Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019:1956:321-336.
doi: 10.1007/978-1-4939-9151-8_15.

Evaluation of Whole Genome Sequencing Data

Daniel Hübschmann  1   2   3 , Matthias Schlesner  4
Affiliations

Evaluation of Whole Genome Sequencing Data

Daniel Hübschmann et al. Methods Mol Biol. 2019.

Abstract

Whole genome sequencing (WGS) can provide comprehensive insights into the genetic makeup of lymphomas. Here we describe a selection of methods for the analysis of WGS data, including alignment, identification of different classes of genomic variants, the identification of driver mutations, and the identification of mutational signatures. We further outline design considerations for WGS studies and provide a variety of quality control measures to detect common quality problems in the data.

Keywords: Mutational signatures; Next-generation sequencing; Quality control; Variant calling.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

  • ZygosityPredictor.
    Rheinnecker M, Fröhlich M, Rübsam M, Paramasivam N, Heilig CE, Fröhling S, Schlenk RF, Hutter B, Hübschmann D. Rheinnecker M, et al. Bioinform Adv. 2024 Feb 6;4(1):vbae017. doi: 10.1093/bioadv/vbae017. eCollection 2024. Bioinform Adv. 2024. PMID: 38560552 Free PMC article.
  • Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.
    Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L; ICGC MMML-Seq consortium; ICGC DE-Mining consortium; BLUEPRINT consortium; Küppers R, Schlesner M, Siebert R. Hübschmann D, et al. Leukemia. 2021 Jul;35(7):2002-2016. doi: 10.1038/s41375-021-01251-z. Epub 2021 May 5. Leukemia. 2021. PMID: 33953289 Free PMC article.
  • Data-driven support to decision-making in molecular tumour boards for lymphoma: A design science approach.
    Rodríguez Ruiz N, Abd Own S, Ekström Smedby K, Eloranta S, Koch S, Wästerlid T, Krstic A, Boman M. Rodríguez Ruiz N, et al. Front Oncol. 2022 Nov 15;12:984021. doi: 10.3389/fonc.2022.984021. eCollection 2022. Front Oncol. 2022. PMID: 36457495 Free PMC article.
  • Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives.
    Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Brlek P, et al. Cells. 2024 Mar 13;13(6):504. doi: 10.3390/cells13060504. Cells. 2024. PMID: 38534348 Free PMC article. Review.
  • Targeted therapy of advanced parathyroid carcinoma guided by genomic and transcriptomic profiling.
    Teleanu MV, Fuss CT, Paramasivam N, Pirmann S, Mock A, Terkamp C, Kircher S, Landwehr LS, Lenschow C, Schlegel N, Stenzinger A, Jahn A, Fassnacht M, Glimm H, Hübschmann D, Fröhling S, Kroiss M. Teleanu MV, et al. Mol Oncol. 2023 Jul;17(7):1343-1355. doi: 10.1002/1878-0261.13398. Epub 2023 Apr 11. Mol Oncol. 2023. PMID: 36808802 Free PMC article.

Publication types

LinkOut - more resources