A genome-wide scan for copy number variations using high-density single nucleotide polymorphism array in Simmental cattle

2015 ◽  
Vol 46 (3) ◽  
pp. 289-298 ◽  
Author(s):  
Yang Wu ◽  
Huizhong Fan ◽  
Shengyun Jing ◽  
Jiangwei Xia ◽  
Yan Chen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number ◽  
Single Nucleotide Polymorphism Array ◽  
Copy Number Variations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Simmental Cattle ◽  
Genome Wide Scan

scholarly journals A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Nedenia Bonvino Stafuzza ◽  
Rafael Medeiros de Oliveira Silva ◽  
Breno de Oliveira Fragomeni ◽  
Yutaka Masuda ◽  
Yijian Huang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Variation Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Copy Number Variation Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation

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.

scholarly journals Copy-Number Variations Measured by Single-Nucleotide–Polymorphism Oligonucleotide Arrays in Patients with Mental Retardation

2007 ◽  
Vol 81 (4) ◽  
pp. 768-779 ◽  
Author(s):  
Janine Wagenstaller ◽  
Stephanie Spranger ◽  
Bettina Lorenz-Depiereux ◽  
Bernd Kazmierczak ◽  
Michaela Nathrath ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mental Retardation ◽  
Copy Number ◽  
Copy Number Variations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Oligonucleotide Arrays
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