Co-barcoded sequence reads from long DNA fragments: A cost-effective solution for "perfect genome" sequencing

Frontiers in Genetics

Volumn 5, Issue JAN, 2015, Pages

  Peters, Brock A ^a,b   Liu, Jia ^a   Drmanac, Radoje ^a,b  

^a Complete Genomics Inc ^*  (United States)

^b BGI SHENZHEN   (China)

Author keywords

"Perfect genome"; De novo assembly; Haplotyping; LFR; MPS; NGS; WGS; Whole genome sequencing

Indexed keywords

DNA FRAGMENT;

ARTICLE; COST EFFECTIVENESS ANALYSIS; DNA BARCODING; DNA PURIFICATION; DNA SEQUENCE; GENE DELETION; GENE DUPLICATION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; HAPLOTYPE; HUMAN; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION;

EID: 84924269700     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00466     Document Type: Article

References (38)

1. Adey, A., Kitzman, J. O., Burton, J. N., Daza, R., Kumar, A., Christiansen, L.,et al. (2014). In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res. 24, 2041-2049. doi: 10.1101/gr.178319.114
2. Ahn, S. M., Kim, T. H., Lee, S., Kim, D., Ghang, H., Kim, D. S.,et al. (2009). The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19, 1622-1629. doi: 10.1101/gr.092197.109
3. Al Turki, S., Manickaraj, A. K., Mercer, C. L., Gerety, S. S., Hitz, M. P., Lindsay, S.,et al. (2014). Rare variants in NR2F2 cause congenital heart defects in humans. Am. J. Hum. Genet. 94, 574-585. doi: 10.1016/j.ajhg.2014.03.007
4. Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G.,et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59. doi: 10.1038/nature07517
5. Bolnick, J. M., Kilburn, B. A., Bajpayee, S., Reddy, N., Jeelani, R., Crone, B.,et al. (2014). Trophoblast retrieval and isolation from the cervix (TRIC) for noninvasive prenatal screening at 5 to 20 weeks of gestation. Fertil. Steril. 102, 135-142.e6. doi: 10.1016/j.fertnstert.2014.04.008
6. Carnevali, P., Baccash, J., Halpern, A. L., Nazarenko, I., Nilsen, G. B., Pant, K. P.,et al. (2012). Computational techniques for human genome resequencing using mated gapped reads. J. Comput. Biol. 19, 279-292. doi: 10.1089/cmb.2011.0201
7. Dean, F. B., Hosono, S., Fang, L., Wu, X., Faruqi, A. F., Bray-Ward, P.,et al. (2002). Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U.S.A. 99, 5261-5266. doi: 10.1073/pnas.082089499
8. de Koning, A. P., Gu, W., Castoe, T. A., Batzer, M. A., and Pollock, D. D. (2011). Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 7:e1002384. doi: 10.1371/journal.pgen.1002384
9. de Vree, P. J., De Wit, E., Yilmaz, M., Van De Heijning, M., Klous, P., Verstegen, M. J.,et al. (2014). Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat. Biotechnol. 32, 1019-1025. doi: 10.1038/nbt.2959
10. Drmanac, R. (2006). Nucleic acid analysis by random mixtures of non-overlapping Fragments. Patent WO 2006/138284 A2.
11. Drmanac, R. (2012). Medicine. The ultimate genetic test. Science 336, 1110-1112. doi: 10.1126/science.1221037
12. Drmanac, R., and Crkvenjakov, R. (1990). Prospects for a miniaturized, simplified, and frugal human genome project. Sci. Yugoslavica 16, 97-107.
13. Drmanac, R., Peters, B. A., Alexeev, A., and Hong, P. (2011). Methods and Compositions for Long Fragment Read Sequencing. Patent US 8592150 B2.
14. Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G.,et al. (2010). Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78-81. doi: 10.1126/science.1181498
15. Epi, K. C., Epilepsy Phenome/Genome, P., Allen, A. S., Berkovic, S. F., Cossette, P., Delanty, N.,et al. (2013). De novo mutations in epileptic encephalopathies. Nature 501, 217-221. doi: 10.1038/nature12439
16. Fromer, M., Pocklington, A. J., Kavanagh, D. H., Williams, H. J., Dwyer, S., Gormley, P.,et al. (2014). De novo mutations in schizophrenia implicate synaptic networks. Nature 506, 179-184. doi: 10.1038/nature12929
17. Gilissen, C., Hehir-Kwa, J. Y., Thung, D. T., Van De Vorst, M., Van Bon, B. W., Willemsen, M. H.,et al. (2014). Genome sequencing identifies major causes of severe intellectual disability. Nature 511, 344-347. doi: 10.1038/nature13394
18. Green, E. D., Guyer, M. S., and National Human Genome Research, I. (2011). Charting a course for genomic medicine from base pairs to bedside. Nature 470, 204-213. doi: 10.1038/nature09764
19. Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G.,et al. (2012). Rate of de novo mutations and the importance of father's age to disease risk. Nature 488, 471-475. doi: 10.1038/nature11396
20. Kuleshov, V., Xie, D., Chen, R., Pushkarev, D., Ma, Z., Blauwkamp, T.,et al. (2014). Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol. 32, 261-266. doi: 10.1038/nbt.2833
21. Lawrence, M. S., Stojanov, P., Mermel, C. H., Robinson, J. T., Garraway, L. A., Golub, T. R.,et al. (2014). Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501. doi: 10.1038/nature12912
22. Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P.,et al. (2007). The diploid genome sequence of an individual human. PLoS Biol. 5:e254. doi: 10.1371/journal.pbio.0050254
23. MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K.,et al. (2012). A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828. doi: 10.1126/science.1215040
24. Michaelson, J. J., Shi, Y., Gujral, M., Zheng, H., Malhotra, D., Jin, X.,et al. (2012). Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 151, 1431-1442. doi: 10.1016/j.cell.2012.11.019
25. O'Roak, B. J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B. P.,et al. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246-250. doi: 10.1038/nature10989
26. Peters, B. A., Kermani, B. G., Sparks, A. B., Alferov, O., Hong, P., Alexeev, A.,et al. (2012). Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487, 190-195. doi: 10.1038/nature11236
27. Purcell, S. M., Moran, J. L., Fromer, M., Ruderfer, D., Solovieff, N., Roussos, P.,et al. (2014). A polygenic burden of rare disruptive mutations in schizophrenia. Nature 506, 185-190. doi: 10.1038/nature12975
28. Rios, J., Stein, E., Shendure, J., Hobbs, H. H., and Cohen, J. C. (2010). Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum. Mol. Genet. 19, 4313-4318. doi: 10.1093/hmg/ddq352
29. Roach, J. C., Glusman, G., Smit, A. F., Huff, C. D., Hubley, R., Shannon, P. T.,et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636-639. doi: 10.1126/science.1186802
30. Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J.,et al. (2012). De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237-241. doi: 10.1038/nature10945
31. Schaaf, C. P., Gonzalez-Garay, M. L., Xia, F., Potocki, L., Gripp, K. W., Zhang, B.,et al. (2013). Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism. Nat. Genet. 45, 1405-1408. doi: 10.1038/ng.2776
32. Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., Mccutcheon, J. P., Rosenbaum, A. M.,et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728-1732. doi: 10.1126/science.1117389
33. Tennessen, J. A., Bigham, A. W., O'connor, T. D., Fu, W., Kenny, E. E., Gravel, S.,et al. (2012). Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69. doi: 10.1126/science.1219240
34. Veltman, J. A., and Brunner, H. G. (2012). De novo mutations in human genetic disease. Nat. Rev. Genet. 13, 565-575. doi: 10.1038/nrg3241
35. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L.,et al. (2008). The diploid genome sequence of an Asian individual. Nature 456, 60-65. doi: 10.1038/nature07484
36. Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., Mcguire, A.,et al. (2008). The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876. doi: 10.1038/nature06884
37. Yang, Y., Muzny, D. M., Reid, J. G., Bainbridge, M. N., Willis, A., Ward, P. A.,et al. (2013). Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N. Engl. J. Med. 369, 1502-1511. doi: 10.1056/NEJMoa1306555
38. Zong, C., Lu, S., Chapman, A. R., and Xie, X. S. (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338, 1622-1626. doi: 10.1126/science.1229164