Prenatal screening for cystic fibrosis: past, present and future

Incidental Finding of a Homozygous p.M348K Asymptomatic Italian Patient Confirms the Many Faces of Cystic Fibrosis

Cystic fibrosis (CF; OMIM number 219700) is an autosomal recessive disease caused by mutations in theCFTR(cystic fibrosis transmembrane conductance regulator) gene, which results in abnormal viscous mucoid secretions in multiple organs and whose main clinical features are pancreatic insufficiency, chronic endobronchial infection, and male infertility. We report the case of a 47-year-old apparently normal male resulting in homozygosity for the mutation p.M348K from nonconsanguineous parents. The proband was screened using a standard panel of 70 different tested on NanoChip 400 platform. The massive parallel pyrosequencing on 454 JS machine allowed the second level analysis. The patient was firstly screened with two different platforms available in our laboratory, obtaining an ambiguous signal for the p.R347P mutation. For this reason we decided to clarify the discordant result ofCFTRstatus by Next Generation Sequencing (NGS) using 454 Junior instrument. The patient is resulted no carrier of the p.R347P mutation, but NGS highlighted a homozygous substitution from T>A at position 1043 in the coding region, causing an amino acid substitution from methionine to lysine (p.M348K). Casual finding of p.M348K homozygote mutation in an individual, without any feature of classical or nonclassical CF form, allowed us to confirm that p.M348K is a benign rare polymorphism.

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.

Evolution of prenatal genetics: from point mutation testing to chromosomal microarray analysis

Molecular genetic testing involves DNA analysis using various methods for the purpose of diagnosing genetic disorders. In the prenatal DNA diagnostic setting, fetal DNA is usually tested for a specific single-gene disorder for which the fetal risk is 25% or more. In contrast, cytogenetic testing is often used to detect fetal chromosomal abnormalities in cases that involve a wider range of indications. Classic cytogenetic and DNA-based testing methods provide a range of aberrations detected with different levels of genomic resolution. More recently developed molecular cytogenetic methods provide powerful tools to bridge the technical divide between these related areas. One such hybrid method is microarray-based comparative genomic hybridization. Chromosomal microarray analysis has been applied to clinical testing for unbalanced gains or losses of genomic regions associated with genetic disorders. This technology is poised to have a substantial impact on clinical genetics, including prenatal genetic testing.

Thin-film technology for direct visual detection of nucleic acid sequences: applications in clinical research

Certain optical conditions permit the unaided eye to detect thickness changes on surfaces on the order of 20 A, which are of similar dimensions to monomolecular interactions between proteins or hybridization of complementary nucleic acid sequences. Such detection exploits specific interference of reflected white light, wherein thickness changes are perceived as surface color changes. This technology, termed thin-film detection, allows for the visualization of subattomole amounts of nucleic acid targets, even in complex clinical samples. Thin-film technology has been applied to a broad range of clinically relevant indications, including the detection of pathogenic bacterial and viral nucleic acid sequences and the discrimination of sequence variations in human genes causally related to susceptibility or severity of disease.

Molecular diagnosis of ATP-binding cassette transporter-related diseases

ATP-binding cassette (ABC) transporters are involved in a variety of physiologic processes such as xenobiotic defense, lipid metabolism, ion homeostasis and immune functions. A large number of ABC proteins have been causatively linked to rare and common human genetic diseases including familial high-density lipoprotein deficiency, retinopathies, cystic fibrosis, diabetes and cardiomyopathies. Furthermore, genetic variations in ABC transporter genes and dysregulated expression patterns of these molecules significantly contribute to drug resistance in human cancer cells and alter the pharmacokinetic properties of a variety of drugs. In order to analyze DNA sequence alterations or define disease-associated mRNA expression patterns of the complete ABC transporter superfamily, novel high-throughput molecular methods such as quantitative real-time PCR and DNA microarray analysis are emerging. The aim of this review is to provide an overview and to present some examples of human ABC transporters involved in monogenic diseases, cancer and pharmacogenetics. Methodologic aspects of molecular diagnostics applied to analyze genetic variations, mRNA and protein expression levels and functional characteristics of ABC transporters are discussed.

Shock, adjust, decide: reproductive decision making in cystic fibrosis (CF) carrier couples--a qualitative study

Cystic fibrosis (CF) is the most common recessive condition affecting the White British population. Facilitating reproductive decision making for couples at genetic risk for CF is an important aspect of genetic counseling practice in the UK. The purpose of this study was to explore the reproductive decision making process for 31 members of CF carrier couples (15 men and 16 women) with or without an affected child. The design involved a qualitative approach consisting of semi-structured interviews and data analysis informed by grounded theory methodology. Sex and personal experience of CF were identified as factors that may influence reproductive decision making. Findings suggest these hypotheses: (1) CF carrier couples who have an affected child/pregnancy, are more likely to embark on another pregnancy than couples who have a healthy child from an at-risk pregnancy, and (2) men and women play different roles in the reproductive decision making process. Data analysis resulted in development of a structured framework modeling the reproductive decision making process, which may be helpful in guiding genetic counseling with CF carrier couples and other at risk couples making reproductive decisions.

Alpha-thalassaemia

Alpha-thalassaemia is inherited as an autosomal recessive disorder characterised by a microcytic hypochromic anaemia, and a clinical phenotype varying from almost asymptomatic to a lethal haemolytic anaemia.

It is probably the most common monogenic gene disorder in the world and is especially frequent in Mediterranean countries, South-East Asia, Africa, the Middle East and in the Indian subcontinent. During the last few decades the incidence of alpha thalassaemia in North-European countries and Northern America has increased because of demographic changes. Compound heterozygotes and some homozygotes have a moderate to severe form of alpha thalassaemia called HbH disease. Hb Bart's hydrops foetalis is a lethal form in which no alpha-globin is synthesized. Alpha thalassaemia most frequently results from deletion of one or both alpha genes from the chromosome and can be classified according to its genotype/phenotype correlation. The normal complement of four functional alpha-globin genes may be decreased by 1, 2, 3 or all 4 copies of the genes, explaining the clinical variation and increasing severity of the disease. All affected individuals have a variable degree of anaemia (low Hb), reduced mean corpuscular haemoglobin (MCH/pg), reduced mean corpuscular volume (MCV/fl) and a normal/slightly reduced level of HbA₂. Molecular analysis is usually required to confirm the haematological observations (especially in silent alpha-thalassaemia and alpha-thalassaemia trait). The predominant features in HbH disease are anaemia with variable amounts of HbH (0.8-40%). The type of mutation influences the clinical severity of HbH disease. The distinguishing features of the haemoglobin Bart's hydrops foetalis syndrome are the presence of Hb Bart's and the total absence of HbF. The mode of transmission of alpha thalassaemia is autosomal recessive. Genetic counselling is offered to couples at risk for HbH disease or haemoglobin Bart's Hydrops Foetalis Syndrome. Carriers of alpha⁺- or alpha⁰-thalassaemia alleles generally do not need treatment. HbH patients may require intermittent transfusion therapy especially during intercurrent illness. Most pregnancies in which the foetus is known to have the haemoglobin Bart's hydrops foetalis syndrome are terminated due to the increased risk of both maternal and foetal morbidity.

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 comparative study of five technologically diverse CFTR testing platforms

Multiple cystic fibrosis (CF) testing platforms, using diverse and rapidly evolving technologies, are available to clinical laboratories commercially or for evaluation. Considerations when choosing a CF platform may include: sensitivity, specificity, accuracy, signal discrimination, ability to genotype, ability to reflex test, no calls/repeat rate, composition of mutation panel, hands-on time, start-to-finish time, integration into laboratory workflow, data analysis methods, flexibility regarding custom test design, and required instrumentation. Mindful of these considerations, we evaluated five technologically diverse CF platforms: 1) eSensor, an electronic detection assay system; 2) InPlex, a signal amplification methodology using a microfluidics card; 3) oligonucleotide ligation assay, an electrophoretic-based separation of amplicon-derived ligation-generated products; and two liquid bead arrays; 4) Signature, a direct hybridization assay using allele-specific capture probes; and 5) Tag-It, an assay using allele-specific primer extension and a universal microarray. A core of 150 samples, focusing on mutations in the American College of Medical Genetics/American College of Obstetricians and Gynecologists mutation panel, was tested throughout several runs for each platform. All of the platforms performed comparably in respect to sensitivity, specificity, and no-call rate. As our results indicate, consideration of all of the parameters evaluated may be useful when selecting the most appropriate platform for the specific setting.

A universal array-based multiplexed test for cystic fibrosis carrier screening

Cystic fibrosis is a multisystem autosomal recessive disorder with high carrier frequencies in caucasians and significant, but lower, carrier frequencies in other ethnicities. Based on technology that allows high detection of mutations in caucasians and significant detection in other ethnic groups, the American College of Medical Genetics (ACMG) and American College of Obstetricians and Gynecologists (ACOG) have recommended pan-ethnic cystic fibrosis carrier screening for all reproductive couples. This paper discusses carrier screening using the Tag-It multiplex mutation platform and the Cystic Fibrosis Mutation Detection Kit. The Tag-It cystic fibrosis assay is a multiplexed genotyping assay that detects a panel of 40 cystic fibrosis transmembrane conductance regulator mutations including the 23 mutations recommended by the ACMG and ACOG for population screening. A total of 16 additional mutations detected by the Tag-It cystic fibrosis assay may also be common. The assay method is described in detail, and its performance in a genetics reference laboratory performing high-volume cystic fibrosis carrier screening is assessed.

Genetic epidemiology and public health: hope, hype, and future prospects

Genetic epidemiology is a rapidly expanding research field, but the implications of findings from such studies for individual or population health are unclear. The use of molecular genetic screening currently has some legitimacy in certain monogenic conditions, but no established value with respect to common complex diseases. Personalised medical care based on molecular genetic testing is also as yet undeveloped for common diseases. Genetic epidemiology can contribute to establishing the causal nature of environmentally modifiable risk factors, through the application of mendelian randomisation approaches and thus contribute to appropriate preventive strategies. Technological and other advances will allow the potential of genetic epidemiology to be revealed over the next few years, and the establishment of large population-based resources for such studies (biobanks) should contribute to this endeavour.

Risk calculations for cystic fibrosis in neonatal screening by immunoreactive trypsinogen and CFTR mutation tests

PURPOSE

Although neonatal screening (or newborn screening) for cystic fibrosis (CF) is commonly practiced, systematic methods for accurate risk calculations are currently lacking.

METHODS AND RESULTS

We evaluated characteristics of the immunoreactive trypsinogen (IRT) test using the published data. The probability that a neonate has a positive IRT test, if the neonate is affected, a carrier, or a noncarrier, is approximately 1, 0.041, or 0.011, respectively. We provide methods to calculate genetic risks for a variety of commonly encountered scenarios in which neonates are positive by the IRT test.

CONCLUSION

Our Bayesian methods permit CF disease probabilities to be calculated accurately, taking into account all relevant information.

Application of fetal DNA detection in maternal plasma: a prenatal diagnosis unit experience

Non-invasive prenatal diagnosis tests based on the analysis of fetal DNA in maternal plasma have potential to be a safer alternative to invasive methods. So far, different studies have shown mainly fetal sex, fetal RhD, and quantitative variations of fetal DNA during gestation with fetal chromosomal anomalies or gestations at risk for preeclampsia. The objective of our research was to evaluate the use of fetal DNA in maternal plasma for clinical application. In our study, we have established the methodology needed for the analysis of fetal DNA. Different methods were used, according to the requirements of the assay. We have used quantitative fluorescent polymerase chain reaction (QF-PCR) to perform fetal sex detection with 90% sensitivity. The same technique permitted the detection of fetal DNA from the 10th week of gestation to hours after delivery. We have successfully carried out the diagnosis of two inherited disorders, cystic fibrosis (conventional PCR and restriction analysis) and Huntington disease (QF-PCR). Ninety percent of the cases studied for fetal RhD by real-time PCR were correctly diagnosed. The detection of fetal DNA sequences is a reality and could reduce the risk of invasive techniques for certain fetal disorders in the near future.

Bayesian analysis for cystic fibrosis risks in prenatal and carrier screening

PURPOSE

Risk assessment is an essential component of genetic counseling and testing, and Bayesian analysis plays a central role in complex risk calculations. We previously developed generalizable Bayesian methods to calculate the autosomal recessive disease risk of a fetus when one or no mutation is detected, and another, independent risk factor is present. Our methods are particularly useful for calculating the CF disease risk for a fetus with echogenic bowel. In genetics practice, however, there are other scenarios for which our previous methods are inadequate.

METHODS AND RESULTS

We provide herein methods for calculating genetic risks in a variety of common clinical scenarios. These scenarios include the following: (1) different mutation panels that have been used for the parents and for a fetus; (2) genetic testing results available on the proband or other relatives, in addition to the consultand; (3) fetal ultrasound negative for echogenic bowel with a positive family history; and (4) a consultand with a mixed ethnic background.

CONCLUSION

Our Bayesian methods have proven their versatility through application to many different common genetic counseling scenarios. These methods permit autosomal recessive disease and carrier probabilities to be calculated accurately, taking into account all relevant information. Our methods allow accurate genetic risk estimates for patients and their family members for CF or other autosomal recessive disorders.