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Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data

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Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data. / Stichel, Damian; Schrimpf, Daniel; Sievers, Philipp; Reinhardt, Annekathrin; Suwala, Abigail K; Sill, Martin; Reuss, David E; Korshunov, Andrey; Casalini, Belén M; Sommerkamp, Alexander C; Ecker, Jonas; Selt, Florian; Sturm, Dominik; Gnekow, Astrid; Koch, Arend; Simon, Michèle; Hernáiz Driever, Pablo; Schüller, Ulrich; Capper, David; van Tilburg, Cornelis M; Witt, Olaf; Milde, Till; Pfister, Stefan M; Jones, David T W; von Deimling, Andreas; Sahm, Felix; Wefers, Annika K.

In: NEUROPATH APPL NEURO, Vol. 47, No. 3, 04.2021, p. 406-414.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Stichel, D, Schrimpf, D, Sievers, P, Reinhardt, A, Suwala, AK, Sill, M, Reuss, DE, Korshunov, A, Casalini, BM, Sommerkamp, AC, Ecker, J, Selt, F, Sturm, D, Gnekow, A, Koch, A, Simon, M, Hernáiz Driever, P, Schüller, U, Capper, D, van Tilburg, CM, Witt, O, Milde, T, Pfister, SM, Jones, DTW, von Deimling, A, Sahm, F & Wefers, AK 2021, 'Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data', NEUROPATH APPL NEURO, vol. 47, no. 3, pp. 406-414. https://doi.org/10.1111/nan.12683

APA

Stichel, D., Schrimpf, D., Sievers, P., Reinhardt, A., Suwala, A. K., Sill, M., Reuss, D. E., Korshunov, A., Casalini, B. M., Sommerkamp, A. C., Ecker, J., Selt, F., Sturm, D., Gnekow, A., Koch, A., Simon, M., Hernáiz Driever, P., Schüller, U., Capper, D., ... Wefers, A. K. (2021). Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data. NEUROPATH APPL NEURO, 47(3), 406-414. https://doi.org/10.1111/nan.12683

Vancouver

Stichel D, Schrimpf D, Sievers P, Reinhardt A, Suwala AK, Sill M et al. Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data. NEUROPATH APPL NEURO. 2021 Apr;47(3):406-414. https://doi.org/10.1111/nan.12683

Bibtex

@article{26104744f0b0457cb88111e36ea830c8,
title = "Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data",
abstract = "AIMS: KIAA1549-BRAF fusions occur in certain brain tumours and provide druggable targets due to a constitutive activation of the MAP-kinase pathway. We introduce workflows for calling the KIAA1549-BRAF fusion from DNA methylation-array-derived copy number as well as DNA panel sequencing data.METHODS: Copy number profiles were analysed by automated screening and visual verification of a tandem duplication on chromosome 7q34, indicative of the KIAA1549-BRAF fusion. Pilocytic astrocytomas of the ICGC cohort with known fusion status were used for validation. KIAA1549-BRAF fusions were called from DNA panel sequencing data using the fusion callers Manta, Arriba with modified filtering criteria and deFuse. We screened DNA methylation and panel sequencing data of 7790 specimens from brain tumour and sarcoma entities.RESULTS: We identified the fusion in 337 brain tumours with both DNA methylation and panel sequencing data. Among these, we detected the fusion from copy number data in 84% and from DNA panel sequencing data in more than 90% using Arriba with modified filters. While in 74% the KIAA1549-BRAF fusion was detected from both methylation-array-derived copy number and panel sequencing data, in 9% it was detected from copy number data only and in 16% from panel data only. The fusion was almost exclusively found in pilocytic astrocytomas, diffuse leptomeningeal glioneuronal tumours and high-grade astrocytomas with piloid features.CONCLUSIONS: The KIAA1549-BRAF fusion can be reliably detected from either DNA methylation array or DNA panel data. The use of both methods is recommended for the most sensitive detection of this diagnostically and therapeutically important marker.",
author = "Damian Stichel and Daniel Schrimpf and Philipp Sievers and Annekathrin Reinhardt and Suwala, {Abigail K} and Martin Sill and Reuss, {David E} and Andrey Korshunov and Casalini, {Bel{\'e}n M} and Sommerkamp, {Alexander C} and Jonas Ecker and Florian Selt and Dominik Sturm and Astrid Gnekow and Arend Koch and Mich{\`e}le Simon and {Hern{\'a}iz Driever}, Pablo and Ulrich Sch{\"u}ller and David Capper and {van Tilburg}, {Cornelis M} and Olaf Witt and Till Milde and Pfister, {Stefan M} and Jones, {David T W} and {von Deimling}, Andreas and Felix Sahm and Wefers, {Annika K}",
note = "This article is protected by copyright. All rights reserved.",
year = "2021",
month = apr,
doi = "10.1111/nan.12683",
language = "English",
volume = "47",
pages = "406--414",
journal = "NEUROPATH APPL NEURO",
issn = "0305-1846",
publisher = "Wiley-Blackwell",
number = "3",

}

RIS

TY - JOUR

T1 - Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data

AU - Stichel, Damian

AU - Schrimpf, Daniel

AU - Sievers, Philipp

AU - Reinhardt, Annekathrin

AU - Suwala, Abigail K

AU - Sill, Martin

AU - Reuss, David E

AU - Korshunov, Andrey

AU - Casalini, Belén M

AU - Sommerkamp, Alexander C

AU - Ecker, Jonas

AU - Selt, Florian

AU - Sturm, Dominik

AU - Gnekow, Astrid

AU - Koch, Arend

AU - Simon, Michèle

AU - Hernáiz Driever, Pablo

AU - Schüller, Ulrich

AU - Capper, David

AU - van Tilburg, Cornelis M

AU - Witt, Olaf

AU - Milde, Till

AU - Pfister, Stefan M

AU - Jones, David T W

AU - von Deimling, Andreas

AU - Sahm, Felix

AU - Wefers, Annika K

N1 - This article is protected by copyright. All rights reserved.

PY - 2021/4

Y1 - 2021/4

N2 - AIMS: KIAA1549-BRAF fusions occur in certain brain tumours and provide druggable targets due to a constitutive activation of the MAP-kinase pathway. We introduce workflows for calling the KIAA1549-BRAF fusion from DNA methylation-array-derived copy number as well as DNA panel sequencing data.METHODS: Copy number profiles were analysed by automated screening and visual verification of a tandem duplication on chromosome 7q34, indicative of the KIAA1549-BRAF fusion. Pilocytic astrocytomas of the ICGC cohort with known fusion status were used for validation. KIAA1549-BRAF fusions were called from DNA panel sequencing data using the fusion callers Manta, Arriba with modified filtering criteria and deFuse. We screened DNA methylation and panel sequencing data of 7790 specimens from brain tumour and sarcoma entities.RESULTS: We identified the fusion in 337 brain tumours with both DNA methylation and panel sequencing data. Among these, we detected the fusion from copy number data in 84% and from DNA panel sequencing data in more than 90% using Arriba with modified filters. While in 74% the KIAA1549-BRAF fusion was detected from both methylation-array-derived copy number and panel sequencing data, in 9% it was detected from copy number data only and in 16% from panel data only. The fusion was almost exclusively found in pilocytic astrocytomas, diffuse leptomeningeal glioneuronal tumours and high-grade astrocytomas with piloid features.CONCLUSIONS: The KIAA1549-BRAF fusion can be reliably detected from either DNA methylation array or DNA panel data. The use of both methods is recommended for the most sensitive detection of this diagnostically and therapeutically important marker.

AB - AIMS: KIAA1549-BRAF fusions occur in certain brain tumours and provide druggable targets due to a constitutive activation of the MAP-kinase pathway. We introduce workflows for calling the KIAA1549-BRAF fusion from DNA methylation-array-derived copy number as well as DNA panel sequencing data.METHODS: Copy number profiles were analysed by automated screening and visual verification of a tandem duplication on chromosome 7q34, indicative of the KIAA1549-BRAF fusion. Pilocytic astrocytomas of the ICGC cohort with known fusion status were used for validation. KIAA1549-BRAF fusions were called from DNA panel sequencing data using the fusion callers Manta, Arriba with modified filtering criteria and deFuse. We screened DNA methylation and panel sequencing data of 7790 specimens from brain tumour and sarcoma entities.RESULTS: We identified the fusion in 337 brain tumours with both DNA methylation and panel sequencing data. Among these, we detected the fusion from copy number data in 84% and from DNA panel sequencing data in more than 90% using Arriba with modified filters. While in 74% the KIAA1549-BRAF fusion was detected from both methylation-array-derived copy number and panel sequencing data, in 9% it was detected from copy number data only and in 16% from panel data only. The fusion was almost exclusively found in pilocytic astrocytomas, diffuse leptomeningeal glioneuronal tumours and high-grade astrocytomas with piloid features.CONCLUSIONS: The KIAA1549-BRAF fusion can be reliably detected from either DNA methylation array or DNA panel data. The use of both methods is recommended for the most sensitive detection of this diagnostically and therapeutically important marker.

U2 - 10.1111/nan.12683

DO - 10.1111/nan.12683

M3 - SCORING: Journal article

C2 - 33336421

VL - 47

SP - 406

EP - 414

JO - NEUROPATH APPL NEURO

JF - NEUROPATH APPL NEURO

SN - 0305-1846

IS - 3

ER -