DNA diagnosis of cystic fibrosis

Technology platforms for molecular diagnosis of cystic fibrosis

Cystic fibrosis (CF) is one of the most common recessive genetic diseases in North America. So far, 1200 mutations causing CF have been identified. Several techniques such as allele specific oligonucleotide (ASO) dot-blot, reverse dot-blot, amplification refractory mutation (ARMS), and an oligo-ligation assay, are available to detect the most common mutations. However, detecting compound heterozygotes between DeltaF508, the most common disease causing mutation, and other mutations which are rare is difficult as some mutations are common only to particular ethnic groups. Therefore, new diagnostic tests such as restriction enzyme assays and single stranded conformational polymorphism (SSCP) have been designed to recognize rare and population-specific mutations. This review will describe the most commonly used CF mutation detecting diagnostic techniques, as well as novel assays and techniques currently in development that might be employed in future.

Optical detection and discrimination of cystic fibrosis-related genetic mutations using oligonucleotide-nanoparticle conjugates

Novel methods for application of oligonucleotide-gold nanoparticle conjugates to selective colorimetric detection and discrimination of cystic fibrosis (CF) related genetic mutations in model oligonucleotide systems are presented. Three-strand oligonucleotide complexes are employed, wherein two probe oligonucleotide-gold nanoparticle conjugates are linked together by a third target oligonucleotide strand bearing the CF-related mutation(s). By monitoring the temperature dependence of the optical properties of the complexes, either in solution or on silica gel plates, melting behaviors may be accurately and reproducibly compared. Using this approach, fully complementary sequences are successfully distinguished from mismatched sequences, with single base mismatch resolution, for Delta F 508, M470V, R74W and R75Q mutations.

Sub-picomole colorimetric single nucleotide polymorphism discrimination using oligonucleotide-nanoparticle conjugates

Oligonucleotide-gold nanoparticle conjugates are employed to demonstrate selective colorimetric discrimination of a cystic fibrosis-related genetic mutation in a model oligonucleotide system. Specifically, three strand oligonucleotide complexes are employed, wherein two probe oligonucleotide-gold nanoparticle conjugates are linked together by a third target oligonucleotide strand bearing the chosen CF-related mutation. By monitoring the solution optical absorption behaviour of the complexes as a function of temperature, melting profiles may be accurately acquired and reproducibly compared. Following this method, fully complementary sequences are successfully distinguished from mismatched sequences, with single base mismatch resolution, for the V232D mutation. To extend the detection sensitivity of this oligonucleotide-nanoparticle conjugate assay, a novel and compact LED-based optical monitoring system capable of sub-picomole level colorimetric SNP discrimination is also demonstrated.

Molecular diagnosis of cystic fibrosis: comparison of four analytical procedures

We compared the analytical accuracy, times, costs and the detection rate of four procedures for the molecular analysis of cystic fibrosis (CF). DNA from 127 subjects bearing different genotypes was tested by denaturating gradient gel electrophoresis followed by sequencing (reference procedure) and, for comparison, by ASO dot-blot (in-house), reverse dot-blot (Innogenetics), ARMS (Zeneca Diagnostics) and OLA-PCR (PE Applied Biosystem). To assess inter-observer variability, all samples were tested twice. To evaluate intra- and between-series variability, two samples were tested twice in each series. All the procedures yielded reproducible results and assigned the correct genotype to each sample. ASO dot-blot is the cheapest procedure but has the longest analytical time (> 24 h) and uses radioactive labeling. It can be adapted to analyze peculiar mutations in specific ethnic groups. ARMS from Zeneca Diagnostics is rapid (4 h), easy to perform, but, except for the AF508 mutation, does not distinguish the homozygote from the heterozygote genotype. It could be used for carrier analysis in families with known mutations. OLA-PCR has the highest detection rate in most ethnic groups, is automated for capillary electrophoresis but requires a high level of operator expertise: it is suitable when collected series of samples are analyzed from large patient cohorts. Reverse dot-blot is easy to perform and can be semiautomated: it can be used as first-line screening test. Given the heterogeneity of CF mutations, commercial kits should be developed to analyze mutations peculiar to specific ethnic groups.