应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

应用Affymetrix全基因组芯片检测染色体7q36区域的DNA拷贝数突变

Objectives To refine the extent of a 7q36 duplication in a Chinese family with triphalangeal thumb-polysyndaetyly syndrome and syndactyly type Ⅳ using the Affymetrix SNP Array combined with quantitative real-time PCR (qPCR). Methods Genomic DNA was extracted and genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0. Copy number analysis was performed on the raw data using the Affymetrix Genotyping Console 3. 0. The qPCR assay was carried out using the AACT method to validate the duplication. Results With use of the combined approach, we were able to narrow down the breakpoint intervals from 113 kb and 33 kb to 5.4 kb and 1.8 kb, respectively. These allowed us to refine the extent of the 7q36 duplication from 291-437 kb to 379-387kb. Conclusion Screening with the Affymetrix Genome-Wide Human SNP Array 6. 0 followed by the validation using qPCR is a reliable approach for high-resolution detection of copy number mutations.     

一个先天性主动脉瓣上狭窄家系的分子遗传性分析

目的 检测一个临床诊断为"先天性升主动脉狭窄"家系患者的基因组拷贝数变异,明确其发病的遗传学基础.方法 以一个先天性升主动脉狭窄家系为研究对象,收集患儿及其患病父亲、正常母亲外周血标本,常规提取基因组DNA.应用Affymetrix人类全基因组SNP 6.0芯片对患儿及1例正常健康对照个体进行检测,应用实时定量PCR(real-time quantitative polymerase-chain-reaction,qPCR)方法对芯片分析结果进行验证.结果 经Affymetrix SNP 6.0 芯片分析显示患儿染色体7q11.23区域内弹力蛋白基因(elastin,ELN)5′端大部分及基因上游区域共约80 kb发生杂合性缺失.在ELN基因内设计4对qPCR引物,在家系内进行验证,结果显示ELN的缺失向下游至少累及至第22外显子,且患儿父亲携带与患儿相同的杂合性缺失.结论 ELN 基因部分杂合性缺失为该患儿及其父亲发病的原因,二者之先天异常为主动脉瓣上狭窄(supravalvular aortic stenosis,SVAS).

Abstract：

Objective To detect the copy number variations(CNVs)in a family with congenital narrowing of the ascending aorta,and to explore the underlying genetic causes of the disease.Methods Peripheral blood samples were collected from an affected boy,his affected father and his apparently normal mother.Genomic DNA Was extracted and genotyped using Affymetrix Genome-Wide Human SNP Array 6.0.CNVs were confirmed by real-time quantitative PCR(qPCR).Results Our SNP Array 6.0analysis showed in the boy an about 80kb heterozygous deletion affecting part of the elastin gene(ELN).Further qPCR assays for four confirmed the presence of the deletion in the boy and his father,and indieated that the deletion involved at least the first 22 ELN exons.Conclusion A heterozygous deletion affecting part of the ELN gene has been identified in the boy and his father, A diagnosis of supravalvular aortic stenosis(SVAS)could he made based on the molecular finding.     

SNP array and cytogenetic analysis of a patient with unexplained mental retardation北大核心CSCD

Objective: To analyze a patient with unexplained mental retardation by using three primer PCR(TP-PCR) and single nucleotide polymorphisms array(SNP-array), and to correlate the genotype with phenotype. Methods: Peripheral blood sample was taken from the patient for the extraction of DNA. TP-PCR was used to determine the copy number of CGG repeats in the 5′-UTR of the FMR1 gene. SNP array was used for high resolution analysis of the patient's genome. Results: TP-PCR has shown no abnormal amplification of CGG in the 5′-UTR of FMR1 gene. Hence, Fragile X syndrome was excluded as the cause for mental retardation. SNP array analysis has identified a 0.93 Mb duplication at 7q36.1-q36.2 and a 2.2 Mb deletion at 12p13.1-p13.2 in the patient. Conclusion: The microduplication and microdeletion discovered in the patient probably underlies the intelligence disability. The high-resolution SNP array can provide accurate information for the identification of pathogenesis, and is the preferred method for the diagnosis of unexplained mental retardation. © 2016, West China University of Medical Sciences. All rights reserved.