Neurofibromatosis type 1 syndrome (NF1) is caused by mutations in the NF1 gene. Availability of new sequencing technology prompted us to search for an alternative method for NF1 mutation analysis. Genomic DNA was isolated from saliva avoiding invasive sampling. The NF1 exons with an additional 50bp of flanking intronic sequences were captured and enriched using the SeqCap EZ Choice Library protocol. The captured DNA was sequenced with the Roche/454 GS Junior system. The mean coverages of the targeted regions were 41x and 74x in 2 separate sets of samples. An NF1 mutation was discovered in 10 out of 16 separate patient samples. Our study provides proof of principle that the sequence capture methodology combined with high-throughput sequencing is applicable to NF1 mutation analysis. Deep intronic mutations may however remain undetectable, and change at the DNA level may not predict the outcome at the mRNA or protein levels.
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http://dx.doi.org/10.2340/00015555-1843 | DOI Listing |
World J Surg Oncol
January 2025
Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tiantan Hospital, Capital Medical University, No. 119, South Fourth Ring Road West, Fengtai District, Beijing, 100070, China.
Background: This study aims to identify a pathogenic SDHD mutation associated with hereditary head and neck paraganglioma (HNPGL) in a Chinese family and to explore its implications for genetic counseling.
Methods: The study involved a family with 15 members spanning three generations. A 31-year-old patient (II-4) was diagnosed with a left parotid gland tumor and a right carotid body tumor, while both the father and elder sister had right carotid body tumors, and the third sister had bilateral carotid body tumors.
Clin Exp Med
January 2025
Liver & Peritonectomy Unit, Department of Surgery, St George Hospital, Pitney Building, Short Street, Kogarah, NSW, 2217, Australia.
Purpose: This study seeks to resolve a fundamental question in oncology: Why do appendiceal and colorectal adenocarcinomas exhibit distinct liver metastasis rates? Building on our prior hypothesis published in the British Journal of Surgery, our institution has investigated potential DNA mutations within the carcinoembryonic antigen-related cell adhesion molecule (CEACAM5) gene's Pro-Glu-Leu-Pro-Lys (PELPK) motif to evaluate its role as a biomarker for liver metastasis risk.
Methods: Partnering with the Australian Genome Research Facility, the PELPK motif of CEACAM5 was analysed in colorectal and appendiceal adenocarcinomas to detect DNA mutations associated with liver metastasis. Additionally, our institution performed the COPPER trial to assess carcinoembryonic antigen (CEA) levels in portal versus peripheral blood in patients with appendiceal adenocarcinoma and a systematic review and meta-analysis of 136 studies on CEA's prognostic significance among patients with colorectal and appendiceal adenocarcinoma.
Nat Genet
January 2025
Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.
Understanding the molecular landscape of nonmuscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and treatment regimens. We performed a comprehensive genomic analysis of patients with NMIBC using whole-exome sequencing (n = 438), shallow whole-genome sequencing (n = 362) and total RNA sequencing (n = 414). A large genomic variation within NMIBC was observed and correlated with different molecular subtypes.
View Article and Find Full Text PDFNPJ Precis Oncol
January 2025
Athinoula A. Martinos Center for Biomedical Imaging, 149 13th St, Charlestown, MA, 02129, USA.
Recent progress in deep learning (DL) is producing a new generation of tools across numerous clinical applications. Within the analysis of brain tumors in magnetic resonance imaging, DL finds applications in tumor segmentation, quantification, and classification. It facilitates objective and reproducible measurements crucial for diagnosis, treatment planning, and disease monitoring.
View Article and Find Full Text PDFSci Rep
January 2025
Jiangxi Key Laboratory of Molecular Medicine, Jiangxi Medical College, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, China.
SMAD3, a protein-coding gene, assumes a pivotal role within the transforming growth factor-beta (TGF-β) signaling pathway. Notably, aberrant SMAD3 expression has been linked to various malignancies. Nevertheless, an extensive examination of the comprehensive pan-cancer impact on SMAD3's diagnostic, prognostic, and immunological predictive utility has yet to be undertaken.
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