Evaluation of a new NGS method based on a custom AmpliSeq library and Ion Torrent PGM sequencing for the fast detection of genetic variations in cardiomyopathies

Clinica Chimica Acta

Volumn 433, Issue , 2014, Pages 266-271

  Millat, Gilles ^a,b   Chanavat, Valérie ^a   Rousson, Robert ^a,b  

^a HOSPICES CIVILS DE LYON   (France)

^b UNIVERSITÉ LYON 1   (France)

Author keywords

Dilated cardiomyopathy; Hypertrophic cardiomyopathy; Molecular diagnosis; Mutations; NGS sequencing

Indexed keywords

GENOMIC DNA; SODIUM CHANNEL NAV1.5;

AMINO ACID SUBSTITUTION; ANALYTICAL EQUIPMENT; ARTICLE; CARDIOMYOPATHY; CLINICAL PROTOCOL; COHORT ANALYSIS; COMPUTER MODEL; COMPUTER PROGRAM; CONGESTIVE CARDIOMYOPATHY; COST EFFECTIVENESS ANALYSIS; FALSE POSITIVE RESULT; GENE; GENE LIBRARY; GENE SEQUENCE; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; HYPERTROPHIC CARDIOMYOPATHY; INDEL MUTATION; LMNA GENE; MAJOR CLINICAL STUDY; MUTATIONAL ANALYSIS; MYBPC3 GENE; MYH7 GENE; MYL2 GENE; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; SCN5A GENE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; TNNI3 GENE; TNNT2 GENE; TPM1 GENE; WORKFLOW; BIOLOGY; DNA SEQUENCE; EVALUATION STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; TIME;

CARDIOMYOPATHIES; COHORT STUDIES; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; SEQUENCE ANALYSIS, DNA; SOFTWARE; TIME FACTORS;

EID: 84899007760     PISSN: 00098981     EISSN: 18733492     Source Type: Journal    
DOI: 10.1016/j.cca.2014.03.032     Document Type: Article

References (17)

1. Rapezzi C., Arbustini E., Caforio A.L., et al. Diagnostic work-up in cardiomyopathies: bridging the gap between clinical phenotypes and final diagnosis. A position statement from the ESC Working Group on Myocardial and Pericardial Diseases. Eur Heart J 2013, 34:1448-1458.
2. Jacoby D., McKenna W.J. Genetics of inherited cardiomyopathy. Eur Heart J 2012, 33:296-304.
3. Millat G., Chanavat V., Créhalet H., Rousson R. Development of a high resolution melting method for the detection of genetic variations in hypertrophic cardiomyopathy. Clin Chim Acta 2010, 411:1983-1991.
4. Millat G., Bouvagnet P., Chevalier P., et al. Prevalence and spectrum of mutations in a cohort of 192 unrelated patients with hypertrophic cardiomyopathy. Eur J Med Genet 2010, 53:261-267.
5. Millat G., Chanavat V., Julia S., Crehalet H., Bouvagnet P., Rousson R. Validation of high-resolution DNA melting analysis for mutation scanning of the LMNA gene. Clin Biochem 2009, 42:892-898.
6. Millat G., Chanavat V., Rodriguez-Lafrasse C., Rousson R. Rapid, sensitive and inexpensive detection of SCN5A genetic variations by high resolution melting analysis. Clin Biochem 2009, 42:491-499.
7. Sikkema-Raddatz B., Johansson L.F., de Boer E.N., et al. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Hum Mutat 2013, 34:1035-1042.
8. Mook O.R., Haagmans M.A., Soucy J.F., et al. Targeted sequence capture and GS-FLX Titanium sequencing of 23 hypertrophic and dilated cardiomyopathy genes: implementation into diagnostics. J Med Genet 2013, 50:614-626.
9. Dames S., Durtschi J., Geiersbach K., Stephens J., Voelkerding K.V. Comparison of the Illumina Genome Analyzer and Roche 454 GS FLX for resequencing of hypertrophic cardiomyopathy-associated genes. J Biomol Tech 2010, 21:73-80.
10. Teekakirikul P., Kelly M.A., Rehm H.L., Lakdawala N.K., Funke B.H. Inherited cardiomyopathies: molecular genetics and clinical genetic testing in the postgenomic era. J Mol Diagn 2013, 15:158-170.
11. Meder B., Haas J., Keller A., et al. Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies. Circ Cardiovasc Genet 2011, 4:110-122.
12. Li X., Buckton A.J., Wilkinson S.L., et al. Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers. PLoS One 2013, 8(7):e6774.
13. Tarabeux J., Zeitouni B., Moncoutier V., et al. Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model. Eur J Hum Genet 2014, 22:535-541.
14. Abou Tayoun A.N., Tunkey C.D., Pugh T.J., et al. A comprehensive assay for CFTR mutational analysis using next-generation sequencing. Clin Chem 2013, 59:1481-1488.
15. Elliott A.M., Radecki J., Moghis B., Li X., Kammesheidt A. Rapid detection of the ACMG/ACOG-recommended 23 CFTR disease-causing mutations using ion torrent semiconductor sequencing. J Biomol Tech 2012, 23:24-30.
16. Yeo Z.X., Chan M., Yap Y.S., Ang P., Rozen S., Lee A.S. Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer. PLoS One 2012, 7(9):e45798.
17. Chin E.L., da Silva C., Hegde M. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet 2013, 14:6.