Assessment of the latest NGS enrichment capture methods in clinical context

Scientific Reports

Volumn 6, Issue , 2016, Pages

  García García, Gema ^a   Baux, David ^b   Faugère, Valérie ^b   Moclyn, Mélody ^b   Koenig, Michel ^a,b   Claustres, Mireille ^a,b   Roux, Anne Françoise ^a,b  

^a UNIVERSITÉ DE MONTPELLIER   (France)

^b MONTPELLIER UNIVERSITY HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEVICES; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; HEARING LOSS, FUNCTIONAL; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; RECESSIVE GENE; RETINITIS PIGMENTOSA; USHER SYNDROMES;

BASE COMPOSITION; GENES, RECESSIVE; HEARING LOSS, FUNCTIONAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RETINITIS PIGMENTOSA; SEQUENCE ANALYSIS, DNA; USHER SYNDROMES;

EID: 84958582482     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep20948     Document Type: Article

References (42)

1. Gullapalli, R., Desai, K., Santana-Santos, L., Kant, J. & Becich, M. Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J. Pathol. Inform. 3, 40 (2012).
2. Alazami, A. M. et al. Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Cell Rep. 10, 148-61 (2015).
3. Yu, T. W. et al. Using whole-exome sequencing to identify inherited causes of autism. Neuron 77, 259-73 (2013).
4. Rehm, H. L. Disease-targeted sequencing: a cornerstone in the clinic. Nat. Rev. Genet. 14, 295-300 (2013).
5. Wooderchak-Donahue, W. L. et al. A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel-clinical diagnostics perspective. BMC Med. Genomics 5, 50 (2012).
6. Lu, Y. et al. Resolving the genetic heterogeneity of prelingual hearing loss within one family: Performance comparison and application of two targeted next generation sequencing approaches. J. Hum. Genet. 59, 599-607 (2014).
7. Consugar, M. B. et al. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet. Med. 17, 253-261 (2015).
8. Hehir-Kwa, J. Y. et al. Towards a European consensus for reporting incidental findings during clinical NGS testing. Eur. J. Hum. Genet. 1-6 (2015).
9. Samorodnitsky, E. et al. Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing. Hum. Mutat. 36, 903-914 (2015).
10. Asan et al. Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 12, R95 (2011).
11. Chilamakuri, C. S. R. et al. Performance comparison of four exome capture systems for deep sequencing. BMC Genomics 15, 449 (2014).
12. Parla, J. S. et al. A comparative analysis of exome capture. Genome Biol. 12, R97 (2011).
13. Sulonen, A.-M. et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 12, R94 (2011).
14. Teer, J. K. et al. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res. 20, 1420-1431 (2010).
15. Clark, M. J. et al. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908-14 (2011).
16. Meienberg, J. et al. New insights into the performance of human whole-exome capture platforms. Nucleic Acids Res. 43, 1-14 (2015).
17. Bodi, K. et al. Comparison of commercially available target enrichment methods for next-generation sequencing. J. Biomol. Tech. 24, 73-86 (2013).
18. Ware, J. S. et al. Next generation diagnostics in inherited arrhythmia syndromes: A comparison of two approaches. J. Cardiovasc. Transl. Res. 6, 94-103 (2013).
19. Hedges, D. J. et al. Comparison of three targeted enrichment strategies on the Solid sequencing platform. PLoS One 6, 1-8 (2011).
20. Gargis, A. S. et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat. Biotechnol. 30, 1033-6 (2012).
21. Rehm, H. L. et al. ACMG clinical laboratory standards for next-generation sequencing. Genet. Med. 15, 733-47 (2013).
22. Matthijs et al. Guidelines for diagnostic next-generation sequencing. Eur J Hum Genet. 24, 2-5 (2016).
23. Mokry, M. et al. Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries. Nucleic Acids Res. 38, e116-e116 (2010).
24. Vona, B. et al. DFNB16 is a frequent cause of congenital hearing impairment: implementation of STRC mutation analysis in routine diagnostics. Clin. Genet. 87, 49-55 (2015).
25. Besnard, T. et al. Experience of targeted Usher exome sequencing as a clinical test. Mol. Genet. genomic Med. 2, 30-43 (2014).
26. van Dijk, E. L., Jaszczyszyn, Y. & Thermes, C. Library preparation methods for next-generation sequencing: Tone down the bias. Exp. Cell Res. 322, 12-20 (2014).
27. Green, B., Bouchier, C., Fairhead, C., Craig, N. L. & Cormack, B. P. Insertion site preference of Mu, Tn5, and Tn7 transposons. Mob. DNA 3, 3 (2012).
28. Lelieveld, S. H., Spielmann, M., Mundlos, S., Veltman, J. A. & Gilissen, C. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions. Hum. Mutat. 36, 815-822 (2015).
29. Aird, D. et al. Analyzing and minimizing bias in Illumina sequencing libraries. Genome Biol. 11, P3 (2010).
30. Quail, M. A. et al. Optimal enzymes for amplifying sequencing libraries. Nat. Methods 9, 10-11 (2011).
31. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
32. Ebersberger, I., Metzler, D., Schwarz, C. & Pääbo, S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70, 1490-1497 (2002).
33. Freudenberg-Hua, Y. et al. Single nucleotide variation analysis in 65 candidate genes for CNS disorders in representative sample of the European population. Genome Res. 13, 2271-2276 (2003).
34. Qi, X. P. et al. Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: Utility and limitations. Gene 516, 93-100 (2013).
35. Mandelker, D. et al. Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology. J. Mol. Diagn. 16, 639-47 (2014).
36. Francey, L. J. et al. Genome-wide SNP genotyping identifies the Stereocilin (STRC) gene as a major contributor to pediatric bilateral sensorineural hearing impairment. Am. J. Med. Genet. Part A 158 A, 298-308 (2012).
37. Claes, K. B. M. & De Leeneer, K. Dealing with pseudogenes in molecular diagnostics in the next-generation sequencing era. Methods Mol. Biol. 1167, 303-15 (2014).
38. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
39. McKenna, A. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
40. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
41. R Development Core Team. Computational Many-Particle Physics. R Foundation for Statistical Computing 739, (Springer Berlin Heidelberg, 2008).
42. Thorvaldsdóttir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178-192 (2013).