Guidelines for Splicing Analysis in Molecular Diagnosis Derived from a Set of 327 Combined In Silico/In Vitro Studies on BRCA1 and BRCA2 Variants

被引：192

作者：

Houdayer, Claude ^{[1
,2
]}

Caux-Moncoutier, Virginie ^{[1
,2
]}

Krieger, Sophie ^{[3
]}

Barrois, Michel ^{[4
]}

Bonnet, Francoise ^{[5
]}

Bourdon, Violaine ^{[6
]}

Bronner, Myriam ^{[7
]}

Buisson, Monique ^{[8
]}

Coulet, Florence ^{[9
]}

Gaildrat, Pascaline ^{[10
]}

Lefol, Cedrick ^{[11
]}

Leone, Melanie ^{[12
]}

Mazoyer, Sylvie ^{[8
]}

Muller, Danielle ^{[13
]}

Remenieras, Audrey ^{[4
]}

Revillion, Francoise ^{[14
]}

Rouleau, Etienne ^{[11
]}

Sokolowska, Joanna ^{[7
]}

Vert, Jean-Philippe ^{[15
,17
]}

Lidereau, Rosette ^{[11
]}

Soubrier, Florent ^{[9
]}

Sobol, Hagay ^{[6
]}

Sevenet, Nicolas ^{[5
]}

Bressac-de Paillerets, Brigitte ^{[4
,16
]}

Hardouin, Agnes ^{[3
]}

Tosi, Mario ^{[10
]}

Sinilnikova, Olga M. ^{[2
,8
,12
]}

Stoppa-Lyonnet, Dominique ^{[1
,2
,18
]}

机构：

[1] Inst Curie, Serv Genet Oncol, F-75005 Paris, France

[2] Univ Paris 05, Paris, France

[3] Univ Caen Basse Normandie, Lab Biol Clin & Oncol, Ctr Francois Baclesse, Caen, France

[4] Inst Cancerol Gustave Roussy, Dept Biopathol, Serv Genet, Villejuif, France

[5] Inst Bergonie, INSERM, U916, Dept Pathol,Lab Genet Constitut, Bordeaux, France

[6] Inst Paoli Calmettes, Lab Oncogenet Mol, Marseille, France

[7] CHU Nancy Brabois, Serv Genet, Nancy, France

[8] Univ Lyon 1, CNRS INSERM U1052 UMR5286, Canc Res Ctr Lyon, Ctr Leon Berard, F-69365 Lyon, France

[9] Hop La Pitie Salpetriere, AP HP, Serv Genet, Paris, France

[10] Univ Rouen, INSERM, U1079, Inst Res & Innovat Biomed, Rouen, France

[11] Hop Rene Huguenin, Inst Curie, St Cloud, France

[12] Hosp Civils Lyon, Unite Mixte Genet Constitut Cancers Frequents, Ctr Leon Berard, Lyon, France

[13] Ctr Paul Strauss, Lab Oncogenet, Strasbourg, France

[14] Ctr Oscar Lambret, Lab Oncol Mol Humaine, F-59020 Lille, France

[15] Mines ParisTech, Ctr Computat Biol, Fontainebleau, France

[16] INSERM, U946, Paris, France

[17] INSERM, U900, Inst Curie, Paris, France

[18] INSERM, U830, Inst Curie, Paris, France

来源：

HUMAN MUTATION | 2012年 / 33卷 / 08期

关键词：

splice prediction; BRCA1; BRCA2; VUS; variants of unknown significance; guidelines; UNCLASSIFIED VARIANTS; RNA; MUTATIONS; EXON; TOOL; GENE; MSH2; CLASSIFICATION; PREDICTION; NONSENSE;

D O I：

10.1002/humu.22101

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Assessing the impact of variants of unknown significance (VUS) on splicing is a key issue in molecular diagnosis. This impact can be predicted by in silico tools, but proper evaluation and user guidelines are lacking. To fill this gap, we embarked upon the largest BRCA1 and BRCA2 splice study to date by testing 272 VUSs (327 analyses) within the BRCA splice network of Unicancer. All these VUSs were analyzed by using six tools (splice site prediction by neural network, splice site finder (SSF), MaxEntScan (MES), ESE finder, relative enhancer and silencer classification by unanimous enrichment, and human splicing finder) and the predictions obtained were compared with transcript analysis results. Combining MES and SSF gave 96% sensitivity and 83% specificity for VUSs occurring in the vicinity of consensus splice sites, that is, the surrounding 11 and 14 bases for the 5' and 3' sites, respectively. This study was also an opportunity to define guidelines for transcript analysis along with a tentative classification of splice variants. The guidelines drawn from this large series should be useful for the whole community, particularly in the context of growing sequencing capacities that require robust pipelines for variant interpretation. Hum Mutat 33:1228-1238, 2012. (c) 2012 Wiley Periodicals, Inc.

引用

页码：1228 / 1238

页数：11

共 42 条

[1] Unclassified variants identified in BRCA1 exon 11:: Consequences on splicing [J].