Mutational scanning of large genes by extensive PCR multiplexing and two-dimensional electrophoresis: application to the RB1 gene. 1996

N J Van Orsouw, and D Li, and P van der Vlies, and H Scheffer, and C Eng, and C H Buys, and F P Li, and J Vijg
Department of Medicine, Beth Israel Hospital, Boston, MA 02215, USA.

With the rapid increase in the number of identified human disease genes, the development of accurate and cost-efficient mutation tests has become opportune. Here we present a combination of extensive PCR multiplexing and two-dimensional (2-D) DNA electrophoresis to screen for mutations in 26 exons of the retinoblastoma (RB1) tumor suppressor gene. In 2-D electrophoresis, fragments are separated according to size and base pair sequence in non-denaturing and denaturing gradient gels, respectively. All target fragments, designed to have optimal melting characteristics, were prepared in a two-step PCR (a 6-plex long-PCR pre-amplification and a subsequent 25-plex short-PCR) followed by heteroduplexing. The mixture of PCR amplicons was then subjected to 2-D electrophoresis under a single set of experimental conditions. With this design, 35 previously identified mutations in 18 different exons were detected in 33 bilateral retinoblastoma patients. These results suggest that 2-D electrophoresis in this format provides a generally applicable, practical and fast way to diagnose with high accuracy large genes for a broad spectrum of possible disease-causing mutations.

UI MeSH Term Description Entries
D011110 Polymorphism, Genetic The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level. Gene Polymorphism,Genetic Polymorphism,Polymorphism (Genetics),Genetic Polymorphisms,Gene Polymorphisms,Polymorphism, Gene,Polymorphisms (Genetics),Polymorphisms, Gene,Polymorphisms, Genetic
D004252 DNA Mutational Analysis Biochemical identification of mutational changes in a nucleotide sequence. Mutational Analysis, DNA,Analysis, DNA Mutational,Analyses, DNA Mutational,DNA Mutational Analyses,Mutational Analyses, DNA
D005091 Exons The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA. Mini-Exon,Exon,Mini Exon,Mini-Exons
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D012175 Retinoblastoma A malignant tumor arising from the nuclear layer of the retina that is the most common primary tumor of the eye in children. The tumor tends to occur in early childhood or infancy and may be present at birth. The majority are sporadic, but the condition may be transmitted as an autosomal dominant trait. Histologic features include dense cellularity, small round polygonal cells, and areas of calcification and necrosis. An abnormal pupil reflex (leukokoria); NYSTAGMUS, PATHOLOGIC; STRABISMUS; and visual loss represent common clinical characteristics of this condition. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2104) Glioblastoma, Retinal,Glioma, Retinal,Neuroblastoma, Retinal,Eye Cancer, Retinoblastoma,Familial Retinoblastoma,Hereditary Retinoblastoma,Sporadic Retinoblastoma,Cancer, Retinoblastoma Eye,Cancers, Retinoblastoma Eye,Eye Cancers, Retinoblastoma,Familial Retinoblastomas,Glioblastomas, Retinal,Gliomas, Retinal,Hereditary Retinoblastomas,Neuroblastomas, Retinal,Retinal Glioblastoma,Retinal Glioblastomas,Retinal Glioma,Retinal Gliomas,Retinal Neuroblastoma,Retinal Neuroblastomas,Retinoblastoma Eye Cancer,Retinoblastoma Eye Cancers,Retinoblastoma, Familial,Retinoblastoma, Hereditary,Retinoblastoma, Sporadic,Retinoblastomas,Retinoblastomas, Familial,Retinoblastomas, Hereditary,Retinoblastomas, Sporadic,Sporadic Retinoblastomas
D015180 Electrophoresis, Gel, Two-Dimensional Electrophoresis in which a second perpendicular electrophoretic transport is performed on the separate components resulting from the first electrophoresis. This technique is usually performed on polyacrylamide gels. Gel Electrophoresis, Two-Dimensional,Polyacrylamide Gel Electrophoresis, Two-Dimensional,2-D Gel Electrophoresis,2-D Polyacrylamide Gel Electrophoresis,2D Gel Electrophoresis,2D PAGE,2D Polyacrylamide Gel Electrophoresis,Electrophoresis, Gel, 2-D,Electrophoresis, Gel, 2D,Electrophoresis, Gel, Two Dimensional,Polyacrylamide Gel Electrophoresis, 2-D,Polyacrylamide Gel Electrophoresis, 2D,Two Dimensional Gel Electrophoresis,2 D Gel Electrophoresis,2 D Polyacrylamide Gel Electrophoresis,Electrophoresis, 2-D Gel,Electrophoresis, 2D Gel,Electrophoresis, Two-Dimensional Gel,Gel Electrophoresis, 2-D,Gel Electrophoresis, 2D,Gel Electrophoresis, Two Dimensional,PAGE, 2D,Polyacrylamide Gel Electrophoresis, 2 D,Polyacrylamide Gel Electrophoresis, Two Dimensional,Two-Dimensional Gel Electrophoresis
D016133 Polymerase Chain Reaction In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships. Anchored PCR,Inverse PCR,Nested PCR,PCR,Anchored Polymerase Chain Reaction,Inverse Polymerase Chain Reaction,Nested Polymerase Chain Reaction,PCR, Anchored,PCR, Inverse,PCR, Nested,Polymerase Chain Reactions,Reaction, Polymerase Chain,Reactions, Polymerase Chain
D016147 Genes, Tumor Suppressor Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible. Antioncogenes,Cancer Suppressor Genes,Emerogenes,Genes, Cancer Suppressor,Genes, Growth Suppressor,Genes, Metastasis Suppressor,Growth Suppressor Genes,Metastasis Suppressor Genes,Tumor Suppressor Genes,Anti-Oncogenes,Genes, Onco-Suppressor,Oncogenes, Recessive,Tumor Suppressing Genes,Anti Oncogenes,Anti-Oncogene,Antioncogene,Cancer Suppressor Gene,Emerogene,Gene, Cancer Suppressor,Gene, Growth Suppressor,Gene, Metastasis Suppressor,Gene, Onco-Suppressor,Gene, Tumor Suppressing,Gene, Tumor Suppressor,Genes, Onco Suppressor,Genes, Tumor Suppressing,Growth Suppressor Gene,Metastasis Suppressor Gene,Onco-Suppressor Gene,Onco-Suppressor Genes,Oncogene, Recessive,Recessive Oncogene,Recessive Oncogenes,Suppressor Gene, Cancer,Suppressor Gene, Growth,Suppressor Gene, Metastasis,Suppressor Genes, Cancer,Suppressor Genes, Growth,Suppressor Genes, Metastasis,Tumor Suppressing Gene,Tumor Suppressor Gene
D016160 Retinoblastoma Protein Product of the retinoblastoma tumor suppressor gene. It is a nuclear phosphoprotein hypothesized to normally act as an inhibitor of cell proliferation. Rb protein is absent in retinoblastoma cell lines. It also has been shown to form complexes with the adenovirus E1A protein, the SV40 T antigen, and the human papilloma virus E7 protein. Rb Protein,Retinoblastoma Nuclear Phosphoprotein p105-Rb,p105-Rb Protein,Rb Gene Product,Rb1 Gene Product,Retinoblastoma Nuclear Phosphoprotein p105 Rb,p105 Rb Protein
D018807 Polymorphism, Single-Stranded Conformational Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels. SSCP,Single-Stranded Conformational Polymorphism,Conformational Polymorphism, Single-Stranded,Conformational Polymorphisms, Single-Stranded,Polymorphism, Single Stranded Conformational,Polymorphisms, Single-Stranded Conformational,Single Stranded Conformational Polymorphism,Single-Stranded Conformational Polymorphisms

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