Exome-Wide Analysis of the DiscovEHR Cohort Reveals Novel Candidate Pharmacogenomic Variants for Clinical Pharmacogenomics.

Abstract:

:Recent advances in next-generation sequencing technology have led to the production of an unprecedented volume of genomic data, thus further advancing our understanding of the role of genetic variation in clinical pharmacogenomics. In the present study, we used whole exome sequencing data from 50,726 participants, as derived from the DiscovEHR cohort, to identify pharmacogenomic variants of potential clinical relevance, according to their occurrence within the PharmGKB database. We further assessed the distribution of the identified rare and common pharmacogenomics variants amongst different GnomAD subpopulations. Overall, our findings show that the use of publicly available sequence data, such as the DiscovEHR dataset and GnomAD, provides an opportunity for a deeper understanding of genetic variation in pharmacogenes with direct implications in clinical pharmacogenomics.

journal_name

Genes (Basel)

journal_title

Genes

authors

Pandi MT,Williams MS,van der Spek P,Koromina M,Patrinos GP

doi

10.3390/genes11050561

subject

Has Abstract

pub_date

2020-05-18 00:00:00

issue

5

issn

2073-4425

pii

genes11050561

journal_volume

11

pub_type

杂志文章

相关文献

Genes文献大全
  • Molecular Cloning and Characterization of Three Glucosinolate Transporter (GTR) Genes from Chinese Kale.

    abstract::Chinese kale is a native vegetable in Southern China and the flowering stalk is the most commonly used edible part due to its high glucosinolate content and other nutritional qualities. The GTR protein played important roles in the glucosinolate transport process. In this study, three BocGTR1 genes were cloned from Ch...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10030202

    authors: Jiang D,Lei J,Cao B,Wu S,Chen G,Chen C

    更新日期:2019-03-08 00:00:00

  • Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses.

    abstract::Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. T...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10050355

    authors: Qanmber G,Ali F,Lu L,Mo H,Ma S,Wang Z,Yang Z

    更新日期:2019-05-09 00:00:00

  • Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations.

    abstract::Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype-phenotype associations is still ...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11080892

    authors: Ramzan F,Gültas M,Bertram H,Cavero D,Schmitt AO

    更新日期:2020-08-05 00:00:00

  • Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential.

    abstract::Several transcription factors (TFs) coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to under...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes5041115

    authors: Kurihara Y,Makita Y,Kawashima M,Hamasaki H,Yamamoto YY,Matsui M

    更新日期:2014-12-19 00:00:00

  • Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes.

    abstract::B chromosomes (Bs) were discovered a century ago, and since then, most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin,...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes9120610

    authors: Clark FE,Conte MA,Kocher TD

    更新日期:2018-12-05 00:00:00

  • Evolution of Tandem Repeat Satellite Sequences in Two Closely Related Caenorhabditis Species. Diminution of Satellites in Hermaphrodites.

    abstract::The availability of the genome sequence of the unisexual (male-female) Caenorhabditis nigoni offers an opportunity to compare its non-coding features with the related hermaphroditic species Caenorhabditis briggsae; to understand the evolutionary dynamics of their tandem repeat sequences (satellites), as a result of ev...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8120351

    authors: Subirana JA,Messeguer X

    更新日期:2017-11-28 00:00:00

  • 46,XY,r(8)/45,XY,-8 Mosaicism as a Possible Mechanism of the Imprinted Birk-Barel Syndrome: A Case Study.

    abstract::Ring chromosome 8 (r(8)) is one of the least frequent ring chromosomes. Usually, maternal chromosome 8 forms a ring, which can be lost from cells due to mitotic instability. The 8q24 region contains the imprinted KCNK9 gene, which is expressed from the maternal allele. Heterozygous KCNK9 mutations are associated with ...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11121473

    authors: Kashevarova AA,Nikitina TV,Mikhailik LI,Belyaeva EO,Vasilyev SA,Lopatkina ME,Fedotov DA,Fonova EA,Zarubin AA,Sivtsev AA,Skryabin NA,Nazarenko LP,Lebedev IN

    更新日期:2020-12-09 00:00:00

  • Evolutionary Insights of the ZW Sex Chromosomesin Snakes: A New Chapter Added by the AmazonianPuffing Snakes of the Genus Spilotes.

    abstract::Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and tre...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10040288

    authors: Viana PF,Ezaz T,de Bello Cioffi M,Jackson Almeida B,Feldberg E

    更新日期:2019-04-09 00:00:00

  • A Third MLPH Variant Causing Coat Color Dilution in Dogs.

    abstract::Altered melanosome transport in melanocytes, resulting from variants in the melanophilin (MLPH) gene, are associated with inherited forms of coat color dilution in many species. In dogs, the MLPH gene corresponds to the D locus and two variants, c.-22G > A (d1) and c.705G > C (d2), leading to the dilution of coat colo...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11060639

    authors: Van Buren SL,Minor KM,Grahn RA,Mickelson JR,Grahn JC,Malvick J,Colangelo JR,Mueller E,Kuehnlein P,Kehl A

    更新日期:2020-06-10 00:00:00

  • The Role of Wnt Signal in Glioblastoma Development and Progression: A Possible New Pharmacological Target for the Therapy of This Tumor.

    abstract::Wnt is a complex signaling pathway involved in the regulation of crucial biological functions such as development, proliferation, differentiation and migration of cells, mainly stem cells, which are virtually present in all embryonic and adult tissues. Conversely, dysregulation of Wnt signal is implicated in developme...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes9020105

    authors: Zuccarini M,Giuliani P,Ziberi S,Carluccio M,Iorio PD,Caciagli F,Ciccarelli R

    更新日期:2018-02-17 00:00:00

  • Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm.

    abstract::Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We pr...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11070737

    authors: Žulj Mihaljević M,Maletić E,Preiner D,Zdunić G,Bubola M,Zyprian E,Pejić I

    更新日期:2020-07-02 00:00:00

  • Telomere and Centromere Staining Followed by M-FISH Improves Diagnosis of Chromosomal Instability and Its Clinical Utility.

    abstract::Dicentric chromosomes are a relevant marker of chromosomal instability. Their appearance is associated with telomere dysfunction, leading to cancer progression and a poor clinical outcome. Here, we present Telomere and Centromere staining followed by M-FISH (TC+M-FISH) for improved detection of telomere dysfunction an...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11050475

    authors: M'kacher R,Colicchio B,Borie C,Junker S,Marquet V,Heidingsfelder L,Soehnlen K,Najar W,Hempel WM,Oudrhiri N,Wilhelm-Murer N,Miguet M,Arnoux M,Ferrapie C,Kerbrat W,Plesch A,Dieterlen A,Girinsky T,Voisin P,Deschenes G

    更新日期:2020-04-27 00:00:00

  • Transitions from Single- to Multi-Locus Processes during Speciation with Gene Flow.

    abstract::During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitat...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes9060274

    authors: Schilling MP,Mullen SP,Kronforst M,Safran RJ,Nosil P,Feder JL,Gompert Z,Flaxman SM

    更新日期:2018-05-24 00:00:00

  • Study of the Relationship between Polymorphisms in the IL-8 Gene Promoter Region and Coccidiosis Resistance Index in Jinghai Yellow Chickens.

    abstract::Interleukin 8 (IL-8) participates in the immune response and has the function of inducing neutrophils to release lysosomal enzymes and eliminate pathogens. This study was to investigate the effect of single nucleotide mutations in the IL-8 gene promoter region on the coccidiosis resistance index. In this study, 180 in...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11050476

    authors: Wang XH,Yu HL,Zou WB,Mi CH,Dai GJ,Zhang T,Zhang GX,Xie KZ,Wang JY

    更新日期:2020-04-27 00:00:00

  • Identification of Genetic Locus Underlying Easy Dehulling in Rice-Tartary for Easy Postharvest Processing of Tartary Buckwheat.

    abstract::As a highly nutritious crop, Tartary buckwheat (Fagopyrum tartaricum) strongly adapts and grows in adverse environments and is widely grown in Asia. However, its flour contains a large proportion of the hull that adheres to the testa layer of the groats and is difficult to be removed in industrial processing. Fortunat...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11040459

    authors: Zhang L,Ma M,Liu L

    更新日期:2020-04-23 00:00:00

  • K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features.

    abstract::In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8040122

    authors: Sievers A,Bosiek K,Bisch M,Dreessen C,Riedel J,Froß P,Hausmann M,Hildenbrand G

    更新日期:2017-04-19 00:00:00

  • Investigation of Precise Molecular Mechanistic Action of Tobacco-Associated Carcinogen `NNK´ Induced Carcinogenesis: A System Biology Approach.

    abstract::Cancer is the second deadliest disease listed by the WHO. One of the major causes of cancer disease is tobacco and consumption possibly due to its main component, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). A plethora of studies have been conducted in the past aiming to decipher the association of NNK with o...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10080564

    authors: Anukriti.,Dhasmana A,Uniyal S,Somvanshi P,Bhardwaj U,Gupta M,Haque S,Lohani M,Kumar D,Ruokolainen J,Kesari KK

    更新日期:2019-07-26 00:00:00

  • Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig.

    abstract::There are major differences between Yorkshire (lean-type) and Wannanhua pig (fat-type) in terms of growth performance and meat quality. Long intergenic noncoding RNAs (lincRNAs) are a class of regulators that are involved in numerous biological processes and widely identified in many species. However, the role of linc...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8080203

    authors: Zou C,Li S,Deng L,Guan Y,Chen D,Yuan X,Xia T,He X,Shan Y,Li C

    更新日期:2017-08-18 00:00:00

  • Identification of the Ovine Keratin-Associated Protein 22-1 (KAP22-1) Gene and Its Effect on Wool Traits.

    abstract::Keratin-associated proteins (KAPs) are structural components of wool and hair fibers. To date, eight high glycine/tyrosine KAP (HGT-KAP) families have been identified in humans, but only three have been identified in sheep. In this study, the putative ovine homolog of the human KAP22-1 gene (KRTAP22-1) was amplified u...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes8010027

    authors: Li S,Zhou H,Gong H,Zhao F,Wang J,Liu X,Luo Y,Hickford JG

    更新日期:2017-01-11 00:00:00

  • Identification of Long Non-Coding RNAs Deregulated in Multiple Myeloma Cells Resistant to Proteasome Inhibitors.

    abstract::While the clinical benefit of proteasome inhibitors (PIs) for multiple myeloma (MM) treatment remains unchallenged, dose-limiting toxicities and the inevitable emergence of drug resistance limit their long-term utility. Disease eradication is compromised by drug resistance that is either present de novo or therapy-ind...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes7100084

    authors: Malek E,Kim BG,Driscoll JJ

    更新日期:2016-10-06 00:00:00

  • Transcriptome Analysis Reveals Inhibitory Effects of Lentogenic Newcastle Disease Virus on Cell Survival and Immune Function in Spleen of Commercial Layer Chicks.

    abstract::As a major infectious disease in chickens, Newcastle disease virus (NDV) causes considerable economic losses in the poultry industry, especially in developing countries where there is limited access to effective vaccination. Therefore, enhancing resistance to the virus in commercial chickens through breeding is a prom...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11091003

    authors: Zhang J,Kaiser MG,Gallardo RA,Kelly TR,Dekkers JCM,Zhou H,Lamont SJ

    更新日期:2020-08-26 00:00:00

  • Identification of QTLs for Resistance to Fusarium Head Blight Using a Doubled Haploid Population Derived from Southeastern United States Soft Red Winter Wheat Varieties AGS 2060 and AGS 2035.

    abstract::Fusarium head blight (FHB), caused primarily by the fungus Fusarium graminearum, is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high inoculum pressure from corn stubble contribute...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11060699

    authors: Castro Aviles A,Alan Harrison S,Joseph Arceneaux K,Brown-Guidera G,Esten Mason R,Baisakh N

    更新日期:2020-06-25 00:00:00

  • Comparative Transcriptome Profiling of Skeletal Muscle from Black Muscovy Duck at Different Growth Stages Using RNA-seq.

    abstract::In China, the production for duck meat is second only to that of chicken, and the demand for duck meat is also increasing. However, there is still unclear on the internal mechanism of regulating skeletal muscle growth and development in duck. This study aimed to identity candidate genes related to growth of duck skele...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11101228

    authors: Hu Z,Cao J,Liu G,Zhang H,Liu X

    更新日期:2020-10-20 00:00:00

  • RNA Modifications Modulate Activation of Innate Toll-Like Receptors.

    abstract::Self/foreign discrimination by the innate immune system depends on receptors that identify molecular patterns as associated to pathogens. Among others, this group includes endosomal Toll-like receptors, among which Toll-like receptors (TLR) 3, 7, 8, and 13 recognize and discriminate mammalian from microbial, potential...

    journal_title:Genes

    pub_type: 杂志文章,评审

    doi:10.3390/genes10020092

    authors: Freund I,Eigenbrod T,Helm M,Dalpke AH

    更新日期:2019-01-29 00:00:00

  • Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors.

    abstract::In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient editing of human i...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11050511

    authors: Sürün D,Schneider A,Mircetic J,Neumann K,Lansing F,Paszkowski-Rogacz M,Hänchen V,Lee-Kirsch MA,Buchholz F

    更新日期:2020-05-06 00:00:00

  • Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas.

    abstract::Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region o...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11060695

    authors: Tunjić Cvitanić M,Vojvoda Zeljko T,Pasantes JJ,García-Souto D,Gržan T,Despot-Slade E,Plohl M,Šatović E

    更新日期:2020-06-24 00:00:00

  • Mutational Spectrum and Clinical Features of Patients with LOXHD1 Variants Identified in an 8074 Hearing Loss Patient Cohort.

    abstract::Variants of the LOXHD1 gene, which are expressed in hair cells of the cochlea and vestibule, have been reported to cause a progressive form of autosomal recessive non-syndromic hereditary hearing loss, DFNB77. In this study, genetic screening was conducted on 8074 Japanese hearing loss patients utilizing massively par...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10100735

    authors: Maekawa K,Nishio SY,Abe S,Goto SI,Honkura Y,Iwasaki S,Kanda Y,Kobayashi Y,Oka SI,Okami M,Oshikawa C,Sakuma N,Sano H,Shirakura M,Uehara N,Usami SI

    更新日期:2019-09-23 00:00:00

  • Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes.

    abstract::Architectural proteins play key roles in genome construction and regulate the expression of many genes, albeit the modulation of genome plasticity by these proteins is largely unknown. A critical screening of the architectural proteins in five crop species, viz., Oryza sativa, Zea mays, Sorghum bicolor, Cicer arietinu...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes9040183

    authors: Verma JK,Wardhan V,Singh D,Chakraborty S,Chakraborty N

    更新日期:2018-03-28 00:00:00

  • Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey (Petromyzon marinus).

    abstract::The sea lamprey (Petromyzon marinus) is one of few vertebrate species known to reproducibly eliminate large fractions of its genome during normal embryonic development. This germline-specific DNA is lost in the form of large fragments, including entire chromosomes, and available evidence suggests that DNA elimination ...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes10100832

    authors: Timoshevskiy VA,Timoshevskaya NY,Smith JJ

    更新日期:2019-10-22 00:00:00

  • PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids.

    abstract::Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimenta...

    journal_title:Genes

    pub_type: 杂志文章

    doi:10.3390/genes11121431

    authors: Singh V,Sharma A,Dehzangi A,Tsunoda T

    更新日期:2020-11-28 00:00:00