Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: An ENIGMA report

Irene Lopez-Perolio, Raphaël Leman, Raquel Behar, Vanessa Lattimore, John F. Pearson, Laurent Castéra, Alexandra Martins, Dominique Vaur, Nicolas Goardon, Grégoire Davy, Pilar Garre, Vanesa García-Barberán, Patricia Llovet, Pedro Pérez-Segura, Eduardo Díaz-Rubio, Trinidad Caldés, Kathleen S. Hruska, Vickie Hsuan, Sitao Wu, Tina Pesaran & 14 others Rachid Karam, Johan Vallon-Christersson, Ake Borg, Kconfab Investigators, Alberto Valenzuela-Palomo, Eladio A. Velasco, Melissa Southey, Maaike P.G. Vreeswijk, Peter Devilee, Anders Kvist, Amanda B. Spurdle, Logan C. Walker, Sophie Krieger, Miguel De La Hoya

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Background PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. Methods Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. Results We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. Conclusions PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.

Original languageEnglish
Pages (from-to)453-460
Number of pages8
JournalJournal of Medical Genetics
Volume56
Issue number7
DOIs
Publication statusPublished - 1 Jul 2019
Externally publishedYes

Keywords

  • acmg-Amp guidelines
  • palb2
  • pvs1
  • splicing
  • variant classification

Cite this

Lopez-Perolio, I., Leman, R., Behar, R., Lattimore, V., Pearson, J. F., Castéra, L., ... De La Hoya, M. (2019). Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: An ENIGMA report. Journal of Medical Genetics, 56(7), 453-460. https://doi.org/10.1136/jmedgenet-2018-105834
Lopez-Perolio, Irene ; Leman, Raphaël ; Behar, Raquel ; Lattimore, Vanessa ; Pearson, John F. ; Castéra, Laurent ; Martins, Alexandra ; Vaur, Dominique ; Goardon, Nicolas ; Davy, Grégoire ; Garre, Pilar ; García-Barberán, Vanesa ; Llovet, Patricia ; Pérez-Segura, Pedro ; Díaz-Rubio, Eduardo ; Caldés, Trinidad ; Hruska, Kathleen S. ; Hsuan, Vickie ; Wu, Sitao ; Pesaran, Tina ; Karam, Rachid ; Vallon-Christersson, Johan ; Borg, Ake ; Investigators, Kconfab ; Valenzuela-Palomo, Alberto ; Velasco, Eladio A. ; Southey, Melissa ; Vreeswijk, Maaike P.G. ; Devilee, Peter ; Kvist, Anders ; Spurdle, Amanda B. ; Walker, Logan C. ; Krieger, Sophie ; De La Hoya, Miguel. / Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants : An ENIGMA report. In: Journal of Medical Genetics. 2019 ; Vol. 56, No. 7. pp. 453-460.
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abstract = "Background PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. Methods Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. Results We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. Conclusions PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.",
keywords = "acmg-Amp guidelines, palb2, pvs1, splicing, variant classification",
author = "Irene Lopez-Perolio and Rapha{\"e}l Leman and Raquel Behar and Vanessa Lattimore and Pearson, {John F.} and Laurent Cast{\'e}ra and Alexandra Martins and Dominique Vaur and Nicolas Goardon and Gr{\'e}goire Davy and Pilar Garre and Vanesa Garc{\'i}a-Barber{\'a}n and Patricia Llovet and Pedro P{\'e}rez-Segura and Eduardo D{\'i}az-Rubio and Trinidad Cald{\'e}s and Hruska, {Kathleen S.} and Vickie Hsuan and Sitao Wu and Tina Pesaran and Rachid Karam and Johan Vallon-Christersson and Ake Borg and Kconfab Investigators and Alberto Valenzuela-Palomo and Velasco, {Eladio A.} and Melissa Southey and Vreeswijk, {Maaike P.G.} and Peter Devilee and Anders Kvist and Spurdle, {Amanda B.} and Walker, {Logan C.} and Sophie Krieger and {De La Hoya}, Miguel",
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Lopez-Perolio, I, Leman, R, Behar, R, Lattimore, V, Pearson, JF, Castéra, L, Martins, A, Vaur, D, Goardon, N, Davy, G, Garre, P, García-Barberán, V, Llovet, P, Pérez-Segura, P, Díaz-Rubio, E, Caldés, T, Hruska, KS, Hsuan, V, Wu, S, Pesaran, T, Karam, R, Vallon-Christersson, J, Borg, A, Investigators, K, Valenzuela-Palomo, A, Velasco, EA, Southey, M, Vreeswijk, MPG, Devilee, P, Kvist, A, Spurdle, AB, Walker, LC, Krieger, S & De La Hoya, M 2019, 'Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: An ENIGMA report' Journal of Medical Genetics, vol. 56, no. 7, pp. 453-460. https://doi.org/10.1136/jmedgenet-2018-105834

Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants : An ENIGMA report. / Lopez-Perolio, Irene; Leman, Raphaël; Behar, Raquel; Lattimore, Vanessa; Pearson, John F.; Castéra, Laurent; Martins, Alexandra; Vaur, Dominique; Goardon, Nicolas; Davy, Grégoire; Garre, Pilar; García-Barberán, Vanesa; Llovet, Patricia; Pérez-Segura, Pedro; Díaz-Rubio, Eduardo; Caldés, Trinidad; Hruska, Kathleen S.; Hsuan, Vickie; Wu, Sitao; Pesaran, Tina; Karam, Rachid; Vallon-Christersson, Johan; Borg, Ake; Investigators, Kconfab; Valenzuela-Palomo, Alberto; Velasco, Eladio A.; Southey, Melissa; Vreeswijk, Maaike P.G.; Devilee, Peter; Kvist, Anders; Spurdle, Amanda B.; Walker, Logan C.; Krieger, Sophie; De La Hoya, Miguel.

In: Journal of Medical Genetics, Vol. 56, No. 7, 01.07.2019, p. 453-460.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants

T2 - An ENIGMA report

AU - Lopez-Perolio, Irene

AU - Leman, Raphaël

AU - Behar, Raquel

AU - Lattimore, Vanessa

AU - Pearson, John F.

AU - Castéra, Laurent

AU - Martins, Alexandra

AU - Vaur, Dominique

AU - Goardon, Nicolas

AU - Davy, Grégoire

AU - Garre, Pilar

AU - García-Barberán, Vanesa

AU - Llovet, Patricia

AU - Pérez-Segura, Pedro

AU - Díaz-Rubio, Eduardo

AU - Caldés, Trinidad

AU - Hruska, Kathleen S.

AU - Hsuan, Vickie

AU - Wu, Sitao

AU - Pesaran, Tina

AU - Karam, Rachid

AU - Vallon-Christersson, Johan

AU - Borg, Ake

AU - Investigators, Kconfab

AU - Valenzuela-Palomo, Alberto

AU - Velasco, Eladio A.

AU - Southey, Melissa

AU - Vreeswijk, Maaike P.G.

AU - Devilee, Peter

AU - Kvist, Anders

AU - Spurdle, Amanda B.

AU - Walker, Logan C.

AU - Krieger, Sophie

AU - De La Hoya, Miguel

PY - 2019/7/1

Y1 - 2019/7/1

N2 - Background PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. Methods Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. Results We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. Conclusions PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.

AB - Background PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. Methods Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. Results We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. Conclusions PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.

KW - acmg-Amp guidelines

KW - palb2

KW - pvs1

KW - splicing

KW - variant classification

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U2 - 10.1136/jmedgenet-2018-105834

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EP - 460

JO - Journal of Medical Genetics

JF - Journal of Medical Genetics

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