Presentation on theme: "Genetic Testing for Cystic Fibrosis"— Presentation transcript:
1 Genetic Testing for Cystic Fibrosis Dee Quinn, MS, CGCAugust, 2006
2 “Gene Testing Going Mainstream” Cystic Fibrosis Gene Test OfferedBy Lauran NeergaardAP Medical WriterMonday, Oct. 1, 2001; 9:53 p.m. EDTWASHINGTON –– Gene testing is going mainstream: Starting this month, tens of thousands of white Americans will be offered testing to see if they carry a gene mutation that causes cystic fibrosis even if no one in their family has the disease.
3 CFTR Gene Identified in 1989 Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)27 exons, 250kB of genomic DNAChromosome 7qLap-Chee Tsui and Francis Collins headed team that reported the discovery of the gene, linkage analysis (a lot of families to use) and positional cloningName CFTR-they hypothesized the gene was involved with transport and conductance across the membraneLarge geneLocated on the long arm of chromosome 7
6 CFTR Gene cAMP-dependent chloride channel Expressed in epithelial cells of:respiratory tractsweat and salivary glandspancreasintestinereproductive tractReason CF has the clinical presentation that it does:CFTR forms a regulated cell membrane Cl channel with several domains, allowing chloride to be transported out of the cell to the epithelial surface, so mutations cause defective chloride transportLook at each individually2. Respiratory: too much chloride kept in cell, leads to dehydrated secretions, thick mucus instead of thin watery secretionsSweat glands: high levels of NaCl (salt) not reabsorbedPancreas-obstruct the digestive system and prevent pancreatic enzymes from reaching the small intestineIntestine-presence of thickened mucus and lack of digestive enzymes, lead to increased risk for bowel obstruction, can sometimes be seen by ultrasound echogenic bowel (1-13% risk)Reproductive
7 Clinical Phenotype Respiratory GI, pancreas Reproductive CF is typically a multi-system disease. Most patients have both respiratory and digestive problems, while others only have respiratory problems.Pulmonary manifestations-range from very mild pulmonary symptoms to severe progressive chronic lung disease, vast majority of patients with CF die as a result of pulmonary complicationsPancreatic insufficiency and intestinal malabsorption are present in 85% of affected individualsMen with CF (more than 95%) are infertile due to azoospermia, because of congenital bilateral absence of the vas deferensAlso see men without any pulmonary or gastrointestinal manifestations of CF may have CBAVD resulting in azoospermiaSalt loss syndromes like salt depletion or chronic metabolic alkalosisIntelligence and appearance are typically not affected in those with CF.
8 CFTR Mutations Over 1,000 mutations identified Most labs test for mutations13 of the identified CF mutations occur in more than 1% of CF chromosomes72% of whites with CF are homozygous or heterozygous for 8 mutations5 classes of CFTR mutationsGenotype/phenotype correlations may not be helpfulWith that many mutations, how could screening possibly be accomplished?Most of the remaining mutations occur infrequently, usually only in a particular familyHelpful to organize into 5 classes
9 Class I premature termination signals and splicing abnormalities, no protein production Class II- defective folding and disruption of protein biosynthesis, can’t make to membraneClass III- generate protein that reaches the plasma membrane but channels show defective regulationClass IV- generate correcting localized CFTR with defective pore properties, reduced Cl current, less Cl in and out and the channel is open a shorter timeClass V-reduced protein productionIn general Class 1,2 or 3 mutations are expected to have more serious phenotypic consequences than class 4 or 5Call attention to deltaF508 and R117h
10 CFTR Mutations- ΔF508Most common mutation in North America, 70-75% of the mutationsDeletion of codon 508 Results in shortening of the protein productProtein product still functioning as Cl channel, but is retained in the endoplasmic reticulumΔF508 (homozygosity): classical phenotypeVaries from ethnic groupClassical phenotype-typically have severe pancreatic insufficiency combined with variable pulmonary function
11 EpidemiologyOne of the most common autosomal recessive diseases in CaucasiansOccurs in 1 in 3300 births30,000 affected persons in the United StatesProposed advantages cholera infection, higher fertility and resistance to a variety of infectious agents.
14 Epidemiology 97 1/29 1/3,300 Ashkenazi Jews 30 1/90 1/32,100 Asian Americans691/60-651/15,300African Americans80-901/521/3,970-1/1,500Native Americans571/461/8-9,000HispanicsCaucasians(United States)SensitivityCarrierFrequencyIncidenceGroup80-90 Sensitivity depends on ethnic background of Caucasians, N. Europeans have 90% detection rate, S. Europeans 80%Native Americans founder effect, geographic isolation
15 Congenital Bilateral Absence of the Vas Deferens (CBAVD) Vas deferens – carries sperm from the epididymis to the ejaculatory ductsAbsence of vas occurs in 95% of males with CFCBAVD: distinct genetic disorder which overlaps with CF and causes infertilityNoncoding region of CFTR gene involved: intron 8 with thymidine tracts (5T/7T/9T)60-70% of men with CBAVD carry one mutation in the CFTR gene.5T reduces the number of functional Cl channelsIntricately tied to CFCBAVD is a distinct genetic disorder. Condition overlaps with CF, but also represents a distinct entity so it occurs outside of the CF phenotype and is responsible for 1-2% of infertility due to azoospermiaMutations in the CFTR gene have also been identified in patients with CBAVD which suggests this condition is a genital form of CF % of men with CBAVD carry one mutation in the CFTR gene.5T reduces the number of functional Cl channels
16 Congenital Bilateral Absence of the Vas Deferens (CBAVD)
17 Genotype - Phenotype Correlation CFTR Genotype First Allele Second Allele Range of Phenotypes Classic (e.g., F508) Classic Classic >> nonclassic Mild (e.g., A455E) Classic or mild Nonclassic > classic R117H/5T Classic or mild Nonclassic > classic R117H/7T Classic or mild Asymptomatic female or CBAVD > nonclassic 5T/TG13 or TG12 Classic or mild CBAVD or nonclassic CF >> asymptomatic carrier 5T/TG11 Classic or mild Asymptomatic > CBAVD 7T or 9T Classic or mild Asymptomatic 7T or 9T 7T or 9T Asymptomatic (From1. Patterns reflect dominant effect of "milder” alleles in compound heterozygotes. Classic alleles generally refer to Class I-III mutations; mild alleles refer to Class IV-V mutations exclusive of R117H and 5T alleles.
18 Newborn ScreeningBlood spots from infants taken within days of birth to identify infants at increased risk for a specific genetic disordersJustifications:Early treatment of respiratory illnessesEvidence for nutritional benefitCurrently offered or in planning in many states – AZ to begin newborn screening by 9/07
19 Newborn ScreeningInitial screen tests levels of IRT (immunoreactive trypsinogen)Screening program should include:Specific provider and patient educational materialsProtocol for addressing positive screening resultsSweat chlorideDNA testingDevelopment of systems in collaboration with specialty care providers to track short-term and long-term child outcomes and identify resources to support this activity
20 Carrier Screening for CF 1997- NIH convened a Consensus Conference1998- ACOG/ACMG formed Steering Committee10/2001- “Preconception and Prenatal Carrier Screening for Cystic Fibrosis”1997- several pilot studies before consensus, recommended that CFTR mutation testing be available to all pregnant couples and those contemplating pregnancy1998-steering committee to coordinate the implementation of the consensus conference recommendations, develop guidelines for provider education, laboratory testing, interpretation and genetic counseling, and patient education and informed consent10/2001- document includes guidelines for providers, patient education, and informed consent.
21 ACOG/ACMG Recommendations Offer screening to:Individuals with a family history of CFReproductive partners of individuals with CFCouples in whom one or both are Caucasian and are planning a pregnancy or seeking prenatal careOther individuals must be given written informationElicit family history, determine who in family has CF, refer to genetics professional because of interpretation of test results and estimation of risk may be more complex than in the general population (bring up referral to genetic professional, clearly states so that obs and PCPs will not have to provide these services and so that insurance will cover)Clarify couple’s risk of having a child with CF, majority are aware of their increased risk for having a child with CF, again referral to genetics professionalOffered when both the frequency of carriers and the detection rate of the carrier test are relatively high in the ethnic groups of the partnersMade available to other ethnic and racial groups, informed of their delectability through educational brochures. For example, Asian Americans w/o significant Caucasian admixture should be informed of the rarity of the disease and the very low yield of the test in their population.Problem may be difficult to classify patients ethnic background, especially in a busy clinical setting, advocate universal screening, most often happen in the PCP’s office or the OB’s office
22 ACOG/ACMG Recommendations Provider’s Role:Purpose of screeningVoluntary nature of screeningSymptoms of CF, treatment andprognosisGenetics of CF and populationfrequenciesMeaning of positive and negative testresultsFactors to consider in deciding to haveor not to have screeningCommon patient belief that any test offered by a physician must be necessary and advantageous, see this with amnioBooklet address these issues, makes explicit the optional nature of the testing and presents information in written form so that the patient and partner can consider their concerns and formulate questions about testing before discussing it with the support staff or provider, suggested that booklet be sent to a woman before her initial clinic visit, reinforces idea that CF screening is a personal decision between the coupleFactors for screening, if risk seems high and insurance covers, against doesn’t detect all carriersBooklets are intended to supplement not replace communication with providersInformed consent: counseling and offer of screening and the couple’s decision about screening should be discussed and documented in the medical record, written informed consent should be obtained only after the woman and her partner have opportunity to review the educational material and receive pretest counseling.Lower risk ethnic groups, CF screening should be made available, printed information provided, screening and counseling provided upon request
23 Additional Indications for Screening Echogenic bowel detected on prenatal ultrasoundInfertility in males
24 Diagnostic Prenatal Tests Testing offered when:When both members of a couple are carriers, ie: 25% risk of having a baby with CFWhen one member of a couple is carrier and other member not available for testingTesting options:Chorionic villus sampling (CVS)9-11 weeksAmniocentesisAfter 14 weeks
25 Other Approaches Procedure Caveats In vitro fertilization One cell removed from early embryo to test for mutations which were found in parentsCell without a CF genotype transferred to mother’s uterusCaveatsTechnically demanding and complex procedureAvailable on a limited basisExpensive: $4,000 - $12,000Ethical implications
26 ACOG/ACMG Recommendations Laboratory’s Role:Reports should include results of screening and an interpretation:Negative Residual risk givenPositive Test other partnerSo doctor can easily understand and have available residual riskSee chart 1QA:Time constraint, expect in 2 weeksUse accredited labs that will provide high quality testing and interpretationDNA based test, use oligonucetide primers
27 Limitations of CF Screening Does not detect all carriersEstimate of residual risk applies only when family history is negative and to the current pregnancyCannot make reliable predictions for outcome based on mutationsNon-paternityNot all CF mutations can be detected in screening panels. Impt to go over residual risk based on the racial or ethnic group of the partner, the specific mutations the test covered, and whether one or both partners were tested like we just looked atAt end: All of these issues should be discussed with couple before testing and reviewed after results given
28 Genetic CounselingVarious outcomes of prenatal and newborn will generate need for genetic counseling:Newly diagnosed child with CFHealthy males who carry mutations associated with infertilityIdentification of positive/negative couples who request additional mutational analyses or counseling to clarify residual riskPositive/positive couples
29 Ethical, Legal, and Social Implications of CF Screening Unnecessary anxiety createdInadequate pretest informationLegalInformed ConsentInsurance discriminationSocialExpense swell health costsSocietal pressure not to bear affected offspringNIH conducted pilot studies before issuing consensus statement. Ethical, legal and social issues were looked at in deciding whether CF screening should be implemented.Ethical:Anxiety levels: no increase in anxiety levels by CF education or DNA testingLess than half (44%) whose result was negative understood that they could still have a child with CF, providers in that study spent little time explaining CF carrier screening and generally relied in patient comprehending written material (article)Legal:Without proper education, can’t really be considered an informed consent to testing, suggestions have been made to use quizzes that would test patient understanding, provider cannot be held liable for couples that have children with CF1/3 of those express concern about insurance discrimination, laws in place that prevent discrimination, most of the concern with insurance discrimination is with predictive gene tests and insurance companies reducing benefits on the basis of predictive gene test.Social:57% offered screening accepted, factors against religious beliefs, 1/3 insurance fearsMost decided on their own rather than on the basis of physician, reasons were logical, most women who would not terminate a pregnancy for CF chose not to be testedOverall, NIH pilot studies have not shown results that substantiate concern over any of these implications, except for adequate pretest education. Several studies have been done since then and these same issue has arisen, that providers aren’t familiar with the information about CF and in turn do not pass along to their patients
30 Resources Cystic Fibrosis Foundation http://www.cff.org GeneTests and GeneReviewsNational Society of Genetic CounselorsMountain States Genetics Network
31 Conclusions“It will be very important to see how this goes. Certainly it requires the obstetricians to become more familiar with genetics than many of them have previously had occasion to do.”-Francis CollinsImplications for other gene testing