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van der Klift HM, Jansen AM, van der Steenstraten N, et al. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med. 2015;3(4):327-45doi: 10.1002/mgg3.145.
van der Klift, H. M., Jansen, A. M., van der Steenstraten, N., Bik, E. C., Tops, C. M., Devilee, P., & Wijnen, J. T. (2015). Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Molecular genetics & genomic medicine, 3(4), 327-45. https://doi.org/10.1002/mgg3.145
van der Klift, Heleen M, et al. "Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses." Molecular genetics & genomic medicine vol. 3,4 (2015): 327-45. doi: https://doi.org/10.1002/mgg3.145
van der Klift HM, Jansen AM, van der Steenstraten N, Bik EC, Tops CM, Devilee P, Wijnen JT. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med. 2015 Jul;3(4):327-45. doi: 10.1002/mgg3.145. Epub 2015 Apr 23. PMID: 26247049; PMCID: PMC4521968.
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Mol Genet Genomic Med. 2015 Jul;3(4):327-45. doi: 10.1002/mgg3.145. Epub 2015 Apr 23.

Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses.

Molecular genetics & genomic medicine

Heleen M van der Klift, Anne M L Jansen, Niki van der Steenstraten, Elsa C Bik, Carli M J Tops, Peter Devilee, Juul T Wijnen

Affiliations

  1. Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands.
  2. Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands.
  3. Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands.
  4. Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Pathology, Leiden University Medical Center Leiden, The Netherlands.

PMID: 26247049 PMCID: PMC4521968 DOI: 10.1002/mgg3.145

Abstract

A subset of DNA variants causes genetic disease through aberrant splicing. Experimental splicing assays, either RT-PCR analyses of patient RNA or functional splicing reporter minigene assays, are required to evaluate the molecular nature of the splice defect. Here, we present minigene assays performed for 17 variants in the consensus splice site regions, 14 exonic variants outside these regions, and two deep intronic variants, all in the DNA mismatch-repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, associated with Lynch syndrome. We also included two deep intronic variants in APC and PKD2. For one variant (MLH1 c.122A>G), our minigene assay and patient RNA analysis could not confirm the previously reported aberrant splicing. The aim of our study was to further investigate the concordance between minigene splicing assays and patient RNA analyses. For 30 variants results from patient RNA analyses were available, either performed by our laboratory or presented in literature. Some variants were deliberately included in this study because they resulted in multiple aberrant transcripts in patient RNA analysis, or caused a splice effect other than the prevalent exon skip. While both methods were completely concordant in the assessment of splice effects, four variants exhibited major differences in aberrant splice patterns. Based on the present and earlier studies, together showing an almost 100% concordance of minigene assays with patient RNA analyses, we discuss the weight given to minigene splicing assays in the current criteria proposed by InSiGHT for clinical classification of MMR variants.

Keywords: Aberrant splicing; Lynch syndrome; minigene assay; mismatch repair genes; patient RNA analysis; variant classification

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