The minimal amount of starting DNA for Agilent's hybrid capturebased targeted massively parallel sequencing

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Chung, Jongsuk ^a,b,c   Son, Dae Soon ^a,b   Jeon, Hyo Jeong ^b   Kim, Kyoung Mee ^c   Park, Gahee ^b   Ryu, Gyu Ha ^b   Park, Woong Yang ^b,c   Park, Donghyun ^a,b  

^a SAMSUNG Electronics   (South Korea)

^b Samsung Medical Center   (South Korea)

^c Sungkyunkwan University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

LIGATION; PRACTICE GUIDELINE; CHEMISTRY; COMPARATIVE STUDY; DEVICES; DIAGNOSTIC KIT; DNA SEQUENCE; GENETICS; PROCEDURES;

DNA;

DNA; REAGENT KITS, DIAGNOSTIC; SEQUENCE ANALYSIS, DNA;

EID: 84971353886     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep26732     Document Type: Article

References (40)

1. Collins, F. S., Varmus, H. A new initiative on precision medicine. N Engl J Med 372, 793-5 (2015).
2. de Bono, J. S., Ashworth, A. Translating cancer research into targeted therapeutics. Nature 467, 543-9 (2010).
3. Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333-9 (2013).
4. Choi, M. et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 106, 19096-101 (2009).
5. Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27, 182-9 (2009).
6. Summerer, D. et al. Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform. Genomics 95, 241-6 (2010).
7. Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 12, R1 (2011).
8. Mamanova, L. et al. Target-enrichment strategies for next-generation sequencing. Nat Methods 7, 111-8 (2010).
9. Frampton, G. M. et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol 31, 1023-31 (2013).
10. Vigliar, E., Malapelle, U., de Luca, C., Bellevicine, C., Troncone, G. Challenges and opportunities of next-generation sequencing: a cytopathologist's perspective. Cytopathology 26, 271-83 (2015).
11. Bedard, P. L., Hansen, A. R., Ratain, M. J., Siu, L. L. Tumour heterogeneity in the clinic. Nature 501, 355-64 (2013).
12. Young, G. et al. Clinical next-generation sequencing successfully applied to fine-needle aspirations of pulmonary and pancreatic neoplasms. Cancer Cytopathol 121, 688-94 (2013).
13. Lozano, M. D. et al. Assessment of EGFR and KRAS mutation status from FNAs and core-needle biopsies of non-small cell lung cancer. Cancer Cytopathol 123, 230-6 (2015).
14. Kerick, M. et al. Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics 4, 68 (2011).
15. Zhu, Q. et al. The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology. Cancer Epidemiol Biomarkers Prev 24, 1207-13 (2015).
16. Diaz, L. A. Jr. et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 486, 537-40 (2012).
17. Ramos, E. et al. Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing. BMC Genomics 13, 683 (2012).
18. Rykalina, V. N. et al. Exome sequencing from nanogram amounts of starting DNA: comparing three approaches. Plos One 9, e101154 (2014).
19. Kozarewa, I. et al. A modified method for whole exome resequencing from minimal amounts of starting DNA. Plos One 7, e32617 (2012).
20. Shearer, A. E., Hildebrand, M. S., Smith, R. J. Solution-based targeted genomic enrichment for precious DNA samples. BMC Biotechnol 12, 20 (2012).
21. Chilamakuri, C. S. et al. Performance comparison of four exome capture systems for deep sequencing. BMC Genomics 15, 449 (2014).
22. Shigemizu, D. et al. Performance comparison of four commercial human whole-exome capture platforms. Sci Rep 5, 12742 (2015).
23. Gundry, M., Vijg, J. Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat Res 729, 1-15 (2012).
24. Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci USA 109, 14508-13 (2012).
25. Shin, J., Ming, G. L., Song, H. Decoding neural transcriptomes and epigenomes via high-throughput sequencing. Nat Neurosci 17, 1463-75 (2014).
26. Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2, 82-93 (2012).
27. Diaz, L. A. Jr., Bardelli, A. Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol 32, 579-86 (2014).
28. Diehl, F. et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA 102, 16368-73 (2005).
29. Newman, A. M. et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med 20, 548-54 (2014).
30. Diehl, F. et al. Circulating mutant DNA to assess tumor dynamics. Nat Med 14, 985-90 (2008).
31. Murtaza, M. et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497, 108-12 (2013).
32. Ross, M. G. et al. Characterizing and measuring bias in sequence data. Genome Biol 14, R51 (2013).
33. Benjamini, Y., Speed, T. P. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40, e72 (2012).
34. Oyola, S. O. et al. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13, 1 (2012).
35. Li, H., Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-95 (2010).
36. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-9 (2009).
37. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297-303 (2010).
38. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31, 213-9 (2013).
39. Ye, K., Schulz, M. H., Long, Q., Apweiler, R., Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-71 (2009).
40. Siva, N. 1000 Genomes project. Nat Biotechnol 26, 256 (2008).