Identification of PATCHED mutations in medulloblastomas by direct sequencing
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Updated: Aug 10, 2026
Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
Published on: September 20, 2016
J Dong1, M R Gailani, S L Pomeroy
1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA.
Abstract:
Medulloblastoma is the most common malignant embryonic tumors of the central nervous system. The nevoid basal cell carcinoma syndrome (NBCCS), which is caused by mutations of PTCH gene on chromosome 9q22, accounts for about 2% of all medulloblastomas. Previous studies of PTCH in sporadic medulloblastomas using single strand conformational polymorphism (SSCP) detected mutations in about 10% of the tumors. In this study, we directly sequenced the PTCH gene in 20 sporadic medulloblastoma DNA samples. A nonsense mutation (Q694X) and a splice site alteration (2875+1G>A) were identified in two of the samples. The mutations are predicted to result in a truncated PTCH protein and aberrant splicing, respectively. In both cases, only the mutant alleles were identified, indicating that the mutations were associated with loss of the wild-type PTCH allele in the tumor cells. Several novel variants, including 1653T>C, 1672C>T, and 2292C>T, were also found in these tumor samples. One of the two mutations detected in this study had been missed by SSCP, suggesting that the true rate of PTCH mutations in sporadic medulloblastomas may be underestimated by SSCP screening. Nevertheless, the frequency of mutations in this study did not differ from previous reports.
Insights
Directly sequencing the PTCH gene in sporadic medulloblastoma identified two mutations, Q694X and 2875+1G>A. These PTCH gene mutations suggest a potential underestimation of mutation rates in medulloblastoma by previous screening methods.
Area of Science:
- Neuro-oncology
- Molecular genetics
- Cancer research
Background:
- Medulloblastoma is a common malignant embryonic central nervous system tumor.
- Nevoid basal cell carcinoma syndrome (NBCCS), linked to PTCH gene mutations, accounts for ~2% of medulloblastomas.
- Previous studies using SSCP detected PTCH mutations in ~10% of sporadic medulloblastomas.
Purpose of the Study:
- To directly sequence the PTCH gene in sporadic medulloblastoma samples.
- To identify mutations in the PTCH gene associated with sporadic medulloblastomas.
- To compare the efficacy of direct sequencing versus SSCP for PTCH mutation detection.
Main Methods:
- Direct sequencing of the PTCH gene in 20 sporadic medulloblastoma DNA samples.
- Analysis of mutation types (nonsense, splice site) and their impact on protein.
- Assessment of allele status (mutant vs. wild-type) in tumor cells.
Main Results:
- Identified a nonsense mutation (Q694X) and a splice site alteration (2875+1G>A) in two samples.
- Mutations predicted to cause truncated PTCH protein and aberrant splicing.
- Loss of wild-type PTCH allele observed in both cases; one mutation missed by SSCP.
- Several novel PTCH variants (1653T>C, 1672C>T, 2292C>T) were also identified.
Conclusions:
- Direct sequencing identified PTCH mutations in sporadic medulloblastomas, including one missed by SSCP.
- The frequency of PTCH mutations in this study aligns with previous reports.
- SSCP may underestimate the true rate of PTCH mutations in sporadic medulloblastomas.
