Approaches for analyzing human mutations and nucleotide sequence variation: A report from the Seventh International Mutation Detection meeting, 2003

Syvänen, Ann‐Christine; Taylor, Graham R.

doi:10.1002/humu.20031

Cited by 9 publications

(8 citation statements)

References 8 publications

(8 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is higher than that of other gel-based mutationscreening methods, such as SSCP, which has a detection rate of approximately 90% [Moyret et al, 1994]. Furthermore, DGGE analysis can be used for routine mutation scanning in capillary sequencing instruments [Syvanen and Taylor, 2004]. Like DGGE, the DHPLC technique fulfills several of the criteria for an optimal genetic test and has proven to be efficient and more sensitive than SSCP and HD for detecting mutations in the TSC genes [Dabora et al, 2001;Cheadle et al, 2000].…”

Section: Discussionmentioning

confidence: 99%

Analysis of 65 tuberous sclerosis complex (TSC) patients byTSC2DGGE,TSC1/TSC2MLPA, andTSC1long-range PCR sequencing, and report of 28 novel mutations

Rendtorff

Bjerregaard

Frödin³

et al. 2005

Hum. Mutat.

View full text Add to dashboard Cite

Tuberous sclerosis complex (TSC) is a severe autosomal-dominant disorder characterized by the development of benign tumors (hamartomas) in many organs. It can lead to intellectual handicap, epilepsy, autism, and renal or heart failure. An inactivating mutation in either of two tumor-suppressor genes-TSC1 and TSC2-is the cause of this syndrome, with TSC2 mutations accounting for 80-90% of all mutations. Molecular diagnosis of TSC is challenging, since TSC1 and TSC2 consist of 21 and 41 coding exons, respectively, and the mutation spectrum is very heterogeneous. Here we report a new approach for detecting mutations in TSC: a denaturing gradient gel electrophoresis (DGGE) analysis for small TSC2 mutations, a multiplex ligation-dependent probe amplification (MLPA) analysis for large deletions and duplications in TSC1 or TSC2, and a long-range PCR/sequencing-based analysis for small TSC1 mutations. When applied in this order, the three methods provide a new sensitive and time- and cost-efficient strategy for the molecular diagnosis of TSC. We analyzed 65 Danish patients who had been clinically diagnosed with TSC, and identified pathogenic mutations in 51 patients (78%). These included 36 small TSC2 mutations, four large deletions involving TSC2, and 11 small TSC1 mutations. Twenty-eight of the small mutations are novel. For the missense mutations, we established a functional assay to demonstrate that the mutations impair TSC2 protein function. In conclusion, the strategy presented may greatly help small- and medium-sized laboratories in the pre- and postnatal molecular diagnosis of TSC.

show abstract

Section: Discussionmentioning

confidence: 99%

Analysis of 65 tuberous sclerosis complex (TSC) patients byTSC2DGGE,TSC1/TSC2MLPA, andTSC1long-range PCR sequencing, and report of 28 novel mutations

Rendtorff

Bjerregaard

Frödin³

et al. 2005

Hum. Mutat.

View full text Add to dashboard Cite

show abstract

“…It is sometimes necessary to show not only the presence or absence of SNP in sample, but also to determine the quantitative ratio of normal and mutant alleles. This is important, e.g., in the work with tumor tissues or in the determination of the ratio of different alleles in total genomic DNA samples taken from many donors [12]. We showed in a model experiment that DSNP can be used for the semiquantitative determination of the mutant gene content in a complex DNA sample.…”

Section: Introductionmentioning

confidence: 98%

“…or peculiarities of their interactions with special probes (fluorescent and luminescent probes, allele-specific primers, etc.) [10][11][12][13][14]. Many of the methods are adapted to the SNP analysis both in solution and on solid phase [15,16].…”

Section: Introductionmentioning

confidence: 99%

“…Many of the methods are adapted to the SNP analysis both in solution and on solid phase [15,16]. As a rule, methods of SNP analysis involve the stage of preliminary amplification (usually using PCR) of DNA fragments carrying polymorphic regions [10][11][12][13][14]. The advantages and drawbacks of these methods have comprehensively been discussed in a number of reviews [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Application of the Duplex-Specific Nuclease Preference Method to the Analysis of Single Nucleotide Polymorphisms in Human Genes

Altshuler¹,

Zhulidov

Богданова

et al. 2005

Russ J Bioorg Chem

View full text Add to dashboard Cite

A new modification of the single nucleotide polymorphism (SNP) analysis (DSNP, duplex-specific nuclease preference) method using the duplex-specific nuclease from the king crab was proposed. The method was used to study SNPs in the following human genes: kRAS , nRAS , hRAS , and p53 , the genes of blood coagulation factor V, methyltetrahydrofolate reductase, prothrombin, and apolipoprotein E and a deletion in the BRCA1 gene. DSNP was shown to be useful for the estimation of the mutant allele content in DNA samples. A system for the simultaneous identification of several adjacent single-nucleotide polymorphisms in the kRAS gene was proposed. The approaches could be used to develop test systems for the detection of SNPs in human genes.

show abstract

“…Both approaches can be used for mutational scanning in homogeneous assays performed in closed tubes or on solid-phase assays in microarray platforms (1 ).…”

mentioning

confidence: 99%

Genotyping β-Globin Gene Mutations on Copolymer-Coated Glass Slides with the Ligation Detection Reaction

et al. 2008

View full text Add to dashboard Cite

Background: Methods are needed to analyze small amounts of samples for variation in disease-causing genes. One means is to couple the sensitivity and multiplexing capability of the ligation detection reaction (LDR) with the use of simple glass slides specifically functionalized with a novel polymer coating to enhance sensitivity. Methods: We developed an array-based genotyping assay based on glass slides coated with copolymer (N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and 3-(trimethoxysilyl)propyl methacrylate). The assay consists of an LDR with genomic DNA followed by a universal PCR (U-PCR) of genomic DNA–templated LDR product. The LDR occurs in the presence of 3 primers for each sequence variant under investigation: 2 distinguishing primers (allele specific and perfectly complementary to wild-type and mutant alleles) and 1 common locus-specific primer. The 2 allele-specific primers have different capture sequences for binding different complementary probes on a tag array. The LDR product templated from genomic DNA is made fluorescent during the U-PCR via incorporation of a Cy5-labeled universal primer into all LDR products; detection occurs on the coated glass slides. Results: The assay was designed to detect 7 prevalent mutations in the β-globin gene (HBB, hemoglobin, beta) in a multiplex format, and signals for the different alleles are detected by their fluorescence. The assay was applied to 40 genomic DNA samples from both control individuals and patients with known β-thalassemia mutations. Results show good correspondence between the patients’ genotypes as assessed by DNA sequence analysis and those generated from the LDR assays. Conclusions: The developed technology allows accurate identification of sequence variants in a simple, cost-effective way and offers good flexibility for scaling to other applications with different numbers of single-nucleotide polymorphisms or mutations to be detected.

show abstract

Approaches for analyzing human mutations and nucleotide sequence variation: A report from the Seventh International Mutation Detection meeting, 2003

Cited by 9 publications

References 8 publications

Analysis of 65 tuberous sclerosis complex (TSC) patients byTSC2DGGE,TSC1/TSC2MLPA, andTSC1long-range PCR sequencing, and report of 28 novel mutations

Analysis of 65 tuberous sclerosis complex (TSC) patients byTSC2DGGE,TSC1/TSC2MLPA, andTSC1long-range PCR sequencing, and report of 28 novel mutations

Application of the Duplex-Specific Nuclease Preference Method to the Analysis of Single Nucleotide Polymorphisms in Human Genes

Genotyping β-Globin Gene Mutations on Copolymer-Coated Glass Slides with the Ligation Detection Reaction

Contact Info

Product

Resources

About