Copy number alterations determined by single nucleotide polymorphism array testing in the clinical laboratory are indicative of gene fusions in pediatric cancer patients

2017 ◽  
Vol 56 (10) ◽  
pp. 730-749 ◽  
Author(s):  
Tracy M. Busse ◽  
Jacquelyn J. Roth ◽  
Donna Wilmoth ◽  
Luanne Wainwright ◽  
Laura Tooke ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Pediatric Cancer ◽  
Copy Number ◽  
Clinical Laboratory ◽  
Single Nucleotide Polymorphism Array ◽  
Gene Fusions ◽  
Copy Number Alterations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pediatric Cancer Patients

scholarly journals Analysis of somatic copy number alterations in biliary tract carcinoma using a single nucleotide polymorphism array

2021 ◽  
Author(s):  
Yoshihiro Shioi ◽  
Mitsumasa Osakabe ◽  
Naoki Yanagawa ◽  
Hiroyuki Nitta ◽  
Akira Sasaki ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Biliary Tract ◽  
Copy Number ◽  
Single Nucleotide Polymorphism Array ◽  
Biliary Tract Carcinoma ◽  
Copy Number Alterations ◽  
Nucleotide Polymorphism ◽  
Duct Carcinoma ◽  
Single Nucleotide ◽  
Somatic Copy Number Alterations

Aim: Biliary tract carcinoma (BTC), including gall bladder carcinoma (GBC) and biliary duct carcinoma (BDC), has a poor prognosis. Comprehensive genomic profiling has important roles in evaluation of the carcinogenesis of BTC. Materials & methods: We examined somatic copy number alterations (SCNAs) using a single nucleotide polymorphism array system to analyze 36 BTC samples (11 GBCs and 25 BDCs). Results: In hierarchical cluster analysis, two clusters were identified (subgroup 1 with low SCNAs and subgroup 2 with high SCNAs). GBC was predominant in subgroup 1, whereas BDC was predominant in subgroup 2, suggesting that GBC and BDC had different genetic backgrounds in terms of SCNAs. Conclusion: These findings could be helpful for establishing the molecular carcinogenesis of BTCs.

scholarly journals Prenatal Diagnosis of 17p11.2 Copy Number Abnormalities Associated With Smith–Magenis and Potocki–Lupski Syndromes in Fetuses

2021 ◽  
Vol 12 ◽  
Author(s):  
Meiying Cai ◽  
Xianguo Fu ◽  
Liangpu Xu ◽  
Na Lin ◽  
Hailong Huang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Prenatal Diagnosis ◽  
Copy Number ◽  
De Novo ◽  
Single Nucleotide Polymorphism Array ◽  
Copy Number Variant ◽  
Prenatal Ultrasound ◽  
Nucleotide Polymorphism ◽  
Array Analysis ◽  
Single Nucleotide

Smith-Magenis syndrome and Potocki-Lupski syndrome are rare autosomal dominant diseases. Although clinical phenotypes of adults and children have been reported, fetal ultrasonic phenotypes are rarely reported. A retrospective analysis of 6,200 pregnant women who received invasive prenatal diagnosis at Fujian Provincial Maternal and Child Health Hospital between October 2016 and January 2021 was performed. Amniotic fluid or umbilical cord blood was extracted for karyotyping and single nucleotide polymorphism array analysis. Single nucleotide polymorphism array analysis revealed six fetuses with copy number variant changes in the 17p11.2 region. Among them, one had a copy number variant microdeletion in the 17p11.2 region, which was pathogenically analyzed and diagnosed as Smith-Magenis syndrome. Five fetuses had copy number variant microduplications in the 17p11.2 region, which were pathogenically analyzed and diagnosed as Potocki-Lupski syndrome. The prenatal ultrasound phenotypes of the six fetuses were varied. The parents of two fetuses with Potocki-Lupski syndrome refused verification. Smith-Magenis syndrome in one fetus and Potocki-Lupski in another were confirmed as de novo. Potocki-Lupski syndrome in two fetuses was confirmed to be from maternal inheritance. The prenatal ultrasound phenotypes of Smith-Magenis syndrome and Potocki-Lupski syndrome in fetuses vary; single nucleotide polymorphism array analysis is a powerful diagnostic tool for these diseases. The ultrasonic phenotypes of these cases may enrich the clinical database.

scholarly journals Genome-Wide Copy Number Analysis in a Family With p.G533C RET Mutation and Medullary Thyroid Carcinoma Identified Regions Potentially Associated With a Higher Predisposition to Lymph Node Metastasis

2014 ◽  
Vol 99 (6) ◽  
pp. E1104-E1112 ◽  
Author(s):  
Aline N. Araujo ◽  
Lais Moraes ◽  
Maria Inez C. França ◽  
Hakon Hakonarson ◽  
Jin Li ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Lymph Node ◽  
Lymph Node Metastasis ◽  
Copy Number ◽  
Single Nucleotide Polymorphism Array ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Medullary Thyroid ◽  
Node Metastasis ◽  
Genome Wide

Context: Our group described a p.G533C RET gene mutation in a large family with multiple endocrine neoplasia type 2 syndrome. Clinical heterogeneity, primarily associated with the presence of lymph node metastases, was observed among the p.G533C carriers. Objective: The aim of this study was to use single-nucleotide polymorphism-array technology to identify copy number variations (CNVs), which are present in the constitutional DNA and associated with the established clinical and pathological features of aggressive medullary thyroid carcinoma (MTC), primarily the presence of lymph node metastasis. Design: Fifteen p.G533C carriers with MTC were chosen for the initial screening. The subjects were divided into two groups according the presence (n = 8) or absence (n = 7) of lymph node metastasis. Peripheral blood DNA was independently hybridized using a genome-wide single-nucleotide polymorphism Array 6.0 platform. The results were analyzed using both Genotyping Console and PennCNV software. To identify the possible candidate regions associated with the presence of lymph node metastasis, cases (metastatic MTC) were compared with controls (nonmetastatic MTC). The identified CNVs were validated by quantitative PCR in an extended cohort (n = 32). Results: Using two different algorithms, we identified nine CNV regions that may contribute to susceptibility to lymph node metastasis. The validation step confirmed that a CNV loss impacting the FMN2 gene was potentially associated with a greater predisposition to lymph node metastasis in this family (P = .0179). Finally, we sought to investigate whether the development of lymph node metastasis might not depend on a single CNV but rather a combination of various CNVs. These analyses defined a CNV pattern related to a more aggressive phenotype in this family, with CNV deletions being enriched in the metastatic group (P = .0057). Conclusion: Although hereditable specific RET mutations are important to determine cancer risk, germline CNVs in disease-affected individuals may predispose them to MTC aggressiveness.

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