Systematic Pharmacogenomics Analysis of a Malay Whole Genome: Proof of Concept for Personalized Medicine

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  Salleh, Mohd Zaki ^a   Teh, Lay Kek ^a   Lee, Lian Shien ^a   Ismet, Rose Iszati ^a   Patowary, Ashok ^b   Joshi, Kandarp ^b   Pasha, Ayesha ^b   Ahmed, Azni Zain ^a   Janor, Roziah Mohd ^a   Hamzah, Ahmad Sazali ^a   Adam, Aishah ^a   Yusoff, Khalid ^a   Hoh, Boon Peng ^a   Hatta, Fazleen Haslinda Mohd ^a   Ismail, Mohamad Izwan ^a   Scaria, Vinod ^b   Sivasubbu, Sridhar ^b  

^a UNIVERSITI TEKNOLOGI MARA   (Malaysia)

^b CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ADULT; ARTICLE; CONTROLLED STUDY; DISEASE MARKER; DRUG RESPONSE; ETHNIC GROUP; FAMILY HISTORY; GENE FREQUENCY; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; MALAY; MALE; OUTCOME ASSESSMENT; PATIENT ASSESSMENT; PERSONALIZED MEDICINE; PHARMACOGENOMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

ASIAN CONTINENTAL ANCESTRY GROUP; BIOLOGICAL MARKERS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDIVIDUALIZED MEDICINE; MALAYSIA; MALE; MIDDLE AGED; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; QUANTITATIVE TRAIT, HERITABLE;

EID: 84882970247     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071554     Document Type: Article

References (39)

1. Mardis ER, (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
2. Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, et al. (2010) Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2: 20ra14.
3. ten BoschJR, Grody WW, (2008) Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J Mol Diagn 10: 484-492.
4. Pool JE, Hellmann I, Jensen JD, Nielsen R, (2010) Population genetic inference from genomic sequence variation. Genome Res 20: 291-300.
5. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, et al. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 19: 1622-1629.
6. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, et al. (2010) Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet 42: 931-936.
7. Kim JI, Ju YS, Park H, Kim S, Lee S, et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460: 1011-1015.
8. Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, et al. (2012) Systematic analysis and functional annotation of variations in the genome of an Indian individual. Human Mutation 33: 1133-1140.
9. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The Diploid Genome Sequence of an Individual Human. PLoSBIOLOGY 5: 2113-2144.
10. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463: 943-947.
11. Wang J, Wang W, Li R, Li Y, Tian G, et al. (2008) The diploid genome sequence of an Asian individual. Nature 456: 60-65.
12. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876.
13. Genomes Project C (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
14. Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, et al. (2012) Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics 13: 440.
15. Dissanayake VHW, Samarakoon PS, Scaria V, Patowary A, Sivasubbu S, et al. (2011) The Sri Lankan Personal Genome Project: an overview. Sri Lanka Journal of Bio-Medical Informatics 2.
16. Cordero P, Ashley EA, (2012) Whole-Genome Sequencing in Personalized Therapeutics. Clinical Pharmacology & Therapeutics 91: 1001-1009.
17. Belle DJ, Singh H (2008) Genetic factors in drug metabolism. Am Fam Physician.
18. Shukla P, Gupta D, Pant MC, Parmar D, (2012) CYP 2D6 polymorphism: a predictor of susceptibility and response to chemoradiotherapy in head and neck cancer. J Cancer Res Ther 8: 40-45.
19. Yoo HD, Lee YB, (2011) Interplay of pharmacogenetic variations in ABCB1 transporters and cytochrome P450 enzymes. Arch Pharm Res 34: 1817-1828.
20. Pirmohamed M (2001) Pharmacogenetics and pharmacogenomics. Br J Clin Pharmacol.
21. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, et al. (2007) The NCBI dbGaP database of genotypes and phenotypes. Nat Genet 39: 1181-1186.
22. Hatin WI, Nur-Shafawati AR, Zahri M-K, Xu S, Jin L, et al. (2011) Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups. PLoS ONE 6: e18312.
23. The HUGO Pan-Asian SNP Consortium, et al. (2009) Mapping Human Genetic Diversity in Asia (2009) Science. 326: 1541-1545.
24. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
25. Karolchik D, (2003) The UCSC Genome Browser Database. Nucleic Acids Research 31: 51-54.
26. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
27. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, et al. (2011) The variant call format and VCFtools. Bioinformatics 27: 2156-2158.
28. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Research 29: 308-311.
29. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW, (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenetic and Genome Research 115: 205-214.
30. Wang K, Li M, Hakonarson H, (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38: e164-e164.
31. Moore B, Fan G, Eilbeck K, (2010) SOBA: sequence ontology bioinformatics analysis. Nucleic Acids Research 38: W161-W164.
32. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research 36: D901-D906.
33. Sangkuhl K, Berlin DS, Altman RB, Klein TE, (2008) PharmGKB: Understanding the Effects of Individual Genetic Variants. Drug Metabolism Reviews 40: 539-551.
34. Cariaso M, Lennon G, (2012) SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. Nucleic Acids Research 40: D1308-D1312.
35. Ng PC, (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Research 31: 3812-3814.
36. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
37. Donlin MJ (2002) Using the Generic Genome Browser (GBrowse). Current Protocols in Bioinformatics: John Wiley & Sons, Inc.
38. Van Hemert JL, Dickerson JA, (2010) PathwayAccess: CellDesigner plugins for pathway databases. Bioinformatics 26: 2345-2346.
39. Kawamoto K, Lobach DF, Willard HF, Ginsburg GS, (2009) A national clinical decision support infrastructure to enable the widespread and consistent practice of genomic and personalized medicine. BMC Med Inform Decis Mak 9: 17.