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Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms

Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms
Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A>C (IVS9-2A>C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A>C. The combined odds for causality considering case-control, segregation, and breast tumor pathology information was 3.23x10-8. Our data indicate that c.594-2A>C is always in cis with c.641A>G.

The spliceogenic effect of c.[594-2A>C;641A>G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A>C; 641A>G] caused exon 10 skipping, albeit not due to c.594-2A>C impairing the acceptor site but rather by c.641A>G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile comprised of ?70-80% truncating transcripts, and ?20-30% of in-frame ?9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.

We confirm that BRCA1c.[594-2A>C;641A>G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.
2256-2268
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de la Hoya, M., Soukarieh, O., López-Perolio, I., Vega, A., Walker, L.C., van Ierland, Y., Baralle, D., Santamariña, M., Lattimore, V., Wijnen, J., Whiley, P., Blanco, A., Raponi, M., Hauke, J., Wappenschmidt, B., Becker, A., Hansen, T.V.O., Behar, R., Niederacher, D., Arnold, N., Dworniczak, B., Steinemann, D., Faust, U., Rubinstein, W., Hulick, P.J., Houdayer, C., Caputo, S.M., Castera, L., Peseran, T., Chao, E., Brewer, C., Southey, M.C., van Asperen, C.J., Singer, C.F., Sullivan, J., Poplawski, N., Mai, P., Peto, J., Johnson, N., Burwinkel, B., Surowy, H., Bojesen, S.E., Flyger, H., Lindbolm, A., Margolin, S., Chang-Claude, J., Rudolph, A., Radice, P., Galastri, L., Olson, J.E., Hallberg, E., Giles, G.G., Milne, R.L., Andrulis, I.L., Glendon, G., Hall, P., Czene, K., Blows, F., Shah, M., Wang, Q., Dennis, J., Michailidou, K., McGuffog, L., Bolla, M.K., Antoniou, A.C., Easton, D.F., Couch, F.J., Tavtigian, S., Vreeswijk, M., Parsons, M., Meeks, H., Martins, A., Goldgar, D.E. and Spurdle, A.B. (2016) Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Human Molecular Genetics, 25 (11), 2256-2268. (doi:10.1093/hmg/ddw094). (PMID:27008870)

Record type: Article

Abstract

A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A>C (IVS9-2A>C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A>C. The combined odds for causality considering case-control, segregation, and breast tumor pathology information was 3.23x10-8. Our data indicate that c.594-2A>C is always in cis with c.641A>G.

The spliceogenic effect of c.[594-2A>C;641A>G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A>C; 641A>G] caused exon 10 skipping, albeit not due to c.594-2A>C impairing the acceptor site but rather by c.641A>G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile comprised of ?70-80% truncating transcripts, and ?20-30% of in-frame ?9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.

We confirm that BRCA1c.[594-2A>C;641A>G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.

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Accepted/In Press date: 17 March 2016
e-pub ahead of print date: 23 March 2016
Published date: June 2016
Organisations: Human Development & Health

Identifiers

Local EPrints ID: 390355
URI: http://eprints.soton.ac.uk/id/eprint/390355
PURE UUID: 5211651d-cc09-4df3-adb1-d18f81efd4ee
ORCID for D. Baralle: ORCID iD orcid.org/0000-0003-3217-4833

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Date deposited: 24 Mar 2016 13:52
Last modified: 17 Dec 2019 06:53

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Contributors

Author: M. de la Hoya
Author: O. Soukarieh
Author: I. López-Perolio
Author: A. Vega
Author: L.C. Walker
Author: Y. van Ierland
Author: D. Baralle ORCID iD
Author: M. Santamariña
Author: V. Lattimore
Author: J. Wijnen
Author: P. Whiley
Author: A. Blanco
Author: M. Raponi
Author: J. Hauke
Author: B. Wappenschmidt
Author: A. Becker
Author: T.V.O. Hansen
Author: R. Behar
Author: D. Niederacher
Author: N. Arnold
Author: B. Dworniczak
Author: D. Steinemann
Author: U. Faust
Author: W. Rubinstein
Author: P.J. Hulick
Author: C. Houdayer
Author: S.M. Caputo
Author: L. Castera
Author: T. Peseran
Author: E. Chao
Author: C. Brewer
Author: M.C. Southey
Author: C.J. van Asperen
Author: C.F. Singer
Author: J. Sullivan
Author: N. Poplawski
Author: P. Mai
Author: J. Peto
Author: N. Johnson
Author: B. Burwinkel
Author: H. Surowy
Author: S.E. Bojesen
Author: H. Flyger
Author: A. Lindbolm
Author: S. Margolin
Author: J. Chang-Claude
Author: A. Rudolph
Author: P. Radice
Author: L. Galastri
Author: J.E. Olson
Author: E. Hallberg
Author: G.G. Giles
Author: R.L. Milne
Author: I.L. Andrulis
Author: G. Glendon
Author: P. Hall
Author: K. Czene
Author: F. Blows
Author: M. Shah
Author: Q. Wang
Author: J. Dennis
Author: K. Michailidou
Author: L. McGuffog
Author: M.K. Bolla
Author: A.C. Antoniou
Author: D.F. Easton
Author: F.J. Couch
Author: S. Tavtigian
Author: M. Vreeswijk
Author: M. Parsons
Author: H. Meeks
Author: A. Martins
Author: D.E. Goldgar
Author: A.B. Spurdle

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