Whole exome sequencing of microdissected splenic marginal zone lymphoma: A study to discover novel tumor-specific mutations

Jan Peveling-Oberhag, Franziska Wolters, Claudia Döring, Dirk Walter, Ludger Sellmann, René Scholtysik, Marco Lucioni, Max Schubach, Marco Paulli, Saskia Biskup, Stefan Zeuzem, Ralf Küppers, Martin Leo Hansmann

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Abstract

Background: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking. Methods: We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort. Results: Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15% of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations. Conclusions: In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10% of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.

Original languageEnglish
Article number773
JournalBMC Cancer
Volume15
Issue number1
DOIs
Publication statusPublished - Oct 24 2015

Fingerprint

Exome
Lymphoma
Mutation
Neoplasms
Transcription Factors
Nucleotides
Recurrence
B-Cell Lymphoma
Missense Mutation
Non-Hodgkin's Lymphoma
Lasers
Spleen

Keywords

  • Lymphoma
  • Next generation sequencing
  • NOTCH2
  • SMYD1
  • Splenic marginal zone lymphoma

ASJC Scopus subject areas

  • Oncology
  • Cancer Research
  • Genetics

Cite this

Peveling-Oberhag, J., Wolters, F., Döring, C., Walter, D., Sellmann, L., Scholtysik, R., ... Hansmann, M. L. (2015). Whole exome sequencing of microdissected splenic marginal zone lymphoma: A study to discover novel tumor-specific mutations. BMC Cancer, 15(1), [773]. https://doi.org/10.1186/s12885-015-1766-z

Whole exome sequencing of microdissected splenic marginal zone lymphoma : A study to discover novel tumor-specific mutations. / Peveling-Oberhag, Jan; Wolters, Franziska; Döring, Claudia; Walter, Dirk; Sellmann, Ludger; Scholtysik, René; Lucioni, Marco; Schubach, Max; Paulli, Marco; Biskup, Saskia; Zeuzem, Stefan; Küppers, Ralf; Hansmann, Martin Leo.

In: BMC Cancer, Vol. 15, No. 1, 773, 24.10.2015.

Research output: Contribution to journalArticle

Peveling-Oberhag, J, Wolters, F, Döring, C, Walter, D, Sellmann, L, Scholtysik, R, Lucioni, M, Schubach, M, Paulli, M, Biskup, S, Zeuzem, S, Küppers, R & Hansmann, ML 2015, 'Whole exome sequencing of microdissected splenic marginal zone lymphoma: A study to discover novel tumor-specific mutations', BMC Cancer, vol. 15, no. 1, 773. https://doi.org/10.1186/s12885-015-1766-z
Peveling-Oberhag, Jan ; Wolters, Franziska ; Döring, Claudia ; Walter, Dirk ; Sellmann, Ludger ; Scholtysik, René ; Lucioni, Marco ; Schubach, Max ; Paulli, Marco ; Biskup, Saskia ; Zeuzem, Stefan ; Küppers, Ralf ; Hansmann, Martin Leo. / Whole exome sequencing of microdissected splenic marginal zone lymphoma : A study to discover novel tumor-specific mutations. In: BMC Cancer. 2015 ; Vol. 15, No. 1.
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abstract = "Background: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking. Methods: We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort. Results: Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15{\%} of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations. Conclusions: In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10{\%} of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.",
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AU - Wolters, Franziska

AU - Döring, Claudia

AU - Walter, Dirk

AU - Sellmann, Ludger

AU - Scholtysik, René

AU - Lucioni, Marco

AU - Schubach, Max

AU - Paulli, Marco

AU - Biskup, Saskia

AU - Zeuzem, Stefan

AU - Küppers, Ralf

AU - Hansmann, Martin Leo

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N2 - Background: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking. Methods: We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort. Results: Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15% of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations. Conclusions: In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10% of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.

AB - Background: Splenic marginal zone lymphoma (SMZL) is an indolent B-cell non-Hodgkin lymphoma and represents the most common primary malignancy of the spleen. Its precise molecular pathogenesis is still unknown and specific molecular markers for diagnosis or possible targets for causal therapies are lacking. Methods: We performed whole exome sequencing (WES) and copy number analysis from laser-microdissected tumor cells of two primary SMZL discovery cases. Selected somatic single nucleotide variants (SNVs) were analyzed using pyrosequencing and Sanger sequencing in an independent validation cohort. Results: Overall, 25 nonsynonymous somatic SNVs were identified, including known mutations in the NOTCH2 and MYD88 genes. Twenty-three of the mutations have not been associated with SMZL before. Many of these seem to be subclonal. Screening of 24 additional SMZL for mutations at the same positions found mutated in the WES approach revealed no recurrence of mutations for ZNF608 and PDE10A, whereas the MYD88 L265P missense mutation was identified in 15% of cases. An analysis of the NOTCH2 PEST domain and the whole coding region of the transcription factor SMYD1 in eight cases identified no additional case with a NOTCH2 mutation, but two additional cases with SMYD1 alterations. Conclusions: In this first WES approach from microdissected SMZL tissue we confirmed known mutations and discovered new somatic variants. Recurrence of MYD88 mutations in SMZL was validated, but NOTCH2 PEST domain mutations were relatively rare (10% of cases). Recurrent mutations in the transcription factor SMYD1 have not been described in SMZL before and warrant further investigation.

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