Systematic Pharmacogenomics Analysis of a Malay Whole Genome: Proof of Concept for Personalized Medicine
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{"title"=>"Systematic Pharmacogenomics Analysis of a Malay Whole Genome: Proof of Concept for Personalized Medicine", "type"=>"journal", "authors"=>[{"first_name"=>"Mohd Zaki", "last_name"=>"Salleh", "scopus_author_id"=>"7004532444"}, {"first_name"=>"Lay Kek", "last_name"=>"Teh", "scopus_author_id"=>"7005663493"}, {"first_name"=>"Lian Shien", "last_name"=>"Lee", "scopus_author_id"=>"55835942300"}, {"first_name"=>"Rose Iszati", "last_name"=>"Ismet", "scopus_author_id"=>"55836650900"}, {"first_name"=>"Ashok", "last_name"=>"Patowary", "scopus_author_id"=>"24465559900"}, {"first_name"=>"Kandarp", "last_name"=>"Joshi", "scopus_author_id"=>"55835315900"}, {"first_name"=>"Ayesha", "last_name"=>"Pasha", "scopus_author_id"=>"55835232900"}, {"first_name"=>"Azni Zain", "last_name"=>"Ahmed", "scopus_author_id"=>"7403428697"}, {"first_name"=>"Roziah Mohd", "last_name"=>"Janor", "scopus_author_id"=>"25825047300"}, {"first_name"=>"Ahmad Sazali", "last_name"=>"Hamzah", "scopus_author_id"=>"6701857973"}, {"first_name"=>"Aishah", "last_name"=>"Adam", "scopus_author_id"=>"16183304500"}, {"first_name"=>"Khalid", "last_name"=>"Yusoff", "scopus_author_id"=>"7005545505"}, {"first_name"=>"Boon Peng", "last_name"=>"Hoh", "scopus_author_id"=>"36923912500"}, {"first_name"=>"Fazleen Haslinda Mohd", "last_name"=>"Hatta", "scopus_author_id"=>"54923532700"}, {"first_name"=>"Mohamad Izwan", "last_name"=>"Ismail", "scopus_author_id"=>"55834817700"}, {"first_name"=>"Vinod", "last_name"=>"Scaria", "scopus_author_id"=>"8876981800"}, {"first_name"=>"Sridhar", "last_name"=>"Sivasubbu", "scopus_author_id"=>"8752046300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24009664", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0071554", "scopus"=>"2-s2.0-84882970247", "pui"=>"369642393", "sgr"=>"84882970247"}, "id"=>"0ec4fc6b-7577-3b0e-9919-6cd3df11aca8", "abstract"=>"BACKGROUND: With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine. METHODS: Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences. PRINCIPAL FINDINGS: Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings. CONCLUSIONS: The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.", "link"=>"http://www.mendeley.com/research/systematic-pharmacogenomics-analysis-malay-whole-genome-proof-concept-personalized-medicine", "reader_count"=>63, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>6, "Student > Master"=>12, "Other"=>3, "Student > Bachelor"=>10, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>6, "Student > Master"=>12, "Other"=>3, "Student > Bachelor"=>10, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>20, "Medicine and Dentistry"=>14, "Arts and Humanities"=>2, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Psychology"=>2, "Social Sciences"=>2, "Computer Science"=>6, "Nursing and Health Professions"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>14}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>2}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>6}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>3, "Italy"=>1, "United Kingdom"=>1, "France"=>1}, "group_count"=>4}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1181096"], "description"=>"<p>Summary of the analysis workflow for the Malaysian genome.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "workflow", "malaysian"], "article_id"=>781182, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_analysis_workflow_for_the_Malaysian_genome_/781182", "title"=>"Summary of the analysis workflow for the Malaysian genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181098"], "description"=>"<p>Comparative SNV analysis of other personal genomes with the Malaysian genome.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "snv", "genomes", "malaysian"], "article_id"=>781183, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_SNV_analysis_of_other_personal_genomes_with_the_Malaysian_genome_/781183", "title"=>"Comparative SNV analysis of other personal genomes with the Malaysian genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181108"], "description"=>"<p>Disrupted transporters and targets are depicted in the second and fourth columns of the diagram while enzymes involved in pathways are shown in the third columns. First column shows the drugs which are affected due to disrupted genes in the Malay individual.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "diagram", "pathway", "genes", "disrupted", "malay"], "article_id"=>781191, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_diagram_showing_drug_pathway_for_genes_disrupted_in_the_Malay_genome_/781191", "title"=>"Flow diagram showing drug pathway for genes disrupted in the Malay genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181109"], "description"=>"<p>The bars in blue show risk magnitude for alleles showing association with lung cancer while the bars in red show risk magnitude for prostate cancer associated alleles.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "malay"], "article_id"=>781192, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Disease_risk_plot_for_the_Malay_genome_/781192", "title"=>"Disease risk plot for the Malay genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181110"], "description"=>"<p>$: Positioning of variations to genomic loci with respect to RefGene.</p>*<p>: Including indels.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "snvs", "malay"], "article_id"=>781193, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Database_mapping_of_SNVs_found_in_the_Malay_individual_/781193", "title"=>"Database mapping of SNVs found in the Malay individual.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181111"], "description"=>"<p>Predicted number of potentially damaging and deleterious variants as predicted by computational tools SIFT and Polyphen-2.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "damaging", "deleterious", "variants", "computational", "tools", "sift"], "article_id"=>781194, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Predicted_number_of_potentially_damaging_and_deleterious_variants_as_predicted_by_computational_tools_SIFT_and_Polyphen_2_/781194", "title"=>"Predicted number of potentially damaging and deleterious variants as predicted by computational tools SIFT and Polyphen-2.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181112"], "description"=>"<p>Summary of SNVs found in the Malay genome and overlaps with dbSNP and 1000 Genome datasets.</p>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "snvs", "malay", "genome", "overlaps", "dbsnp", "1000"], "article_id"=>781195, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_SNVs_found_in_the_Malay_genome_and_overlaps_with_dbSNP_and_1000_Genome_datasets_/781195", "title"=>"Summary of SNVs found in the Malay genome and overlaps with dbSNP and 1000 Genome datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-23 01:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1181119", "https://ndownloader.figshare.com/files/1181120", "https://ndownloader.figshare.com/files/1181121", "https://ndownloader.figshare.com/files/1181122", "https://ndownloader.figshare.com/files/1181123", "https://ndownloader.figshare.com/files/1181124", "https://ndownloader.figshare.com/files/1181125", "https://ndownloader.figshare.com/files/1181126", "https://ndownloader.figshare.com/files/1181127", "https://ndownloader.figshare.com/files/1181128"], "description"=>"<div><p>Background</p><p>With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine.</p><p>Methods</p><p>Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences.</p><p>Principal Findings</p><p>Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings.</p><p>Conclusions</p><p>The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.</p></div>", "links"=>[], "tags"=>["biotechnology", "pharmacogenomics", "Computational biology", "genomics", "Genome analysis tools", "Genome databases", "Genome sequencing", "genetics", "Human genetics", "Personalized medicine", "Genomic medicine", "Clinical genetics", "malay", "personalized"], "article_id"=>781202, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mohd Zaki Salleh", "Lay Kek Teh", "Lian Shien Lee", "Rose Iszati Ismet", "Ashok Patowary", "Kandarp Joshi", "Ayesha Pasha", "Azni Zain Ahmed", "Roziah Mohd Janor", "Ahmad Sazali Hamzah", "Aishah Adam", "Khalid Yusoff", "Boon Peng Hoh", "Fazleen Haslinda Mohd Hatta", "Mohamad Izwan Ismail", "Vinod Scaria", "Sridhar Sivasubbu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0071554.s001", "https://dx.doi.org/10.1371/journal.pone.0071554.s002", "https://dx.doi.org/10.1371/journal.pone.0071554.s003", "https://dx.doi.org/10.1371/journal.pone.0071554.s004", "https://dx.doi.org/10.1371/journal.pone.0071554.s005", "https://dx.doi.org/10.1371/journal.pone.0071554.s006", "https://dx.doi.org/10.1371/journal.pone.0071554.s007", "https://dx.doi.org/10.1371/journal.pone.0071554.s008", "https://dx.doi.org/10.1371/journal.pone.0071554.s009", "https://dx.doi.org/10.1371/journal.pone.0071554.s010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Systematic_Pharmacogenomics_Analysis_of_a_Malay_Whole_Genome_Proof_of_Concept_for_Personalized_Medicine_/781202", "title"=>"Systematic Pharmacogenomics Analysis of a Malay Whole Genome: Proof of Concept for Personalized Medicine", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-08-23 01:51:11"}

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Relative Metric

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