Whole genome sequence of a turkish individual

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Dogan, Haluk ^a   Can, Handan ^a   Otu, Hasan H ^a  

^a ISTANBUL BILGI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE SEQUENCE; GENETIC IDENTIFICATION; GENETIC PROCEDURES; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; PAIRED END METHOD; READ DEPTH METHOD; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TURKEY (REPUBLIC); WHOLE GENOME SEQUENCING;

CHROMOSOME MAPPING; CODON; GENE REGULATORY NETWORKS; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDEL MUTATION; MOLECULAR SEQUENCE ANNOTATION; OPEN READING FRAMES; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; TURKEY;

EID: 84897471361     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085233     Document Type: Article

References (38)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921. (Pubitemid 32165345)
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351. (Pubitemid 32173090)
3. Consortium IHGS (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
4. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254.
5. 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. (Pubitemid 351550870)
6. Pritchard JK (2011) Whole-genome sequencing data offer insights into human demography. Nat Genet 43: 923-925.
7. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
8. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
9. Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
10. 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.
11. Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, et al. (2010) Wholegenome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet 42: 931-936.
12. Ju YS, Kim JI, Kim S, Hong D, Park H, et al. (2011) Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet 43: 745-752.
13. Kim JI, Ju YS, Park H, Kim S, Lee S, et al. (2009) A highly annotated wholegenome sequence of a Korean individual. Nature 460: 1011-1015.
14. Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, et al. (2010) Sequencing and analysis of an Irish human genome. Genome Biol 11: R91.
15. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
16. Akin H, Onay H, Turker E, Cogulu O, Ozkinay F (2010) MEFV mutations in patients with Familial Mediterranean Fever from the Aegean region of Turkey. Mol Biol Rep 37: 93-98.
17. Erbilgin Y, Sayitoglu M, Hatirnaz O, Dogru O, Akcay A, et al. (2010) Prognostic significance of NOTCH1 and FBXW7 mutations in pediatric TALL. Dis Markers 28: 353-360.
18. Yazici Y, Yurdakul S, Yazici H (2010) Behcet's syndrome. Curr Rheumatol Rep 12: 429-435.
19. Krueger F, Kreck B, Franke A, Andrews SR (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9: 145-151.
20. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
21. Lassmann T, Hayashizaki Y, Daub CO (2011) SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27: 130-131.
22. Peng Y, Leung H, Yiu S, Chin F. IDBA-A Practical Iterative de Bruijn Graph De Novo Assembler; 2010. Springer. pp. 426-440.
23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
24. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
25. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92.
26. Abyzov A, Urban AE, Snyder M, Gerstein M (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21: 974-984.
27. Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, et al. (2012) CLEVER: clique-enumerating variant finder. Bioinformatics 28: 2875-2882.
28. Colella S, Yau C, Taylor JM, Mirza G, Butler H, et al. (2007) QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 35: 2013-2025. (Pubitemid 47061667)
29. Remmers EF, Cosan F, Kirino Y, Ombrello MJ, Abaci N, et al. (2010) Genome-wide association study identifies variants in the MHC class I, IL10, and IL23RIL12RB2 regions associated with Behcet's disease. Nat Genet 42: 698-702.
30. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909. (Pubitemid 44141658)
31. Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford) 2010: baq020.
32. Becamel C, Alonso G, Galeotti N, Demey E, Jouin P, et al. (2002) Synaptic multiprotein complexes associated with 5-HT(2C) receptors: a proteomic approach. EMBO J 21: 2332-2342. (Pubitemid 34546706)
33. Cheng NH, Zhang W, Chen WQ, Jin J, Cui X, et al. (2011) A mammalian monothiol glutaredoxin, Grx3, is critical for cell cycle progression during embryogenesis. FEBS J 278: 2525-2539.
34. Golebiowski F, Matic I, Tatham MH, Cole C, Yin Y, et al. (2009) System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2: ra24.
35. Ni Z, Karaskov E, Yu T, Callaghan SM, Der S, et al. (2005) Apical role for BRG1 in cytokine-induced promoter assembly. Proc Natl Acad Sci U S A 102: 14611-14616. (Pubitemid 41457105)
36. Bruderer R, Tatham MH, Plechanovova A, Matic I, Garg AK, et al. (2011) Purification and identification of endogenous polySUMO conjugates. EMBO Rep 12: 142-148.
37. Ougolkov AV, Bone ND, Fernandez-Zapico ME, Kay NE, Billadeau DD (2007) Inhibition of glycogen synthase kinase-3 activity leads to epigenetic silencing of nuclear factor kappaB target genes and induction of apoptosis in chronic lymphocytic leukemia B cells. Blood 110: 735-742. (Pubitemid 47105412)
38. Inoue H, Tsukita K, Iwasato T, Suzuki Y, Tomioka M, et al. (2003) The crucial role of caspase-9 in the disease progression of a transgenic ALS mouse model. EMBO J 22: 6665-6674. (Pubitemid 38009612)