Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses.

Abstract

Desmoid-type fibromatoses are locally aggressive and frequently recurrent tumours, and an accurate diagnosis is essential for patient management. The majority of sporadic lesions harbour beta-catenin (CTNNB1) mutations. We used next-generation sequencing to detect CTNNB1 mutations and to compare the sensitivity and specificity of next-generation sequencing with currently employed mutation detection techniques: mutation-specific restriction enzyme digestion and polymerase chain reaction amplification. DNA was extracted from formalin-fixed paraffin-embedded needle biopsy or resection tissue sections from 144 patients with sporadic desmoid-type fibromatoses, four patients with syndrome-related desmoid-type fibromatoses and 11 morphological mimics. Two primer pairs were designed for CTNNB1 mutation hotspots. Using ≥10 ng of DNA, libraries were generated by Fluidigm and sequenced on the Ion Torrent Personal Genome Machine. Next-generation sequencing had a sensitivity of 92.36 % (133/144, 95 % CIs: 86.74 to 96.12 %) and a specificity of 100 % for the detection of CTNNB1 mutations in desmoid-type fibromatoses-like spindle cell lesions. All mutations detected by mutation-specific restriction enzyme digestion were identified by next-generation sequencing. Next-generation sequencing identified additional mutations in 11 tumours that were not detected by mutation-specific restriction enzyme digestion, two of which have not been previously described. Next-generation sequencing is highly sensitive for the detection of CTNNB1 mutations. This multiplex assay has the advantage of detecting additional mutations compared to those detected by mutation-specific restriction enzyme digestion (sensitivity 82.41 %). The technology requires minimal DNA and is time- and cost-efficient.

• Authors: Sarah J Aitken, Nadège Presneau, Sangeetha Kalimuthu, Palma Dileo, Fitim Berisha, Roberto Tirabosco, M Fernanda Amary, Adrienne M Flanagan
• Journal: Virchows Archiv : an international journal of pathology (Virchows Arch) Vol. 467 Issue 2 Pg. 203-10 (Aug 2015) ISSN: 1432-2307 [Electronic] Germany
• PMID: 25838078 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• CTNNB1 protein, human
• beta Catenin

Topics

• Adolescent
• Adult
• Aged
• Aged, 80 and over
• Child
• DNA Mutational Analysis (methods)
• Female
• Fibromatosis, Aggressive (genetics)
• High-Throughput Nucleotide Sequencing (methods)
• Humans
• Male
• Middle Aged
• Mutation
• Polymerase Chain Reaction
• Young Adult
• beta Catenin (genetics)