High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.
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High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors. / Hasselblatt, Martin; Isken, Sarah; Linge, Anna; Eikmeier, Kristin; Jeibmann, Astrid; Oyen, Florian; Nagel, Inga; Richter, Julia; Bartelheim, Kerstin; Kordes, Uwe; Schneppenheim, Reinhard; Frühwald, Michael; Siebert, Reiner; Paulus, Werner.
In: GENE CHROMOSOME CANC, Vol. 52, No. 2, 2, 2013, p. 185-190.Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review
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TY - JOUR
T1 - High-resolution genomic analysis suggests the absence of recurrent genomic alterations other than SMARCB1 aberrations in atypical teratoid/rhabdoid tumors.
AU - Hasselblatt, Martin
AU - Isken, Sarah
AU - Linge, Anna
AU - Eikmeier, Kristin
AU - Jeibmann, Astrid
AU - Oyen, Florian
AU - Nagel, Inga
AU - Richter, Julia
AU - Bartelheim, Kerstin
AU - Kordes, Uwe
AU - Schneppenheim, Reinhard
AU - Frühwald, Michael
AU - Siebert, Reiner
AU - Paulus, Werner
N1 - Copyright © 2012 Wiley Periodicals, Inc.
PY - 2013
Y1 - 2013
N2 - Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high-resolution genome-wide analysis was performed using a molecular inversion probe single-nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin-fixed paraffin-embedded express) on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT.
AB - Atypical teratoid/rhabdoid tumor (AT/RT) is a rare malignant pediatric brain tumor characterized by genetic alterations affecting the SMARCB1 (hSNF5/INI1) locus in chromosome band 22q11.2. To identify potential additional genetic alterations, high-resolution genome-wide analysis was performed using a molecular inversion probe single-nucleotide polymorphism (MIP SNP) assay (Affymetrix OncoScan formalin-fixed paraffin-embedded express) on DNA isolated from 18 formalin-fixed paraffin-embedded archival samples. Alterations affecting the SMARCB1 locus could be demonstrated by MIP SNP in 15 out of 16 evaluable cases (94%). These comprised five tumors with homozygous deletions, six tumors with heterozygous deletions, and four tumors with copy number neutral loss of heterozygosity (LOH) involving chromosome band 22q11.2. Remarkably, MIB SNP analysis did not yield any further recurrent chromosomal gains, losses, or copy neutral LOH. On MIP SNP screening for somatic mutations, the presence of a SMARCB1 mutation (c.472C>T p.R158X) was confirmed, but no recurrent mutations of other cancer relevant genes could be identified. Results of fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, and SMARCB1 sequencing were highly congruent with that of the MIP SNP assay. In conclusion, these data further suggest the absence of recurrent genomic alterations other than SMARCB1 in AT/RT.
KW - Humans
KW - Male
KW - Female
KW - Child, Preschool
KW - Genotype
KW - Infant
KW - Gene Deletion
KW - Infant, Newborn
KW - DNA Mutational Analysis
KW - Chromosome Aberrations
KW - Loss of Heterozygosity
KW - Genome-Wide Association Study
KW - Polymorphism, Single Nucleotide
KW - In Situ Hybridization, Fluorescence
KW - Transcription Factors/genetics
KW - DNA-Binding Proteins/genetics
KW - Mutation
KW - DNA Copy Number Variations
KW - Multiplex Polymerase Chain Reaction
KW - Chromosomal Proteins, Non-Histone/genetics
KW - Chromosomes, Human, Pair 22/genetics
KW - Rhabdoid Tumor/genetics
KW - Humans
KW - Male
KW - Female
KW - Child, Preschool
KW - Genotype
KW - Infant
KW - Gene Deletion
KW - Infant, Newborn
KW - DNA Mutational Analysis
KW - Chromosome Aberrations
KW - Loss of Heterozygosity
KW - Genome-Wide Association Study
KW - Polymorphism, Single Nucleotide
KW - In Situ Hybridization, Fluorescence
KW - Transcription Factors/genetics
KW - DNA-Binding Proteins/genetics
KW - Mutation
KW - DNA Copy Number Variations
KW - Multiplex Polymerase Chain Reaction
KW - Chromosomal Proteins, Non-Histone/genetics
KW - Chromosomes, Human, Pair 22/genetics
KW - Rhabdoid Tumor/genetics
U2 - 10.1002/gcc.22018
DO - 10.1002/gcc.22018
M3 - SCORING: Journal article
VL - 52
SP - 185
EP - 190
JO - GENE CHROMOSOME CANC
JF - GENE CHROMOSOME CANC
SN - 1045-2257
IS - 2
M1 - 2
ER -
