Skip to main content
SpringerLink
Log in

Integrated Analysis of Germ Cell Tumors

  • Protocol
  • First Online:
Testicular Germ Cell Tumors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2195))

Abstract

Somatic analysis of the molecular features of human tumors through numerous efforts including The Cancer Genome Atlas consortium has led to unprecedented insight into the biological basis of cancer behavior. Numerous genomewide sequencing techniques have been utilized in these studies to understand DNA mutations, epigenomic alterations, and ultimately differences in protein expression profiles across various cancers. Due to the dropping costs of next-generation sequencing as well as growing power and ease of use of computational resources, researchers are able to apply these techniques to more specific cancer contexts and/or rarer tumor types. In this chapter, we describe the rationale for and details of methods used in our group for exome analysis of germ cell tumors. The methods described should also be readily applicable to genomic analysis of other tumors.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover 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

Institutional subscriptions

References

  1. Segal R (2006) Surveillance programs for stage I nonseminomatous germ cell tumors of the testis. Urol Oncol Semin Orig Investig 24:68–74. https://doi.org/10.1016/j.urolonc.2005.07.006

    Article  Google Scholar 

  2. Bahrami A, Ro JY, Ayala AG (2007) An overview of testicular germ cell tumors. Arch Pathol Lab Med 131(8):1267. https://doi.org/10.1043/1543-2165(2007)131[1267:AOOTGC]2.0.CO;2

    Article  PubMed  Google Scholar 

  3. American Cancer Society (2018) Cancer facts & figures 2018. https://www.cancer.org/content/dam/cancer-org/research/cancer-facts-and-statistics/annual-cancer-facts-and-figures/2018/cancer-facts-and-figures-2018.pdf

  4. Li C, Ekwueme DU, Rim SH, Tangka FK (2010) Years of potential life lost and productivity losses from male urogenital cancer deaths-United States, 2004. Urology 76:528–535. https://doi.org/10.1016/j.urology.2010.04.030

    Article  PubMed  Google Scholar 

  5. Kemmer K, Corless CL, Fletcher JA et al (2004) KIT mutations are common in testicular seminomas. Am J Pathol 164:305–313. https://doi.org/10.1016/S0002-9440(10)63120-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Honecker F, Wermann H, Mayer F et al (2009) Microsatellite instability, mismatch repair deficiency, and BRAF mutation in treatment-resistant germ cell tumors. J Clin Oncol 27:2129–2136. https://doi.org/10.1200/JCO.2008.18.8623

    Article  CAS  PubMed  Google Scholar 

  7. Feldman DR, Iyer G, Van Alstine L et al (2014) Presence of somatic mutations within PIK3CA, AKT, RAS, and FGFR3 but not BRAF in cisplatin-resistant germ cell tumors. Clin Cancer Res 20:3712–3720. https://doi.org/10.1158/1078-0432.CCR-13-2868

    Article  CAS  PubMed  Google Scholar 

  8. Yang X, Fraser M, Moll UM et al (2006) Akt-mediated cisplatin resistance in ovarian cancer: modulation of p53 action on caspase-dependent mitochondrial death pathway. Cancer Res 66:3126–3136. https://doi.org/10.1158/0008-5472.CAN-05-0425

    Article  CAS  PubMed  Google Scholar 

  9. Koster R, De Jong S (2010) Cytoplasmic p21 expression levels determine cisplatin resistance in human testicular cancer. J Clin Invest 120:3594–3605. https://doi.org/10.1172/JCI41939DS1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Wang L, Yamaguchi S, Burstein MD et al (2014) Novel somatic and germline mutations in intracranial germ cell tumours. Nature 511:241–245. https://doi.org/10.1038/nature13296

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Litchfield K, Summersgill B, Yost S et al (2015) Whole-exome sequencing reveals the mutational spectrum of testicular germ cell tumours. Nat Commun 6:1–8. https://doi.org/10.1038/ncomms6973

    Article  CAS  Google Scholar 

  12. Van Allen EM, Mouw KW, Kim P et al (2014) Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov 4:1140–1153. https://doi.org/10.1158/2159-8290.CD-14-0623

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Liu D, Plimack ER, Hoffman-Censits J et al (2016) Clinical validation of chemotherapy response biomarker ERCC2 in muscle-invasive urothelial bladder carcinoma. JAMA Oncol 4:1140–1153. https://doi.org/10.1001/jamaoncol.2016.1056

    Article  Google Scholar 

  14. Bagrodia A, Lee BH, Lee W et al (2016) Genetic determinants of cisplatin resistance in patients with advanced germ cell tumors. J Clin Oncol 34:4000–4007. https://doi.org/10.1200/JCO.2016.68.7798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Taylor-Weiner A, Zack T, O’Donnell E et al (2016) Genomic evolution and chemoresistance in germ-cell tumours. Nature 540:114–118. https://doi.org/10.1038/nature20596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Shen H, Shih J, Hollern DP et al (2018) Integrated molecular characterization of testicular germ cell tumors. Cell Rep 23:3392–3406. https://doi.org/10.1016/j.celrep.2018.05.039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Van Allen EM, Wagle N, Stojanov P et al (2014) Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med 20:682–688. https://doi.org/10.1038/nm.3559

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Fisher S, Barry A, Abreu J et al (2011) A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 12:1–15. https://doi.org/10.1186/gb-2011-12-1-r1

    Article  Google Scholar 

  19. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv

    Google Scholar 

  20. Cibulskis K, McKenna A, Fennell T et al (2011) ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 27:2601–2602. https://doi.org/10.1093/bioinformatics/btr446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Cibulskis K, Lawrence MS, Carter SL et al (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31:213–219. https://doi.org/10.1038/nbt.2514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Saunders CT, Wong WSW, Swamy S et al (2012) Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28:1811–1817. https://doi.org/10.1093/bioinformatics/bts271

    Article  CAS  PubMed  Google Scholar 

  23. Ramos AH, Lichtenstein L, Gupta M et al (2015) Oncotator: cancer variant annotation tool. Hum Mutat 36:E2423–E2429. https://doi.org/10.1002/humu.22771

    Article  PubMed  PubMed Central  Google Scholar 

  24. Lawrence MS, Stojanov P, Polak P et al (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499:214–218. https://doi.org/10.1038/nature12213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Carter SL, Cibulskis K, Helman E et al (2012) Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 30:413–421. https://doi.org/10.1038/nbt.2203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We thank the members of the Van Allen lab for helpful discussion, especially Brendan Reardon and Eric Kofman.

Author information

Authors and Affiliations

  1. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA

    Alok Tewari & Eliezer Van Allen

Authors
  1. Alok Tewari
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eliezer Van Allen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eliezer Van Allen .

Editor information

Editors and Affiliations

  1. Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA

    Aditya Bagrodia

  2. Cancer and Blood Disease Institute, Children’s Hospital Los Angeles, Departments of Pediatrics and Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    James F. Amatruda

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Tewari, A., Van Allen, E. (2021). Integrated Analysis of Germ Cell Tumors. In: Bagrodia, A., Amatruda, J.F. (eds) Testicular Germ Cell Tumors. Methods in Molecular Biology, vol 2195. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0860-9_13

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0860-9_13

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0859-3

  • Online ISBN: 978-1-0716-0860-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation