Applying and testing the conveniently optimized enzyme mismatch cleavage method to clinical DNA diagnosis

Classification of Uniparental Isodisomy Patterns That Cause Autosomal Recessive Disorders: Proposed Mechanisms of Different Proportions and Parental Origin in Each Pattern

“…The gene mutations were screened by CHIPS (CEL nuclease mediated heteroduplex incision with polyacrylamide gel electrophoresis and silver staining) technology [Niida et al, 2012a[Niida et al, , 2015 and confirmed by direct sequencing with an ABI 3130xl Genetic Analyser and BigDye version 3.1 Cycle Sequencing Kit (Thermo Fisher Scientific). For patient 3, the SNRPN methylation test was performed according to an established protocol [Kosaki et al, 1997] with some modifications.…”

Development of a practical NF1 genetic testing method through the pilot analysis of five Japanese families with neurofibromatosis type 1

“…CHIPS analysis was performed as described in our previous publications [16,17] with the exception of the modification of PCR reagents and cycle parameters required for NF1 gene analysis. The only instance in which a unique protocol and reagents was required was exon 1 of NF1 which was located in a GC rich region.…”

“…After completion of the PCR cycles, heteroduplex DNA was successively produced in a thermal cycler and 1 ll of heteroduplex substrate was digested by SURVEYOR Nuclease S (Transgenomic) as previously described [16,17]. Also, 1 ll of heteroduplex substrate was used for undigested control, and these samples were run on 10% polyacrylamide gels and developed using a modified optimized silver staining method [16,22].…”

“…To solve this problem, over the past few years we have developed a conventional, highly sensitive and inexpensive mutation screening system for large genes. This new technology, CHIPS (CEL nuclease mediated heteroduplex incision with polyacrylamide gel electrophoresis and silver staining) [16,17], has already been successfully applied to our daily clinical genetic service [18]. The aim of this study is to establish a practicable and inexpensive NF1 mutation screening system based on CHIPS technology through the pilot analysis of eight patients with NF1 from five independent families, and prepare for a mutational cohort study of Japan and of molecular pathology of NF1 lesions.…”

How do you Analyze a Mutation of the Gene Consisting of One Hundred Exons?

“…CHIPS is a simple and effective screening method for unknown DNA variations based on the enzyme mismatch cleavage and finely optimized at every step to achieve maximum sensitivity and simplicity [1]. By mixing the sample DNA and control DNA, CHIPS can apply to not only autosomal dominant diseases, but also autosomal recessive and X-linked diseases.…”