High-Throughput Sequencing Technology and Its Applications in Human Disease

Shuyang Deng

2016

Abstract

The high-throughput sequencing technology (HTS), also known as next generation sequencing, refers to the technological advances in DNA sequencing instrumentation that enable the generation of hundreds of thousands to millions of sequence reads per run. The advances of high-throughput, low cost and short timeconsuming democratizes HTS and paves the way for the development of a large number of novel HTS applications in basic science as well as in translational research areas, such as clinical diagnostics, agrigenomics, and forensic science. In recent years, HTS has been widely applied in solving biological problems, especially in human diseases field. In this review, we provide an overview of the evolution of HTS and discuss three important sequencing strategies HTS adopted, Roche/454, Illumina, SOLiD. We also take the example of exome sequencing and ChIP to summarize the application of HTS in human diseases.

References

  1. Chung W. J., Long J., Cheng J., et al., 2015, Next generation sequencing analysis of genetically engineered mouse models of human cancers, Cancer Research, 75(15 Supplement): 2987-2987.
  2. Comas I., Gil A., 2016, Next generation sequencing for the diagnostics and epidemiology of tuberculosis, Enfermedades Infecciosas y Microbiología Clínica, 34: 32.
  3. Cox-Foster, D. L. et al., 2007, A metagenomic survey of microbes in honey bee colony collapse disorder, Science 318, 283-287.
  4. Deeb K. K., Hohman C. M., Risch N. F., et al., 2015, Routine clinical mutation profiling of non-small cell lung cancer using next-generation sequencing, Archives of Pathology and Laboratory Medicine, 139(7): 913-921.
  5. Georgiou G., Ippolito G. C., Beausang J., et al., 2014, The promise and challenge of high-throughput sequencing of the antibody repertoire, Nature biotechnology, 32(2): 158-168.
  6. Glessner J. T., Bick A. G., Ito K., et al., 2014, Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data, Circulation research, 115(10): 884- 896.
  7. Green, R. E. et al., 2006, Analysis of one million base pairs of Neanderthal DNA, Nature 444, 330-336.
  8. Gu Y., Lu K., Yang G., et al., 2014, Mutation spectrum of six genes in Chinese phenylketonuria patients obtained through next-generation sequencing, PLoS One, 9(4): e94100- e94100.
  9. Harbour J. W., Onken M. D., Roberson E. D. O., et al., 2010, Frequent mutation of BAP1 in metastasizing uveal melanomas, Science, 330(6009): 1410-1413.
  10. Hurtado A., Holmes K. A., Ross-Innes C. S., et al., 2011, FOXA1 is a key determinant of estrogen receptor function and endocrine response, Nature genetics, 43(1): 27-33.
  11. Johnson D. S., Mortazavi A., Myers R. M., et al., 2007, Genome-wide mapping of in vivo protein-DNA interactions, Science, 316 (5830): 1497-1502.
  12. Jones S., Wang T. L., Shih I. M., et al., 2010, Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma, Science, 330(6001): 228- 231.
  13. Krauskopf J., Caiment F., Claessen S. M., et al., 2015, Application of high-throughput sequencing to circulating microRNAs reveals novel biomarkers for drug-induced liver injury, Toxicological Sciences, 143(2): 268-276.
  14. Lee B. K., Iyer V. R., 2012, Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation, Journal of Biological Chemistry, 287(37): 30906- 30913.
  15. Li M., Zhao H., Zhang X., et al., 2011, Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma, Nature genetics, 43(9): 828- 829.
  16. Lin B., Wang J., Hong X., et al., 2009, Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor, PloS one, 4(8): e6589.
  17. Liu, L. et al., 2012, Comparison of next-generation sequencing systems, J. Biomed. Biotechnol, 251364.
  18. Mardis E. R., 2008, Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet, 9: 387-402.
  19. Ng S. B., Turner E. H., Robertson P. D., et al., 2009, Targeted capture and massively parallel sequencing of 12 human exomes, Nature, 461(7261): 272-276.
  20. Ng S. B., Buckingham K. J., Lee C., et al., 2010, Exome sequencing identifies the cause of a mendelian disorder, Nature genetics, 42(1): 30-35.
  21. Norton M. E., Jacobsson B., Swamy G. K., et al., 2015, Cell-free DNA analysis for noninvasive examination of trisomy, New England Journal of Medicine, 372(17): 1589-1597.
  22. Park, P. J., 2009, ChIP-seq: advantages and challenges of a maturing technology, Nat. Rev. Genet, 10: 669-680.
  23. Redin C., Gérard B., Lauer J., et al., 2014, Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing. Journal of medical genetics, jmedgenet-2014-102554.
  24. Renkema K. Y., Stokman M. F., Giles R. H., et al., 2014, Next-generation sequencing for research and diagnostics in kidney disease, Nature Reviews Nephrology, 10(8): 433-444.
  25. Reuter J. A., Spacek D. V., Snyder M. P., 2015. Highthroughput sequencing technologies, Molecular cell, 58(4): 586-597.
  26. Robertson G., Hirst M., Bainbridge M., et al., 2007, Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing, Nature methods, 4(8): 651-657.
  27. Ross-Innes C. S., Stark R., Teschendorff A. E., et al., 2012, Differential oestrogen receptor binding is associated with clinical outcome in breast cancer, Nature, 481 (7381): 389-393.
  28. Saare M., Rekker K., Laisk-Podar T., et al., 2014, Highthroughput sequencing approach uncovers the miRNome of peritoneal endometriotic lesions and adjacent healthy tissues, PloS one, 9(11): e112630.
  29. Schones D. E., Zhao K., 2008, Genome-wide approaches to studying chromatin modifications, Nat Rev Genet, 9(3): 179-191.
  30. Seshagiri S., Stawiski E. W., Durinck S., et al., 2012, Recurrent R-spondin fusions in colon cancer, Nature, 488(7413): 660-664.
  31. Tawfik D. S., Griffiths A. D., 1998, Man-made cell-like compartments for molecular evolution, Nat Biotechnol, 16 (7): 652-656.
  32. Thibodeau B., Cardenas P. Y., Ahmed S., et al., 2016, Next generation sequencing of brain metastasis in nonsmall cell lung cancer, Cancer Research, 76(14 Supplement): 1535-1535.
  33. Van Dijk E. L., Auger H., Jaszczyszyn Y., et al., 2014, Ten years of next-generation sequencing technology, Trends in genetics, 30(9): 418-426.
  34. Wang H., Maurano M. T., Qu H., et al., 2012, Widespread plasticity in CTCF occupancy linked to DNA methylation, Genome research, 22(9): 1680-1688.
  35. Wang, Z., et al., 2009, RNA-Seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet, 10: 57-63.
  36. Wilson K. D., Shen P., Fung E., et al., 2015, A rapid, highquality, cost-effective, comprehensive, and expandable targeted next-generation sequencing assay for inherited heart diseases, Circ Res, 117(7): 603-611.
  37. Wolf Z. T., Brand H. A., Shaffer J. R., et al., 2015, Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate, PLoS Genet, 11(3): e1005059-e1005059.
  38. Xu B., Roos J. L., Dexheimer P., et al., 2011 Exome sequencing supports a de novo mutational paradigm for schizophrenia, Nature genetics, 43(9): 864-868.
  39. Xu Y., Chen S., Yin S., et al., 2015, Embryo genome profiling by single-cell sequencing for preimplantation genetic diagnosis in a beta-thalassemia family, Clin Chem, 61(4): 617-626.
  40. Zaghloul N. A., 2010, Katsanis N. Functional modules, mutational load and human genetic disease, Trends Genet, 26(4): 168-76.
Download


Paper Citation


in Harvard Style

Deng S. (2016). High-Throughput Sequencing Technology and Its Applications in Human Disease . In ISME 2016 - Information Science and Management Engineering IV - Volume 1: ISME, ISBN 978-989-758-208-0, pages 318-324. DOI: 10.5220/0006449703180324


in Bibtex Style

@conference{isme16,
author={Shuyang Deng},
title={High-Throughput Sequencing Technology and Its Applications in Human Disease},
booktitle={ISME 2016 - Information Science and Management Engineering IV - Volume 1: ISME,},
year={2016},
pages={318-324},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0006449703180324},
isbn={978-989-758-208-0},
}


in EndNote Style

TY - CONF
JO - ISME 2016 - Information Science and Management Engineering IV - Volume 1: ISME,
TI - High-Throughput Sequencing Technology and Its Applications in Human Disease
SN - 978-989-758-208-0
AU - Deng S.
PY - 2016
SP - 318
EP - 324
DO - 10.5220/0006449703180324