Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors

Neuro-Oncology

Volumn 18, Issue 3, 2016, Pages 379-387

  Nikiforova, Marina N ^a   Wald, Abigail I ^a   Melan, Melissa A ^a   Roy, Somak ^a   Zhong, Shan ^a   Hamilton, Ronald L ^b   Lieberman, Frank S ^c   Drappatz, Jan ^c   Amankulor, Nduka M ^c   Pollack, Ian F ^a   Nikiforov, Yuri E ^a   Horbinski, Craig ^d  

^a UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

^b PRESBYTERIAN UNIVERSITY HOSPITAL   (United States)

^c UNIVERSITY OF PITTSBURGH CANCER INSTITUTE   (United States)

^d NORTHWESTERN UNIVERSITY   (United States)

Author keywords

CNS tumors; gene fusions; mutations; next generation sequencing; paraffin

Indexed keywords

DNA; RNA; B RAF KINASE;

ALLELE; ARTICLE; ATRX GENE; BRAF GENE; BRAIN BIOPSY; CANCER GRADING; CDKN2A GENE; CENTRAL NERVOUS SYSTEM TUMOR; COPY NUMBER VARIATION; EGFR GENE; FGFR3 GENE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE; GENE AMPLIFICATION; GENE FUSION; GENE IDENTIFICATION; GENE MUTATION; GENE STRUCTURE; GENETIC VARIABILITY; GLIOMA; H3F3A GENE; HUMAN; HUMAN TISSUE; IDH1 GENE; INDEL MUTATION; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; NEXT GENERATION SEQUENCING; PTEN GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SANGER SEQUENCING; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TERT GENE; TP53 GENE; ADOLESCENT; ADULT; CHILD; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; PRESCHOOL CHILD;

ADOLESCENT; ADULT; CENTRAL NERVOUS SYSTEM NEOPLASMS; CHILD; CHILD, PRESCHOOL; DNA COPY NUMBER VARIATIONS; GENETIC PREDISPOSITION TO DISEASE; GLIOMA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; PROTO-ONCOGENE PROTEINS B-RAF;

EID: 84960108414     PISSN: 15228517     EISSN: 15235866     Source Type: Journal    
DOI: 10.1093/neuonc/nov289     Document Type: Article

References (46)

1. Kliehues P, Birger PC, Aldape KD, et al. Glioblastoma. In: Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, eds. WHO Classification of Tumours of the Central Nervous System. 4th ed. Lyon: IARC; 2007:33-49.
2. Verhaak RG, Hoadley KA, Purdom E, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010;17(1):98-110.
3. Brennan CW, Verhaak RG, McKenna A, et al. The somatic genomic landscape of glioblastoma. Cell. 2013;155(2):462-477.
4. Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008; 321(5897):1807-1812.
5. Jiao Y, Killela PJ, Reitman ZJ, et al. Frequent ATRX, CIC, FUBP1 and IDH1 mutations refine the classification of malignant gliomas. Oncotarget. 2012;3(7):709-722.
6. Killela PJ, Reitman ZJ, Jiao Y, et al. TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal. Proc Natl Acad Sci USA. 2013; 110(15):6021-6026.
7. Schwartzentruber J, Korshunov A, Liu XY, et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012;482(7384):226-231.
8. Zhang J, Wu G, Miller CP, et al. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet. 2013;45(6):602-612.
9. Schindler G, Capper D, Meyer J, et al. Analysis of BRAF V600E mutation in 1,320 nervous system tumors reveals high mutation frequencies in pleomorphic xanthoastrocytoma, ganglioglioma and extra-cerebellar pilocytic astrocytoma. Acta Neuropathol. 2011;121(3):397-405.
10. Taylor MD, Northcott PA, Korshunov A, et al. Molecular subgroups of medulloblastoma: The current consensus. Acta Neuropathol. 2012;123(4):465-472.
11. Kool M, Korshunov A, Remke M, et al. Molecular subgroups of medulloblastoma: an international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas. Acta Neuropathol. 2012;123(4): 473-484.
12. Jones DT, Jager N, Kool M, et al. Dissecting the genomic complexity underlying medulloblastoma. Nature. 2012;488(7409):100-105.
13. Ramaswamy V, Remke M, Bouffet E, et al. Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis. Lancet Oncol. 2013;14(12):1200-1207.
14. Brastianos PK, Horowitz PM, Santagata S, et al. Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations. Nat Genet. 2013;45(3):285-289.
15. Huse JT, Aldape KD. The evolving role of molecular markers in the diagnosis and management of diffuse glioma. Clin Cancer Res. 2014;20(22):5601-5611.
16. Aldape K, Zadeh G, Mansouri S, Reifenberger G, von Deimling A. Glioblastoma: pathology, molecular mechanisms and markers. Acta Neuropathol. 2015;129(6):829-848.
17. Nikiforova MN, Wald AI, Roy S, Durso MB, Nikiforov YE. Targeted next-generation sequencing panel (ThyroSeq) for detection of mutations in thyroid cancer. J Clin Endocrinol Metab. 2013; 98(11):E1852-E1860.
18. Jennings L, Van Deerlin VM, Gulley ML. Recommended principles and practices for validating clinical molecular pathology tests. Arch Pathol Lab Med. 2009;133(5):743-755.
19. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
20. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812-3814.
21. Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat. Methods. 2010; 7(4):248-249.
22. Sherry ST, Ward MH, Kholodov M, et al. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 2001;29(1):308-311.
23. Forbes SA, Beare D, Gunasekaran P, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43(Database issue):D805-D811.
24. Grasso C, Butler T, Rhodes K, et al. Assessing copy number alterations in targeted, amplicon-based next-generation sequencing data. J Mol Diagn. 2015;17(1):53-63.
25. Martin M. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet.journal. 2011;17(1):10-12.
26. Lassmann T, Hayashizaki Y, Daub CO. SAMStat: monitoring biases in next generation sequencing data. Bioinformatics. 2011;27(1): 130-131.
27. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 2013;14(2):178-192.
28. Liu X, Bishop J, Shan Y, et al. Highly prevalent TERT promoter mutations in aggressive thyroid cancers. Endocr Relat. Cancer. 2013;20(4):603-610.
29. Korshunov A, Meyer J, Capper D, et al. Combined molecular analysis of BRAF and IDH1 distinguishes pilocytic astrocytoma from diffuse astrocytoma. Acta Neuropathol. 2009;118(3): 401-405.
30. Faulkner C, Palmer A, Williams H, et al. EGFR and EGFRvIII analysis in glioblastoma as therapeutic biomarkers. Br J Neurosurg. 2014:1-7.
31. Cin H,Meyer C, Herr R, et al. Oncogenic FAM131B-BRAF fusion resulting from 7q34 deletion comprises an alternative mechanism of MAPK pathway activation in pilocytic astrocytoma. Acta Neuropathol. 2011;121(6):763-774.
32. Mistry M, Zhukova N, Merico D, et al. BRAF mutation and CDKN2A deletion define a clinically distinct subgroup of childhood secondary high-grade glioma. J Clin Oncol. 2015;33(9):1015-1022.
33. Horbinski C, Nikiforova MN, Hagenkord JM, Hamilton RL, Pollack IF. Interplay among BRAF, p16, p53, and MIB1 in pediatric low-grade gliomas. Neuro Oncol. 2012;14(6):777-789.
34. Horbinski C. What do we know about IDH1/2 mutations so far, and how do we use it? Acta Neuropathol. 2013;125(5):621-636.
35. Horbinski C, Kofler J, Yeaney G, et al. Isocitrate dehydrogenase 1 analysis differentiates gangliogliomas from infiltrative gliomas. Brain Pathol. 2011;21(5):564-574.
36. Camelo-Piragua S, Jansen M, Ganguly A, et al. A sensitive and specific diagnostic panel to distinguish diffuse astrocytoma from astrocytosis: chromosome 7 gain with mutant isocitrate dehydrogenase 1 and p53. J Neuropathol Exp Neurol. 2011; 70(2):110-115.
37. Sturm D, Witt H, Hovestadt V, et al. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell. 2012;22(4):425-437.
38. Wu G, Broniscer A, McEachron TA, et al. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet. 2012;44(3):251-253.
39. Koelsche C, Sahm F, Capper D, et al. Distribution of TERT promoter mutations in pediatric and adult tumors of the nervous system. Acta Neuropathol. 2013;126(6):907-915.
40. Yip S, Butterfield YS, Morozova O, et al. Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol. 2012;226(1):7-16.
41. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455(7216): 1061-1068.
42. Eckel-Passow JE, Lachance DH, Molinaro AM, et al. Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. N Engl J Med. 2015;372(26):2499-2508.
43. Di Stefano AL, Fucci A, Frattini V, et al. Detection, Characterization, and Inhibition of FGFR-TACC Fusions in IDH Wild-type Glioma. Clin Cancer Res. 2015;21(14):3307-3317.
44. Clark VE, Erson-Omay EZ, Serin A, et al. Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science. 2013;339(6123):1077-1080.
45. Kieran MW, Roberts CW, Chi SN, et al. Absence of oncogenic canonical pathway mutations in aggressive pediatric rhabdoid tumors. Pediatr Blood Cancer. 2012;59(7):1155-1157.
46. Parker M, Mohankumar KM, Punchihewa C, et al. C11orf95-RELA fusions drive oncogenic NF-kB signalling in ependymoma. Nature. 2014;506(7489):451-455.