and protects against severe malaria in the Dantu blood group. Origins and functional impact of copy number variation in the human genome..

A fast-linear mixed model for genome-wide haplotype association analysis: Application to agronomic traits in maize

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FaST-LMM for genetic units. where y is a vector of the phenotypic values from n indi- viduals, which is justified for systemic factors that in- clude population stratification. β is the additive genetic effect of the tested genetic units, such as the SNP, haplotype (or block), and copy number variations.

Clonal reconstruction from time course genomic sequencing data

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During the course of the evolution exper- iment, bacterial cells accumulate novel mutations form- ing new clones. but the other types of vari- ations (e.g., indels, structural variations and copy number variations) can be modelled in the same way.

Multi-omics approach highlights differences between RLP classes in Arabidopsis thaliana

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AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. Genome-wide Identification, Classification, and Expression Analysis of the Receptor-Like Protein Family in Tomato. Witek K, Lin X, Karki HS, Jupe F, Witek AI, Steuernagel B, et al. Population studies of the wild tomato species Solanum chilense reveal geographically structured major gene-mediated pathogen resistance

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses

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The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease. Proceedings of the International Research Society of Spinal Deformities conference. There may be a same mechanism of the left-right handedness and left-right convex curve pattern of adolescent idiopathic scoliosis. Disorders of the thoracolumbar spine of the horse — a survey of 443 cases.

MONTAGE: A new tool for high-throughput detection of mosaic copy number variation

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ParseCNV integrative copy number variation association software with quality tracking. doi.org/10.1093/nar/gks1346.. https://doi.org/10.1093/hmg/ddv033 Epub 2015 Jan 29.. Mosaic copy number variation in human neurons. Copy number variation and mosaicism.. https://doi.org/10.1159/. doi: https://doi.org/https://doi.org/. https://doi.org/10.1038/s .

A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes

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Global variation in copy number in the human genome. https://doi.org/10.1038/nature05329.. Genova F, Longeri M, Lyons LA, Bagnato A, Gandolfi B, Aberdein D, et al.. https://doi.org/10.1186/s . https://doi.org/10.1111/age.12180.. Gorla E, Cozzi MC, Román-Ponce SI, Ruiz López FJ, Vega-Murillo VE, Cerolini S, et al. https://doi.org/1 0.1186/s . doi.org/10.1186/s z.. https://doi.org/10.1111/jbg.12238.. https://doi.org/10.11 86/s .

Detection of copy number variants in African goats using whole genome sequence data

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A copy number variation map of the human genome. https://doi.. org/10.1038/nrg3871.. https://doi.org/10.1056/. https://doi.org/10.1038/ng.909.. https://doi.org .

Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids

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Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions..

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

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As the dominant copy number was five for both R1 and R2, we used 34 × 5 STR to represent R1 and R2 in the D. which is longer than the reads in the 2 × 150 bp DNA- seq data. However, we did not obtain full-length sequences of LT1 due to sequence- length limitations in the DNA-seq data. Copy number variation of STRs in the mt genomes within an individual animal. We defined the STR position as the genomic position of the first nucleotide of the reference STR.