Diagnostic application of high resolution single nucleotide polymorphism array analysis for children with brain tumors.
Single nucleotide polymorphism (SNP) array analysis is currently used as a first tier test for pediatric brain tumors at The Children's Hospital of Philadelphia. The results from 100 consecutive patients are summarized in the present report. Eighty-seven percent of the tumors had at least one pathogenic copy number alteration. Nineteen of 56 low grade gliomas (LGGs) demonstrated a duplication in 7q34, which resulted in a KIAA1549-BRAF fusion. Chromosome band 7q34 deletions, which resulted in a FAM131B-BRAF fusion, were identified in one pilocytic astrocytoma (PA) and one dysembryoplastic neuroepithelial tumor (DNT). One ganglioglioma (GG) demonstrated a 6q23.3q26 deletion that was predicted to result in a MYB-QKI fusion. Gains of chromosomes 5, 6, 7, 11, and 20 were seen in a subset of LGGs. Monosomy 6, deletion of 9q and 10q, and an i(17)(q10) were each detected in the medulloblastomas (MBs). Deletions and regions of loss of heterozygosity that encompassed TP53, RB1, CDKN2A/B, CHEK2, NF1, and NF2 were identified in a variety of tumors, which led to a recommendation for germline testing. A BRAF p.Thr599dup or p.V600E mutation was identified by Sanger sequencing in one and five gliomas, respectively, and a somatic TP53 mutation was identified in a fibrillary astrocytoma. No TP53 hot-spot mutations were detected in the MBs. SNP array analysis of pediatric brain tumors can be combined with pathologic examination and molecular analyses to further refine diagnoses, offer more accurate prognostic assessments, and identify patients who should be referred for cancer risk assessment.
Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA. Electronic address: rothj@email.chop.edu.
Jacquelyn J
JJ
Roth
Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
Mariarita
M
Santi
Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
Lucy B
LB
Rorke-Adams
Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA.
Brian N
BN
Harding
Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA.
Tracy M
TM
Busse
Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA.
Laura S
LS
Tooke
Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA. Electronic address: biegel@mail.med.upenn.edu.
Jaclyn A
JA
Biegel
D000293:Adolescent; D001932:Brain Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D002648:Child; D002675:Child, Preschool; D002869:Chromosome Aberrations; D056915:DNA Copy Number Variations; D005260:Female; D018303:Ganglioglioma / Q000175:diagnosis / Q000235:genetics; D005910:Glioma / Q000175:diagnosis / Q000235:genetics; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D008527:Medulloblastoma / Q000175:diagnosis / Q000235:genetics; D008579:Meningioma / Q000175:diagnosis / Q000235:genetics; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015514:Oncogene Proteins, Fusion / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D055815:Young Adult
D015514:Oncogene Proteins, Fusion; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf
BRAF; FAM131B; KIAA1549; MYB; QKI; Single nucleotide polymorphism; TP53; astrocytoma; ependymoma; glioma; medulloblastoma