Evaluation of in silico splice tools for decision-making in molecular diagnosis.

PubWeight™: 1.78‹?› | Rank: Top 3%

🔗 View Article (PMID 18449911)

Published in Hum Mutat on July 01, 2008

Authors

Claude Houdayer1, Catherine Dehainault, Christophe Mattler, Dorothée Michaux, Virginie Caux-Moncoutier, Sabine Pagès-Berhouet, Catherine Dubois d'Enghien, Anthony Laugé, Laurent Castera, Marion Gauthier-Villars, Dominique Stoppa-Lyonnet

Author Affiliations

1: Institut Curie, Service de Génétique Oncologique, Paris, France. claude.houdayer@curie.net

Articles citing this

Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res (2009) 10.08

Molecular genetic testing and the future of clinical genomics. Nat Rev Genet (2013) 2.03

Prediction and assessment of splicing alterations: implications for clinical testing. Hum Mutat (2008) 1.73

Clinically applicable models to characterize BRCA1 and BRCA2 variants of uncertain significance. J Clin Oncol (2008) 1.56

Genomic features defining exonic variants that modulate splicing. Genome Biol (2010) 1.46

Progressive familial intrahepatic cholestasis. Orphanet J Rare Dis (2009) 1.38

Missed threads. The impact of pre-mRNA splicing defects on clinical practice. EMBO Rep (2009) 1.32

Classification of missense substitutions in the BRCA genes: a database dedicated to Ex-UVs. Hum Mutat (2011) 1.31

In silico tools for splicing defect prediction: a survey from the viewpoint of end users. Genet Med (2013) 1.22

Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet (2009) 1.18

Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes. Eur J Hum Genet (2011) 1.16

Impact of BRCA1 and BRCA2 variants on splicing: clues from an allelic imbalance study. Eur J Hum Genet (2009) 1.13

Genome-wide discovery of human splicing branchpoints. Genome Res (2015) 1.08

Comparison of mRNA splicing assay protocols across multiple laboratories: recommendations for best practice in standardized clinical testing. Clin Chem (2013) 1.01

Analysis of 30 putative BRCA1 splicing mutations in hereditary breast and ovarian cancer families identifies exonic splice site mutations that escape in silico prediction. PLoS One (2012) 0.98

Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects. Eur J Hum Genet (2015) 0.97

Splicing mutations in glycogen-storage disease type II: evaluation of the full spectrum of mutations and their relation to patients' phenotypes. Eur J Hum Genet (2010) 0.91

Experimental assessment of splicing variants using expression minigenes and comparison with in silico predictions. Hum Mutat (2014) 0.90

Underexpression and abnormal localization of ATM products in ataxia telangiectasia patients bearing ATM missense mutations. Eur J Hum Genet (2011) 0.89

The tumor suppressor gene retinoblastoma-1 is required for retinotectal development and visual function in zebrafish. PLoS Genet (2012) 0.89

The intronic splicing code: multiple factors involved in ATM pseudoexon definition. EMBO J (2010) 0.89

Identification of germline alterations of the mad homology 2 domain of SMAD3 and SMAD4 from the Ontario site of the breast cancer family registry (CFR). Breast Cancer Res (2011) 0.89

The molecular basis of von Willebrand disease: the under investigated, the unexpected and the overlooked. Haematologica (2011) 0.89

Episodic ataxia type 2: phenotype characteristics of a novel CACNA1A mutation and review of the literature. J Neurol (2014) 0.88

Detection of novel mutations that cause autosomal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing. Mol Vis (2013) 0.88

Prediction of disease-related mutations affecting protein localization. BMC Genomics (2009) 0.86

A novel splice-site mutation in angiotensin I-converting enzyme (ACE) gene, c.3691+1G>A (IVS25+1G>A), causes a dramatic increase in circulating ACE through deletion of the transmembrane anchor. PLoS One (2013) 0.85

Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. DNA Res (2010) 0.84

Functional properties and evolutionary splicing constraints on a composite exonic regulatory element of splicing in CFTR exon 12. Nucleic Acids Res (2009) 0.84

Polymorphic variation within the VWF gene contributes to the failure to detect mutations in patients historically diagnosed with type 1 von Willebrand disease from the MCMDM-1VWD cohort. Haematologica (2010) 0.83

Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases. Mol Genet Genomic Med (2013) 0.83

Small-scale high-throughput sequencing-based identification of new therapeutic tools in cystic fibrosis. Genet Med (2015) 0.82

Identification and characterisation of mutations associated with von Willebrand disease in a Turkish patient cohort. Thromb Haemost (2013) 0.81

Diagnostic workup and management of patients with suspected Niemann-Pick type C disease. Ther Adv Neurol Disord (2016) 0.80

Mutation survey of candidate genes in 40 Chinese patients with congenital ectopia lentis. Mol Vis (2014) 0.79

Candidate gene sequencing of SLC11A2 and TMPRSS6 in a family with severe anaemia: common SNPs, rare haplotypes, no causative mutation. PLoS One (2012) 0.79

Integration of molecular and clinical data of 40 unrelated von Willebrand Disease families in a Spanish locus-specific mutation database: first release including 58 mutations. Haematologica (2010) 0.79

Mutation survey of the optic atrophy 1 gene in 193 Chinese families with suspected hereditary optic neuropathy. Mol Vis (2013) 0.79

Genotype-phenotype correlations in sepiapterin reductase deficiency. A splicing defect accounts for a new phenotypic variant. Neurogenetics (2011) 0.79

A retroelement modifies pre-mRNA splicing: the murine Glrb(spa) allele is a splicing signal polymorphism amplified by long interspersed nuclear element insertion. J Biol Chem (2012) 0.79

Exon first nucleotide mutations in splicing: evaluation of in silico prediction tools. PLoS One (2014) 0.78

Computational analysis of the mutations in BAP1, PBRM1 and SETD2 genes reveals the impaired molecular processes in renal cell carcinoma. Oncotarget (2015) 0.77

Functional classification of BRCA2 DNA variants by splicing assays in a large minigene with 9 exons. Hum Mutat (2015) 0.77

A splice mutation and mRNA decay of EXT2 provoke hereditary multiple exostoses. PLoS One (2014) 0.77

Splicing defects caused by exonic mutations in PKD1 as a new mechanism of pathogenesis in autosomal dominant polycystic kidney disease. RNA Biol (2015) 0.76

A Novel Pathogenic BRCA1 Splicing Variant Produces Partial Intron Retention in the Mature Messenger RNA. Int J Mol Sci (2016) 0.75

Mutation survey and genotype-phenotype analysis of COL2A1 and COL11A1 genes in 16 Chinese patients with Stickler syndrome. Mol Vis (2016) 0.75

Articles by these authors

A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor-negative breast cancer in the general population. Nat Genet (2010) 4.96

Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat Genet (2013) 4.35

Protein interaction mapping: a Drosophila case study. Genome Res (2005) 4.15

Salpingo-oophorectomy and the risk of ovarian, fallopian tube, and peritoneal cancers in women with a BRCA1 or BRCA2 Mutation. JAMA (2006) 4.09

RAD51 135G-->C modifies breast cancer risk among BRCA2 mutation carriers: results from a combined analysis of 19 studies. Am J Hum Genet (2007) 3.63

A SUMOylation-defective MITF germline mutation predisposes to melanoma and renal carcinoma. Nature (2011) 3.53

Common breast cancer-predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. Am J Hum Genet (2008) 3.41

Oral contraceptives and the risk of breast cancer in BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst (2002) 3.25

Accuracy of liver stiffness measurement for the diagnosis of cirrhosis in patients with chronic liver diseases. Hepatology (2006) 3.19

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol (2009) 2.88

SAFE biopsy: a validated method for large-scale staging of liver fibrosis in chronic hepatitis C. Hepatology (2009) 2.45

Exposure to diagnostic radiation and risk of breast cancer among carriers of BRCA1/2 mutations: retrospective cohort study (GENE-RAD-RISK). BMJ (2012) 2.44

Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk. PLoS Genet (2013) 2.39

The nonsense-mediated mRNA decay pathway triggers degradation of most BRCA1 mRNAs bearing premature termination codons. Hum Mol Genet (2002) 2.38

A genome wide linkage search for breast cancer susceptibility genes. Genes Chromosomes Cancer (2006) 2.35

Pregnancies, breast-feeding, and breast cancer risk in the International BRCA1/2 Carrier Cohort Study (IBCCS). J Natl Cancer Inst (2006) 2.25

Common variants in LSP1, 2q35 and 8q24 and breast cancer risk for BRCA1 and BRCA2 mutation carriers. Hum Mol Genet (2009) 2.13

Myelodysplasia and leukemia of Fanconi anemia are associated with a specific pattern of genomic abnormalities that includes cryptic RUNX1/AML1 lesions. Blood (2011) 1.99

Pathology of breast and ovarian cancers among BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Cancer Epidemiol Biomarkers Prev (2011) 1.99

2009 version of the Chompret criteria for Li Fraumeni syndrome. J Clin Oncol (2009) 1.97

Partial splenic embolization in patients with cirrhosis: efficacy, tolerance and long-term outcome in 32 patients. Eur J Gastroenterol Hepatol (2005) 1.94

ENIGMA--evidence-based network for the interpretation of germline mutant alleles: an international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes. Hum Mutat (2011) 1.94

Antiviral action of ribavirin in chronic hepatitis C. Gastroenterology (2004) 1.92

Common breast cancer susceptibility alleles and the risk of breast cancer for BRCA1 and BRCA2 mutation carriers: implications for risk prediction. Cancer Res (2010) 1.90

Identification of a BRCA2-specific modifier locus at 6p24 related to breast cancer risk. PLoS Genet (2013) 1.88

Standardization of ROC curve areas for diagnostic evaluation of liver fibrosis markers based on prevalences of fibrosis stages. Clin Chem (2007) 1.84

Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res (2012) 1.78

Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum Mutat (2012) 1.77

Functional consequences of ATM sequence variants for chromosomal radiosensitivity. Genes Chromosomes Cancer (2004) 1.76

AURKA F31I polymorphism and breast cancer risk in BRCA1 and BRCA2 mutation carriers: a consortium of investigators of modifiers of BRCA1/2 study. Cancer Epidemiol Biomarkers Prev (2007) 1.75

Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet (2013) 1.69

Rapid detection of novel BRCA1 rearrangements in high-risk breast-ovarian cancer families using multiplex PCR of short fluorescent fragments. Hum Mutat (2002) 1.66

Prophylactic salpingo-oophorectomy in a series of 89 women carrying a BRCA1 or a BRCA2 mutation. Cancer (2007) 1.63

Professionals assess the acceptability of preimplantation genetic diagnosis and prenatal diagnosis for managing inherited predisposition to cancer. J Clin Oncol (2009) 1.62

High frequency of TP53 mutation in BRCA1 and sporadic basal-like carcinomas but not in BRCA1 luminal breast tumors. Cancer Res (2009) 1.61

Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity. Breast Cancer Res (2007) 1.58

Common genetic variants and modification of penetrance of BRCA2-associated breast cancer. PLoS Genet (2010) 1.56

Factors of accuracy of transient elastography (fibroscan) for the diagnosis of liver fibrosis in chronic hepatitis C. Hepatology (2009) 1.55

Lack of HIN-1 methylation defines specific breast tumor subtypes including medullary carcinoma of the breast and BRCA1-linked tumors. Cancer Biol Ther (2003) 1.52

Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers. Hum Mol Genet (2011) 1.51

Meta-analyses of FibroTest diagnostic value in chronic liver disease. BMC Gastroenterol (2007) 1.49

Retinoblastoma. Orphanet J Rare Dis (2006) 1.44

Should chromosome breakage studies be performed in patients with VACTERL association? Am J Med Genet A (2005) 1.42

Hepatitis B vaccination in HIV-infected patients: a survey of physicians and patients participating in the Aquitaine cohort. Gastroenterol Clin Biol (2006) 1.42

Mood alterations during interferon-alfa therapy in patients with chronic hepatitis C: evidence for an overlap between manic/hypomanic and depressive symptoms. J Clin Psychiatry (2005) 1.41

[Steasis and hepatitis C]. Gastroenterol Clin Biol (2003) 1.41

Genetic variation at 9p22.2 and ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst (2010) 1.41

Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. Breast Cancer Res (2012) 1.38

Does the nonsense-mediated mRNA decay mechanism prevent the synthesis of truncated BRCA1, CHK2, and p53 proteins? Hum Mutat (2008) 1.30

Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. J Clin Oncol (2013) 1.29

A comparison of bilateral breast cancers in BRCA carriers. Cancer Epidemiol Biomarkers Prev (2005) 1.27

Testing for BRCA1 mutations: a cost-effectiveness analysis. Eur J Hum Genet (2002) 1.26

Diagnosis of Fanconi anemia in patients with bone marrow failure. Haematologica (2009) 1.25

Genotype-phenotype correlations in hereditary familial retinoblastoma. Hum Mutat (2007) 1.25

Evolving practices of non-invasive markers of liver fibrosis in patients with chronic hepatitis C in France: time for new guidelines? J Hepatol (2006) 1.25

Contiguous gene deletion within chromosome arm 10q is associated with juvenile polyposis of infancy, reflecting cooperation between the BMPR1A and PTEN tumor-suppressor genes. Am J Hum Genet (2006) 1.24

Frequent hSNF5/INI1 germline mutations in patients with rhabdoid tumor. Clin Cancer Res (2011) 1.24

Evaluation of linkage of breast cancer to the putative BRCA3 locus on chromosome 13q21 in 128 multiple case families from the Breast Cancer Linkage Consortium. Proc Natl Acad Sci U S A (2002) 1.23

Common breast cancer susceptibility alleles are associated with tumour subtypes in BRCA1 and BRCA2 mutation carriers: results from the Consortium of Investigators of Modifiers of BRCA1/2. Breast Cancer Res (2011) 1.22

Significant contribution of germline BRCA2 rearrangements in male breast cancer families. Cancer Res (2004) 1.18

Common variants at the 19p13.1 and ZNF365 loci are associated with ER subtypes of breast cancer and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev (2012) 1.17

On the origin and diffusion of BRCA1 c.5266dupC (5382insC) in European populations. Eur J Hum Genet (2010) 1.17

Common variants associated with breast cancer in genome-wide association studies are modifiers of breast cancer risk in BRCA1 and BRCA2 mutation carriers. Hum Mol Genet (2010) 1.15

Risk of breast cancer recurrence and contralateral breast cancer in relation to BRCA1 and BRCA2 mutation status following breast-conserving surgery and radiotherapy. Eur J Cancer (2005) 1.15

Impact of BRCA1 and BRCA2 variants on splicing: clues from an allelic imbalance study. Eur J Hum Genet (2009) 1.13

Spontaneous abrogation of the G₂DNA damage checkpoint has clinical benefits but promotes leukemogenesis in Fanconi anemia patients. J Clin Invest (2010) 1.13

Neonatal cancer. Lancet Oncol (2013) 1.13

Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol (2011) 1.12

X inactive-specific transcript RNA coating and genetic instability of the X chromosome in BRCA1 breast tumors. Cancer Res (2007) 1.12

A single mutated BRCA1 allele leads to impaired fidelity of double strand break end-joining. Oncogene (2002) 1.12

Alternative Response Criteria (Choi, European association for the study of the liver, and modified Response Evaluation Criteria in Solid Tumors [RECIST]) Versus RECIST 1.1 in patients with advanced hepatocellular carcinoma treated with sorafenib. Oncologist (2014) 1.09

MDM2 as a modifier gene in retinoblastoma. J Natl Cancer Inst (2010) 1.09

EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. Hum Mutat (2011) 1.08

Patients' characteristics and rate of Internet use to obtain cancer information. J Public Health (Oxf) (2006) 1.08

Update on ultrasound imaging of liver fibrosis. J Hepatol (2013) 1.07

Familial breast cancer: clinical response to induction chemotherapy or radiotherapy related to BRCA1/2 mutations status. Am J Clin Oncol (2009) 1.07