Diversity of cystic fibrosis mutation-screening practices

Prenatal screening for cystic fibrosis: past, present and future

Prenatal screening for cystic fibrosis is reviewed. The disease, gene involved, molecular basis of disease, genotype/phenotype correlations and pilot trials are discussed, as well as historical perspectives, background and American College of Medical Genetics/American College of Obstetricians and Gynecologists recommendations. A number of complex challenges to the implementation of cystic fibrosis screening exist, including mutation testing of the cystic fibrosis transmembrane conductance regulator gene (CFTR), as well as laboratory and clinical issues. Current technologies for CFTR testing include reverse dot blots, amplification refractory mutation detection systems, oligonucleotide ligation assays, the Invader assay and NanoChip system. Emerging technologies are also considered, as well as quality assurance measures including analytical and clinical validation, reporting, residual risk calculations and prenatal diagnosis. An even greater challenge is clinical implementation, which focuses upon education and communication, choosing models, reporting, counseling and prenatal diagnosis.

Development and integration of molecular genetic tests into clinical practice: the US experience

The issues that arise in the development of genetic tests for prediction and diagnosis are described in the context of the authors' experience as laboratory directors in the USA. The goal is to identify gaps and weaknesses in the test validation process and to define the pivotal issues. Variables that influence a laboratory director's decision to develop a particular molecular genetic assay, including motivation, economics, intellectual property and the regulatory environment, are described. Issues of clinical and analytic validation are discussed, providing examples of tests with both good (cystic fibrosis carrier screening) and poor (apolipoprotein E genotyping for Alzheimer's disease) clinical utility. The decision-making process that occurs during the considered transition of a research-based molecular genetic assay into routine use in the clinical laboratory is summarized. Different factors will be weighted differently depending on the nature of the disease being tested, the complexity of its gene and mutations, the available technical platforms, potential regulatory and intellectual property restrictions, and whether the proposed test is to be offered by an academic or a commercial laboratory.

Carrier screening for cystic fibrosis in US genetic testing laboratories: a survey of laboratory directors

Initial guidelines for cystic fibrosis (CF) carrier screening were issued in 2001 by the American College of Medical Genetics and the American College of Obstetricians and Gynecologists and updated in 2004. It is unknown how these guidelines have influenced laboratory practice. This study examined the uptake of two components of these guidelines for CF screening in genetic testing laboratories. A survey of directors of US genetic testing laboratories was conducted. Of 190 respondents, 178 answered questions about CF testing. Nearly half (49%) performed some type of DNA testing for CF; most of these (92%) performed CF carrier screening. Ten percent used a 23-mutation panel for CF screening. The results of 5T tests were reported as a reflex test by 79% of laboratories, while 8% always returned 5T results and 7% never returned them. Seven percent of laboratories adopted both guidelines, 80% adopted one of the two guidelines, and 13% had not adopted either recommendation, suggesting that factors other than clinical guidelines may influence laboratories' CF screening practices. Further studies are needed to determine whether the adoption of CF screening guidelines has significant clinical or economic effects on population-based CF screening programs.

A novel method for creating artificial mutant samples for performance evaluation and quality control in clinical molecular genetics

The lack of readily available, patient-derived materials for molecular genetic testing of many heterozygous or rare disorders creates a major impediment for laboratory proficiency and quality control procedures. The paucity of clinically derived mutation-positive samples could be surmounted if it were possible to construct artificial samples containing mutations of interest that would sufficiently resemble natural human samples. Such samples could then function as acceptable and realistic performance evaluation challenges and quality control reagents for recipient laboratories. Using the cystic fibrosis gene (CFTR) as a prototype, we have devised and executed experiments designed to generate unique DNA samples that could be used for these purposes. We used site-directed mutagenesis to generate mutations of interest in plasmid DNA derived from common bacterial artificial chromosome sources containing the cystic fibrosis transmembrane conductance receptor gene. CFTR mutations G85E and 1078delT were chosen to represent mutations in the original American College of Medical Genetics-recommended population-screening panel of 25 mutations. DNA samples containing predetermined concentrations and ratios of wild-type and mutated plasmids, bacterial artificial chromosomes of interest, and nonhuman genomic carrier DNA were characterized and tested in-house and in a group of nine pilot testing laboratories using a variety of technical platforms. The results indicate that these constructs, containing CFTR mutations in heterozygous and homozygous states, can serve as valid and accessible materials for quality assurance, including performance evaluation, proficiency testing, and assay quality control.

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.

Medical genetic test reporting for cystic fibrosis (deltaF508) and factor V Leiden in North American laboratories

PURPOSE

Physicians are ordering an increasing number of genetic tests. Results and additional information provided in the test result report are vital to the physician in making appropriate patient management decisions. Because variability in test result reports can impact patient care, we sought to determine whether variations exist in test reports for cystic fibrosis (CF) and factor V Leiden (fVL) with specific comparison to professional guidelines and recommendations.

METHODS

A cross-sectional study design analyzing for the presence of 16 critical elements in CF reports and 12 critical elements in fVL reports solicited from United States and Canadian laboratories.

RESULTS

Of 44 laboratories performing CF testing and 72 laboratories performing fVL testing, 64% responded. For CF reports, 21% included ethnicity, 64% described methodology, and 61% discussed genetic counseling. For fVL reports, 80% described methodology and 52% discussed the need for genetic counseling in mutation-positive reports.

CONCLUSIONS

Variability exists in report content among North American laboratories performing CF and fVL testing. Many reports lack information deemed critical by professional guidelines and recommendations.

Molecular diagnosis of cystic fibrosis

A review of the current molecular diagnosis of cystic fibrosis including an introduction to cystic fibrosis, the gene function, the phenotypic variation, who should be screened for which mutation, newborn and couple screening, quality assurance, phenotype-genotype correlation, methods and method limitations, options, statements, recommendations, useful Websites and treatments.

Experiences in molecular-based prenatal screening for Ashkenazi Jewish genetic diseases

Multiple-option prenatal carrier testing in the Ashkenazi Jewish community for three and now eight disorders has been readily accepted in this prenatal, health-oriented and knowledgeable population. Counseling of screenees concerning the nature (severity, treatability, etc.), inheritance, and frequencies of each disorder was essential for informed test choices and future reproductive decision making. The value of couple testing for a group of disorders when 1 in about 6 would be found to be a carrier of at least one disease was emphasized. These studies identified issues of education, confidentiality, posttest anxiety, and self-esteem that must be continuously addressed in the Ashkenazi population. However, an important value of these studies is that they provide a framework for the development of mass carrier screening programs in the general population or in specific segments of the population with similar demographic characteristics and in more diverse prenatal populations.

Quality control in molecular genetic testing

DNA-based testing for genetic diseases has developed from nothing into a principal part of laboratory medicine over the past 15 years. In the rush to bring these powerful new technologies into medical use, issues of quality have not always been given sufficient attention. Efforts are now being made to assess the quality of the output of genetic testing laboratories, and the results show that there is room for improvement.

Genetic testing and quality control in diagnostic laboratories

To evaluate the quality of genetic testing for cystic fibrosis, 136, 145 and 159 laboratories participated in a European study in 1996, 1997 and 1998, respectively. We sent six purified DNA samples carrying the more common CFTR mutations with the request to test them using routine protocols. A panel of experts reviewed the results together with the raw data.

Screening practices for mutations in the CFTR gene ABCC7

Cystic fibrosis transmembrane conductance regulator (CFTR) gene studies are now one of the most frequent activities in clinical molecular genetics laboratories. The number of requests is growing, owing to the increasingly wide range of recognized CFTR gene diseases (cystic fibrosis, congenital bilateral absence of the vas deferens, disseminated bronchiectasis, allergic bronchopulmonary aspergillosis and chronic pancreatitis), and the availability of efficient molecular tools for detecting mutations. A growing number of tests capable of simultaneously detecting several frequent CF mutations are being developed, and commercial kits are now available. The most recent kits detect nearly 90% of defective alleles in Caucasians, a rate high enough for carrier screening and for the majority of diagnostic requests. However, because of the wide variety of molecular defects documented in the CFTR gene, only a limited number of laboratories have mastered the entire panoply of necessary techniques, while other laboratories have to refer certain cases to specialized centers with complementary and/or scanning tools at their disposal. A good knowledge of CFTR diseases and their molecular mechanisms, together with expertise in the various techniques, is crucial for interpreting the results. Diagnostic strategies must take into account the indication, the patient's ethnic origin, and the time available in the framework of genetic counseling. This review presents the methods most frequently used for detecting CFTR gene mutations, and discusses the strategies most suited to the different clinical settings.

Cystic fibrosis: molecular diagnosis, population screening, and public policy

OBJECTIVE

To review the current status of scientific knowledge and opinion regarding molecular genetic testing of mutations in the CFTR gene for purposes of diagnosis and population carrier screening of cystic fibrosis (CF).

DATA SOURCES

Published research findings on the nature of the CFTR gene, pilot population screening studies in the United States and Europe, and ongoing deliberations of professional and governmental agencies considering implementation of widespread testing.

STUDY SELECTION

Findings relevant to the molecular heterogeneity of CFTR mutations and its implications for population carrier screening were considered.

DATA EXTRACTION

Information was extracted from studies published by us and others, as made available to recent consensus panels and professional committees.

DATA SYNTHESIS

These data were reevaluated in light of recent movements in professional and public policy regarding acceptability and desirability of widespread CF mutation testing. Effects to date of such testing on patient outcomes is reported.

CONCLUSIONS

The ability to test for CFTR mutations at the molecular level has already improved the diagnosis of symptomatic patients and expanded the reproductive options of family members of CF patients. The same technology also holds promise of identifying asymptomatic carriers and at-risk couples without family history in the general population so that they too might be offered prenatal diagnosis or other options. However, a number of key questions remain to be worked out before a widespread national screening program can be put into practice. These include the target population to be offered testing (the entire population vs high-risk ethnic groups), the size and nature of the mutation test panel (universal vs ethnic specific), the inclusion or exclusion of CFTR variants that do not cause classical CF, the optimal testing technology, appropriate standards for laboratory quality assurance, and the development of sufficient educational materials and genetic counseling resources for test delivery, reporting, and interpretation. The answers to these questions will be relevant not only to CF testing but also to many other large-scale molecular genetic screening programs being considered in the future.

Cystic fibrosis carrier screening practices in an ethnically diverse region: experience of the Genetic Network of the Empire State, Puerto Rico, and the U.S. Virgin Islands

We surveyed clinical genetics centers to assess current cystic fibrosis (CF) screening practices with regard to clinical and laboratory aspects. The survey was developed by the CF committee of the Genetics Network of the Empire State, Puerto Rico, and the U.S. Virgin Islands (GENES) to gauge changes in trends following the April, 1997, NIH Consensus Statement recommending the offering of CF carrier screening to all pregnant patients. Thirty-five of 45 Centers (78%) returned the survey, which was mailed in June, 1998. Sixteen centers currently offer population-based screening, whereas 19 centers do not. Reasons cited for not offering testing included the low risk for CF in ethnic groups served, lack of data about test sensitivity in the populations served, and the absence of CF screening policies in the current standards of care. Approximately half (56%) of genetics centers that are offering testing altered their screening policy following the NIH Consensus statement, either by offering screening to patients of higher-risk ethnicities or by offering it to all patients. Less than half of the Centers that offer routine carrier screening offer screening to all patients regardless of ethnicity. This report is an initial step in documenting and understanding the current service practices regarding CF carrier testing in a diverse region. Our conclusions: (1) Screening practices vary widely among genetic centers in the region. (2) The decision to offer routine CF carrier screening is largely based on ethnicity of the patient population served. (3) Methods used to screen pregnant women and their partners in this part of the country reflect the diversity of models employed throughout the United States. (4) CF screening practices in the GENES region have changed significantly following the April, 1997, NIH consensus statement.

Issues in implementing prenatal screening for cystic fibrosis: results of a working conference

PURPOSE

To summarize a conference convened to examine how cystic fibrosis screening might appropriately be introduced into routine prenatal practice.

METHODS

Participants included experts from various relevant disciplines. Systematic reviews and data from individual trials were presented; issues were identified and discussed.

RESULTS

Judged by published criteria, prenatal cystic fibrosis screening is suitable for introduction. Screening can be performed cost-effectively by identifying racial/ethnic groups at sufficient risk and then using either of two models for delivering laboratory services. Validated educational materials exist. Ethical issues are not unique.

CONCLUSIONS

Once adequate facilities for patient and provider education, testing, counseling, quality control, and monitoring are in place, individual programs can begin prenatal screening for cystic fibrosis.