Accurate diagnosis of spinal muscular atrophy and 22q11.2 deletion syndrome using limited deoxynucleotide triphosphates and high-resolution melting

• Published in: BMC genomics 2018-06, Vol.19 (1), p.485-485, Article 485
• Main Authors: Zhang, Xiaoqing, Wang, Bo, Zhang, Lichen, You, Guoling, Palais, Robert A, Zhou, Luming, Fu, Qihua
• Format: Article
• Language: English
• Subjects: 22q11.2 deletion syndrome; Adaptor Proteins, Signal Transducing - genetics; Analysis; Atrophy; Chromosome 22; Chromosomes, Human, Pair 22 - genetics; Clathrin Heavy Chains - genetics; Copy number; Copy number variation; Copy number variations; Cystic Fibrosis Transmembrane Conductance Regulator - genetics; Deoxynucleotides; Deoxyribonucleic acid; Diagnosis; DiGeorge Syndrome - genetics; Diseases; DNA; DNA Copy Number Variations - genetics; Genes; Genetic aspects; Genetic counseling; Genetic diversity; Genetic testing; Genetics; Genomes; Genomics; Health screening; High resolution; High-resolution melting; Humans; Laboratories; Melting; Minor Histocompatibility Antigens - genetics; Muscular Atrophy, Spinal - diagnosis; Muscular Atrophy, Spinal - genetics; Neuromuscular diseases; Patients; Phosphotransferases (Alcohol Group Acceptor) - genetics; Polymerase chain reaction; SMN protein; Software; Spinal muscular atrophy; Survival of Motor Neuron 1 Protein - genetics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-018-4833-4

Copy number variation (CNV) has been implicated in the genetics of multiple human diseases. Spinal muscular atrophy (SMA) and 22q11.2 deletion syndrome (22q11.2DS) are two of the most common diseases which are caused by DNA copy number variations. Genetic diagnostics for these conditions would be enhanced by more accurate and efficient methods to detect the relevant CNVs. Competitive PCR with limited deoxynucleotide triphosphates (dNTPs) and high-resolution melting (HRM) analysis was used to detect 22q11.2DS, SMA and SMA carrier status. For SMA, we focused on the copy number of SMN1 gene. For 22q11.2DS, we analyzed CNV for 3 genes (CLTCL1, KLHL22, and PI4KA) which are located between different region-specific low copy repeats. CFTR was used as internal reference gene for all targets. Short PCR products with separated Tms were designed by uMelt software. One hundred three clinical patient samples were pretested for possible SMN1 CNV, including carrier status, using multiplex ligation-dependent probe amplification (MLPA) commercial kit as gold standard. Ninety-nine samples consisting of 56 wild-type and 43 22q11.2DS samples were analyzed for CLTCL1, KLHL22, and PI4KA CNV also using MLPA. These samples were blinded and re-analyzed for the same CNVs using the limited dNTPs PCR with HRM analysis and the results were completely consistent with MLPA. Limited dNTPs PCR with HRM analysis is an accurate method for detecting SMN1 and 22q11.2 CNVs. This method can be used quickly, reliably, and economically in large population screening for these diseases.