@article{b8f6f39db36843fda625b3ce817cae21,
title = "Contribution of mRNA Splicing to Mismatch Repair Gene Sequence Variant Interpretation",
abstract = "Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in MLH1, MSH2, and MSH6, including 12 missense variants that were also assessed using a cell-free in vitro MMR activity (CIMRA) assay. Multifactorial likelihood analysis was conducted for each variant, combining CIMRA outputs and clinical data where available. We collated these results with existing public data to provide a dataset of splicing assay results for a total of 671 MMR gene sequence variants (328 missense/in-frame indel), and published and unpublished repair activity measurements for 154 of these variants. There were 241 variants for which a splicing aberration was detected: 92 complete impact, 33 incomplete impact, and 116 where it was not possible to determine complete versus incomplete splicing impact. Splicing results mostly aided in the interpretation of intronic (72%) and silent (92%) variants and were the least useful for missense substitutions/in-frame indels (10%). MMR protein functional activity assays were more useful in the analysis of these exonic variants but by design they were not able to detect clinically important splicing aberrations identified by parallel mRNA assays. The development of high throughput assays that can quantitatively assess impact on mRNA transcript expression and protein function in parallel will streamline classification of MMR gene sequence variants.",
keywords = "Lynch syndrome, mRNA splicing, mismatch repair genes, splicing aberrations, variant interpretation and classification, variant type",
author = "{the InSiGHT Variant Interpretation Committee} and Thompson, {Bryony A.} and Rhiannon Walters and Parsons, {Michael T.} and Troy Dumenil and Mark Drost and Yvonne Tiersma and Lindor, {Noralane M.} and Tavtigian, {Sean V.} and {de Wind}, Niels and Spurdle, {Amanda B.}",
note = "Funding Information: We thank Jannah Shamsani for providing MES-SWA scores for the MMR gene variants. We also acknowledge the Australian Red Cross Blood Services (ARCBS) donors who participated as healthy controls in this study. We are grateful to Rachel Morris and the staff at ARCBS for their assistance with the collection of risk factor information and blood samples, and Melanie Higgins, Kimberley Hinze, Felicity Lose, and members of the Molecular Cancer Epidemiology Laboratory for their assistance with collection and processing of blood samples. Funding. This study was funded by US NIH NCI grants R01 CA164944 and UM1 CA167551 and through U01/U24 cooperative agreements from NCI with the following Colon CFR centers: Mayo Clinic (CA074800 to NL), Ontario (OFCCR) (CA074783), and Seattle (SCCFR) (CA074794). The content of this manuscript does not necessarily reflect the views or policies of the NIH or any of the collaborating centers in the CCFR, nor does the mention of trade names, commercial products, or organizations imply endorsement by the US Government, any cancer registry, or the Colon CFR. NW, MD, and YT were supported by the Dutch Digestive Foundation (Grant FP 16-01) and the Dutch Cancer Society (Grant UL 2013-5939). BT was supported by an NHMRC CJ Martin Early Career Fellowship (ID1091211). AS was supported by an NHMRC Senior Research Fellowship (ID1061779). Funding Information: This study was funded by US NIH NCI grants R01 CA164944 and UM1 CA167551 and through U01/U24 cooperative agreements from NCI with the following Colon CFR centers: Mayo Clinic (CA074800 to NL), Ontario (OFCCR) (CA074783), and Seattle (SCCFR) (CA074794). The content of this manuscript does not necessarily reflect the views or policies of the NIH or any of the collaborating centers in the CCFR, nor does the mention of trade names, commercial products, or organizations imply endorsement by the US Government, any cancer registry, or the Colon CFR. NW, MD, and YT were supported by the Dutch Digestive Foundation (Grant FP 16-01) and the Dutch Cancer Society (Grant UL 2013-5939). BT was supported by an NHMRC CJ Martin Early Career Fellowship (ID1091211). AS was supported by an NHMRC Senior Research Fellowship (ID1061779). Publisher Copyright: {\textcopyright} Copyright {\textcopyright} 2020 Thompson, Walters, Parsons, Dumenil, Drost, Tiersma, Lindor, Tavtigian, de Wind, Spurdle and the InSiGHT Variant Interpretation Committee.",
year = "2020",
month = jul,
day = "27",
doi = "10.3389/fgene.2020.00798",
language = "English (US)",
volume = "11",
journal = "Frontiers in Genetics",
issn = "1664-8021",
publisher = "Frontiers Media S. A.",
}