Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care

npj Genomic Medicine

Volumn 1, Issue , 2016, Pages

  Rennert, Hanna ^a,b   Eng, Kenneth ^a,b   Zhang, Tuo ^a,b   Tan, Adrian ^a,b   Xiang, Jenny ^a,b   Romanel, Alessandro ^c   Kim, Robert ^a,b   Tam, Wayne ^b   Liu, Yen Chun ^b   Bhinder, Bhavneet ^a   Cyrta, Joanna ^a   Beltran, Himisha ^a,b   Robinson, Brian ^a,b   Mosquera, Juan Miguel ^a,b   Fernandes, Helen ^a,b   Demichelis, Francesca ^c   Sboner, Andrea ^a,b   Kluk, Michael ^a,b   Rubin, Mark A ^a,b   Elemento, Olivier ^a,b  

^a NEW YORK PRESBYTERIAN HOSPITAL   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c UNIVERSITY OF TRENTO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85042217284     PISSN: None     EISSN: 20567944     Source Type: Journal    
DOI: 10.1038/npjgenmed.2016.19     Document Type: Article

References (24)

1. Rabbani, B., Tekin, M. & Mahdieh, N. The promise of whole-exome sequencing in medical genetics. J. Hum. Genet. 59, 5-15 (2014).
2. Biesecker, L. G. Exome sequencing makes medical genomics a reality. Nat. Genet. 42, 13-14.
3. Majewski, J., Schwartzentruber, J., Lalonde, E., Montpetit, A. & Jabado, N. What can exome sequencing do for you? J. Med. Genet. 48, 580-589 (2011).
4. Schreiber, M., Dorschner, M. & Tsuang, D. Next-generation sequencing in schizophrenia and other neuropsychiatric disorders. Am. J. Med. Genet. B Neuropsychiatr. Genet. 162, 671-678 (2013).
5. Dias-Santagata, D. et al. Rapid targeted mutational analysis of human tumours: A clinical platform to guide personalized cancer medicine. EMBO Mol. Med. 2, 146-158 (2010).
6. Mahdieh, N. & Rabbani, B. An overview of mutation detection methods in genetic disorders. Iran J. Pediatr. 23, 375-388 (2013).
7. Chan, T. A., Wolchok, J. D. & Snyder, A. Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma. N. Engl. J. Med. 373, 1984 (2015).
8. Van Allen, E. M. et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science 350, 207-211 (2015).
9. Robinson, D. et al. Integrative clinical genomics of advanced prostate cancer. Cell 161, 1215-1228 (2015).
10. Green, R. C. et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet. Med. 15, 565-574 (2013).
11. New York State Department of Health. http://www.wadsworth.org/sites/default/files/WebDoc/1300145166/NextGenSeq-ONCO-Guidelines.pdf Accessed on 2 February 2015.
12. Food and Drug Administration. http://www.fda.gov/downloads/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/UCM416685.pdf. Accessed on 2 July 2016.
13. Collins, F. S. & Varmus, H. A new initiative on precision medicine. N. Engl. J. Med. 372, 793-795 (2015).
14. Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246-251 (2014).
15. Beltran, H. et al. Whole-exome sequencing of metastatic cancer and biomarkers of treatment response. JAMA Oncol. 1, 466-474 (2015).
16. Berglund, E. C. et al. Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment. BMC Genomics 14, 856 (2013).
17. Chilamakuri, C. S. et al. Performance comparison of four exome capture systems for deep sequencing. BMC genomics 15, 449 (2014).
18. Van Allen, E. M. et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat. Med. 20, 682-688 (2014).
19. Green, A. et al. Assessment of HaloPlex amplification for sequence capture and massively parallel sequencing of arrhythmogenic right ventricular cardiomyopathy-Associated genes. J. Mol. Diagn. 17, 31-42 (2015).
20. Alioto, T. S. et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat. Commun. 6, 10001 (2015).
21. Prandi, D. et al. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 15, 439 (2014).
22. Vanneman, M. & Dranoff, G. Combining immunotherapy and targeted therapies in cancer treatment. Nat. Rev. Cancer 12, 237-251 (2012).
23. Coonrod, E. M., Durtschi, J. D., VanSant Webb, C., Voelkerding, K. V. & Kumanovics, A. Next-generation sequencing of custom amplicons to improve coverage of HaloPlex multigene panels. Biotechniques 57, 204-207 (2014).
24. Gullapalli, R. R., Desai, K. V., Santana-Santos, L., Kant, J. A. & Becich, M. J. Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics. J. Pathol. Inform. 3, 40 (2012).