Cystic fibrosis screening using the College panel: Platform comparison and lessons learned from the first 20,000 samples

Abstract

Purpose: To determine the accuracy of two commercially available kits for cystic fibrosis (CF) genotyping and determine allele frequencies for the ACMG/ACOG recommended mutations. Methods: A total of 1,040 consecutive analyses using Roche CF Gold Strips and the ABI CF Genotyper were performed. Subsequently we performed analyses of 20,103 samples. Results: Both kits accurately determined CF genotypes. The I148T mutation was found Ͼ100 times more frequently in carrier screening than in CF patients. Asymptomatic patients were identified who are compound heterozygotes for delta F508 and I148T. Four of 13 patients heterozygous for delta F508 and the IVS8-5T polymorphism had some symptoms of CF. Cystic fibrosis (CF) is one of the most common recessive genetic diseases in North America. In the March/April edition of this Journal, the Subcommittee on Cystic Fibrosis Screening of the American College of Medical Genetics (ACMG) published laboratory standards for population-based CF carrier screening. 1 The Committee recommended a core screening panel of 25 mutations with reflex testing under certain circumstances to four polymorphisms. These recommendations were based on the published frequencies of mutations observed in CF patients and other more subtle considerations such as a reluctance to screen for mutations causing congenital bilateral absence of the vas deferens (CBAVD). In October 2001, the American College of Obstetrics and Gynecology (ACOG) published its anticipated recommendation to College members to offer CF carrier detection to pregnant women. 2 In preparation for the release of the ACOG clinical practice guideline, we evaluated two of the commercially offered analytic platforms available as Analyte Specific Reagents (ASR) by performing blinded side by side analysis of 1,040 samples and determined that both performed acceptably.Our laboratory began screening for the College recommended panel in July 2001. To date, more than 20,000 samples have been analyzed. Many interesting observations are reported here with respect to test volumes, mutation frequencies, and accuracy of commercially available products. We also discuss clinical problems that have arisen. Our data and discussion provide insight into potential problems and solutions as CF population screening becomes integrated into standard obstetric care. MATERIALS AND METHODS Patient populationIn the period between July 1, 2001, and December 1, 2001, 20,103 consecutive samples submitted for CF DNA testing were analyzed for the ACMG recommended panel of mutations. Although information such as patient ethnicity and pertinent family history are requested for each patient, in practice, this information was only sporadically provided. When appropriate, physicians were contacted to obtain clinical information regarding patients with interesting genotypes. Because the indication was not routinely provided, we have no way to determine the number of tests performed for carrier detection versus mutation detection in a patient with CF, or infertility evaluations. The...

CFTR mutation distribution among U.S. Hispanic and African American individuals: Evaluation in cystic fibrosis patient and carrier screening populations

“…D1270N has been identified in individuals with cystic fibrosis 24,33,35,36 as well as in men with congenital absence of the vas deferens. 24,37 Similar discrepancies in mutation frequency between carrier and patient populations are now well known for the R117H 15 and I148T 38,39 sequence changes, each of which has a cis-acting modifier influencing phenotype (5T 21 and 3199del6, 40 respectively). There have been similar reports that R74W may be a potential modifier for the clinical phenotype of D1270N.…”

Detection of an Apparent Homozygous 3120G>A Cystic Fibrosis Mutation on a Routine Carrier Screen

“…Similar to I148T influencing 3199del6 in cis 18,19 or R117H being influenced by the 5T variant, 20 there could be an additional mutation on the same chromosome causing different phenotypes for those who have the same apparent genotype.…”

Molecular screening for diseases frequent in Ashkenazi Jews: Lessons learned from more than 100,000 tests performed in a commercial laboratory

“…11 A detailed description of test methodology is beyond the scope of this publication. In summary, assays for 4 mutations in TSD, 4 mutations in GD, 3 mutations in CD, and 4 mutations in NPD were performed using laboratory developed assays and SnapShot kits provided by Applied Biosystems Incorporated (ABI) under a licensing agreement from Orchid Technologies.…”