Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits

European Journal of Human Genetics

Volumn 20, Issue 1, 2012, Pages 77-83

  Zaboli, Ghazal ^a   Ameur, Adam ^a   Igl, Wilmar ^a   Johansson, Åsa ^a   Hayward, Caroline ^b   Vitart, Veronique ^b   Campbell, Susan ^b   Zgaga, Lina ^c,j   Polasek, Ozren ^c   Schmitz, Gerd ^d   Van Duijn, Cornelia ^e   Oostra, Ben ^e   Pramstaller, Peter ^f,g,h   Hicks, Andrew ^f   Meitinger, Tomas ⁱ   Rudan, Igor ^j,k   Wright, Alan ^b   Wilson, James F ^k   Campbell, Harry ^k   Gyllensten, Ulf ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b WESTERN GENERAL HOSPITAL   (United Kingdom)

^c UNIVERSITY OF ZAGREB   (Croatia)

^d UNIVERSITY HOSPITAL REGENSBURG   (Germany)

^e ERASMUS MEDICAL CENTER   (Netherlands)

^f INSTITUTE FOR RENEWABLE ENERGY   (Italy)

^g General Central Hospital   (Italy)

^h UNIVERSITY OF LÜBECK   (Germany)

ⁱ INSTITUTE OF EPIDEMIOLOGY   (Germany)

^j UNIVERSITY OF SPLIT   (Croatia)

^k UNIVERSITY OF EDINBURGH   (United Kingdom)

more..

Author keywords

indels; next generation DNA sequencing; pooling; SNP; SOLiD

Indexed keywords

DNA;

ARTICLE; CROATIA; DNA SEQUENCE; GENE FREQUENCY; GENETIC TRAIT; GENETIC VARIABILITY; GENOTYPE; HUMAN; INDEL MUTATION; ITALY; LIPID BLOOD LEVEL; NETHERLANDS; POLYMERASE CHAIN REACTION; POPULATION GENETICS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; SWEDEN; UNITED KINGDOM; URIC ACID BLOOD LEVEL;

CHROMOSOMES, HUMAN; COHORT STUDIES; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENETIC TESTING; GENOME, HUMAN; GENOMIC STRUCTURAL VARIATION; GENOTYPE; GLUCOSE TRANSPORT PROTEINS, FACILITATIVE; HUMANS; INDEL MUTATION; LIPASE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 83255185197     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2011.138     Document Type: Article

References (30)

1. Plomin R, Haworth CM, Davis OS: Common disorders are quantitative traits. Nat Rev 2009; 10: 872-878.
2. Sherry ST, Ward MH, Kholodov M et al: dbSNP: the NCBI database of genetic variation. Nucleic acids Res 2001; 29: 308-311. (Pubitemid 32054478)
3. Lango Allen H, Estrada K, Lettre G et al: Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 2010; 467: 832-838.
4. Frazer KA, Murray SS, Schork NJ, Topol EJ: Human genetic variation and its contribution to complex traits. Nature Rev 2009; 10: 241-251.
5. Altshuler DM, Gibbs RA, Peltonen L et al: Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467: 52-58.
6. Li Y, Vinckenbosch N, Tian G et al: Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 2010; 42: 969-972.
7. Durbin RM, Abecasis GR, Altshuler DL et al: A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061-1073.
8. Voelkerding KV, Dames SA, Durtschi JD: Next-generation sequencing: from basic research to diagnostics. Clin Chem 2009; 55: 641-658.
9. Ingman M, Gyllensten U: SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet 2009; 17: 383-386.
10. Out AA, van Minderhout IJ, Goeman JJ et al: Deep sequencing to reveal new variants in pooled DNA samples. Hum Mut 2009; 30: 1703-1712.
11. Druley TE, Vallania FL, Wegner DJ et al: Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 2009; 6: 263-265.
12. Bansal V, Harismendy O, Tewhey R et al: Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res 2010; 20: 537-545.
13. Prabhu S, Pe'er I: Overlapping pools for high-throughput targeted resequencing. Genome Res 2009; 19: 1254-1261.
14. Erlich Y, Chang K, Gordon A et al: DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 2009; 19: 1243-1253.
15. Shental N, Amir A, Zuk O: Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Res 2010.
16. Hicks AA, Pramstaller PP, Johansson A et al: Genetic determinants of circulating sphingolipid concentrations in European populations. PLoS Genetics 2009; 5: e1000672.
17. Vitart V, Rudan I, Hayward C et al: SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout. Nat Genet 2008; 40: 437-442. (Pubitemid 351450879)
18. Mascalzoni D, Janssens AC, Stewart A et al: Comparison of participant information and informed consent forms of five European studies in genetic isolated populations. Eur J Hum Genet 2010; 18: 296-302.
19. Johansson A, Marroni F, Hayward C et al: Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis. Hum Mol Genet 2009; 18: 373-380.
20. McQuillan R, Leutenegger AL, Abdel-Rahman R et al: Runs of homozygosity in European populations. Am J Hum Genet 2008; 83: 359-372.
21. Rudan I, Campbell H, Rudan P: Genetic epidemiological studies of eastern Adriatic Island isolates, Croatia: objective and strategies. Collegium Antropologicum 1999; 23: 531-546.
22. Vitart V, Biloglav Z, Hayward C et al: 3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia. Eur J Hum Genet 2006; 14: 478-487.
23. Pattaro C, Marroni F, Riegler A et al: The genetic study of three population microisolates in South Tyrol (MICROS): study design and epidemiological perspectives. BMC Med Genet 2007; 8: 29.
24. Aulchenko YS, Heutink P, Mackay I et al: Linkage disequilibrium in young genetically isolated Dutch population. Eur J Hum Genet 2004; 12: 527-534. (Pubitemid 39077160)
25. Frey B: SB. Biochemica 1995; 2: 34-35.
26. Ameur A, Wetterbom A, Feuk L, Gyllensten U: Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol 2010; 11: R34.
27. Kaiser J: DNA sequencing. A plan to capture human diversity in 1000 genomes. Science (New York, NY) 2008; 319: 395. (Pubitemid 351160548)
28. Kent WJ, Sugnet CW, Furey TS et al: The human genome browser at UCSC. Genome Res 2002; 12: 996-1006. (Pubitemid 34662293)
29. Sham P, Bader JS, Craig I, O'Donovan M, Owen M: DNA Pooling: a tool for large-scale association studies. Nat Rev 2002; 3: 862-871. (Pubitemid 35303518)
30. Craig DW, Pearson JV, Szelinger S et al: Identification of genetic variants using barcoded multiplexed sequencing. Nat Methods 2008; 5: 887-893.