Movatterモバイル変換

[0]ホーム
URL:

Skip to main content

Advertisement

Springer Nature Link
Log in

Estimating the Length Distributions of Genomic Micro-satellites from Next Generation Sequencing Data

  • Conference paper
  • First Online:

Abstract

Genomic micro-satellites are the genomic regions that consist of short and repetitive DNA motifs. In contrast to unique genome, genomic micro-satellites expose high intrinsic polymorphisms, which mainly derive from variability in length. Length distributions are widely used to represent the polymorphisms. Recent studies report that some micro-satellites alter their length distributions significantly in tumor tissue samples comparing to the ones observed in normal samples, which becomes a hot topic in cancer genomics. Several state-of-the-art approaches are proposed to identify the length distributions from the sequencing data. However, the existing approaches can only handle the micro-satellites shorter than one read length, which limits the potential research on long micro-satellite events. In this article, we propose a probabilistic approach, implemented asELMSI that estimates the length distributions of the micro-satellites longer than one read length. The core algorithm works on a set of mapped reads. It first clusters the reads, and ak-mer extension algorithm is adopted to detect the unit and breakpoints as well. Then, it conducts an expectation maximization algorithm to approach the true length distributions. According to the experiments,ELMSI is able to handle micro-satellites with the length spectrum from shorter than one read length to 10 kbps scale. A series of comparison experiments are applied, which vary the numbers of micro-satellite regions, read lengths and sequencing coverages, andELMSI outperformsMSIsensor in most of the cases.

This is a preview of subscription content,log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
¥17,985 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
JPY 3498
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
JPY 5719
Price includes VAT (Japan)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
JPY 7149
Price includes VAT (Japan)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide -see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Similar content being viewed by others

References

  1. Miesfeld, R., Krystal, M., Arnheim, N.: A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is found between the human delta and beta globin genes. Nucleic Acids Res.9(22), 5931–5947 (1981)

    Article  Google Scholar 

  2. Ashley, C., Warren, S.: Trinucleotide repeat expansion and human disease. Annu. Rev. Genet.16(1), 1698–1704 (1995)

    Google Scholar 

  3. Ellegren, H.: Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet.5(6), 435–445 (2004)

    Article  Google Scholar 

  4. Niu, B., Ye, K., Zhang, Q., et al.: MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics30(7), 1015 (2014)

    Article  Google Scholar 

  5. Murphy, K.M., Zhang, S., Geiger, T., Hafez, M.J., Bacher, J., Berg, K.D., Eshleman, J.R.: Comparison of the microsatellite instability analysis system and the bethesda panel for the determination of micro-satellite instability in colorectal cancers. J. Mol. Diagn.8(3), 305–311 (2006)

    Article  Google Scholar 

  6. Lu, C., Xie, M., Wendl, M., et al.: Patterns and functional implications of rare germline variants across 12 cancer types. Nat. Commun.6(10086), 1–13 (2015)

    Google Scholar 

  7. Markowitz, S.D., Bertagnolli, M.M.: Molecular origins of cancer: molecular basis of colorectal cancer. N. Engl. J. Med.361(25), 2449 (2009)

    Article  Google Scholar 

  8. Kim, T.M., Laird, P.W., Park, P.J.: The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell155(4), 858–868 (2013)

    Article  Google Scholar 

  9. Woerner, S.M., Kloor, M., Mueller, A., et al.: Microsatellite instability of selective target genes in HNPCC-associated colon adenomas. Oncogene24(15), 2523–2535 (2005)

    Article  Google Scholar 

  10. Ritchard, C.C., Morrissey, C., Kumar, A., et al.: Complex MSH2 and MSH6 mutations in hypermutated microsatellite unstable advanced prostate cancer. Nat. Commun.5, 4988 (2014)

    Article  Google Scholar 

  11. Ribic, C.M., Sargent, D.J., Moore, M.J., et al.: Tumor microsatellite instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. N. Engl. J. Med.349(3), 247–257 (2003)

    Article  Google Scholar 

  12. Pawlik, T.M., Raut, C.P., Rodriguez-Bigas, M.A.: Colorectal carcinogenesis: MSI-H versus MSI-L. Dis. Markers20(4–5), 199–206 (2004)

    Article  Google Scholar 

  13. Salipante, S.J., Scroggins, S.M., Hampel, H.L., et al.: Microsatellite instability detection by next generation sequencing. Clin. Chem.60(9), 1192–1199 (2014)

    Article  Google Scholar 

  14. Mi, N.H., Mcpherson, J.R., Cutcutache, I., et al.: MSIseq: software for assessing microsatellite instability from catalogs of somatic mutations. Sci. Rep.5, 13321 (2015)

    Article  Google Scholar 

  15. Wu, C.W., Chen, G.D., Jiang, K.C., et al.: A genome-wide study of microsatellite instability in advanced gastric carcinoma. Cancer92(1), 92–101 (2015)

    Article  Google Scholar 

Download references

Acknowledgement

This work is supported by the National Science Foundation of China (Grant No: 31701150) and the Fundamental Research Funds for the Central Universities (CXTD2017003)

Author information

Authors and Affiliations

  1. School of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, 710049, Shaanxi, China

    Xuan Feng, Huan Hu, Zhongmeng Zhao, Xuanping Zhang & Jiayin Wang

  2. Shaanxi Engineering Research Center of Medical and Health Big Data, Institute of Data Science and Information Quality, Xi’an Jiaotong University, Xi’an, 710049, Shaanxi, China

    Xuan Feng, Huan Hu, Zhongmeng Zhao, Xuanping Zhang & Jiayin Wang

Authors
  1. Xuan Feng

    You can also search for this author inPubMed Google Scholar

  2. Huan Hu

    You can also search for this author inPubMed Google Scholar

  3. Zhongmeng Zhao

    You can also search for this author inPubMed Google Scholar

  4. Xuanping Zhang

    You can also search for this author inPubMed Google Scholar

  5. Jiayin Wang

    You can also search for this author inPubMed Google Scholar

Corresponding author

Correspondence toJiayin Wang.

Editor information

Editors and Affiliations

  1. University of Granada, Granada, Spain

    Ignacio Rojas

  2. University of Granada, Granada, Spain

    Francisco Ortuño

Rights and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Feng, X., Hu, H., Zhao, Z., Zhang, X., Wang, J. (2018). Estimating the Length Distributions of Genomic Micro-satellites from Next Generation Sequencing Data. In: Rojas, I., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2018. Lecture Notes in Computer Science(), vol 10813. Springer, Cham. https://doi.org/10.1007/978-3-319-78723-7_40

Download citation

Publish with us

Access this chapter

Subscribe and save

Springer+ Basic
¥17,985 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
JPY 3498
Price includes VAT (Japan)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
JPY 5719
Price includes VAT (Japan)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
JPY 7149
Price includes VAT (Japan)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide -see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

[8]ページ先頭
©2009-2025 Movatter.jp