Pharmacogenetic testing is becoming more common; however, very few quality control and other reference materials that cover alleles commonly included in such assays are currently available. To address these needs, the Centers for Disease Control and Prevention's Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing community and the Coriell Cell Repositories, have characterized a panel of 107 genomic DNA reference materials for five loci (CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1) that are commonly included in pharmacogenetic testing panels and proficiency testing surveys. Genomic DNA from publicly available cell lines was sent to volunteer laboratories for genotyping. Each sample was tested in three to six laboratories using a variety of commercially available or laboratory-developed platforms. The results were consistent among laboratories, with differences in allele assignments largely related to the manufacturer's assay design and variable nomenclature, especially for CYP2D6. The alleles included in the assay platforms varied, but most were identified in the set of 107 DNA samples. Nine additional pharmacogenetic loci (CYP4F2, EPHX1, ABCB1, HLAB, KIF6, CYP3A4, CYP3A5, TPMT, and DPD) were also tested. These samples are publicly available from Coriell and will be useful for quality assurance, proficiency testing, test development, and research. Many laboratories are testing for pharmacogenetic (PGx) markers, common genetic variants that are usually considered only when a patient is likely to be exposed to a Accepted for publication June 21, 2010. R.B., A.E.-B., C.S., A.V., and M.Z. are employees of AutoGenomics (manufacturer of several pharmacogenetic assays used in this study); M.B., A.B., and K.M. are employees of Quest Diagnostics Inc.; J.M. is an employee of Idaho Technology (manufacturer of the reagents used to genotype CYP2C9 and VKORC1 loci for this project);

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...

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Purpose: To develop a sequencing assay for the CFTR gene to identify mutations in patients with cystic fibrosis (CF). Methods: An automated assay format was developed to sequence all exons and splice junctional sequences, the promotor region, and parts of introns 11 and 19. Results: After validating the assay using 20 known samples, DNA of seven patients, four of whom were heterozygous for a known CF mutation, was sequenced. Known CF mutations were detected in seven of the eight chromosomes, and a novel missense mutation was detected in the eighth. In addition, this assay allowed 14 ambiguous results obtained using the Roche CF gold strips to be resolved. Three false-positive diagnoses were prevented; a different mutation at the same codon was identified in two patients and confirmation was provided in the remaining nine cases.

Cystic fibrosis (CF) is one of the most common monogenic diseases affecting Caucasians and has an incidence of approximately 1:3,300 births. Currently recommended screening panels for mutations in the responsible gene (CF transmembrane regulator gene, CFTR) do not detect all disease-associated mutations. Our laboratory offers extensive sequencing of the CFTR (ABCC7) gene (including the promoter, all exons and splice junction sites, and regions of selected introns) as a clinical test to detect mutations which are not found with conventional screening. The objective of this report is to summarize the findings of extensive CFTR sequencing from our first 157 consecutive patient samples. In most patients with classic CF symptoms (18/24, 75%), extensive CFTR sequencing confirmed the diagnosis by finding two disease-associated mutations. In contrast, only 5 of 75 (7%) patients with atypical CF had been identified with two CFTR mutations. A diagnosis of CF was confirmed in 10 of 17 (58%) newborns with either positive sweat chloride readings or positive immunoreactive trypsinogen (IRT) screen results. We ascertained ten novel sequence variants that are potentially disease-associated: two deletions (c.1641AG>T, c.2949_2853delTACTC), seven missense mutations (p.S158T, p.G451V, p.K481E, p.C491S, p.H949L, p.T1036N, p.F1099L), and one complex allele ([p.356_A357del; p.358I]). We ascertained three other apparently novel complex alleles. Finally, several patients were found to carry partial CFTR gene deletions. In summary, extensive CFTR gene sequencing can detect rare mutations which are not found with other screening and diagnostic tests, and can thus establish a definitive diagnosis in symptomatic patients with previously negative results. This enables carrier detection and prenatal diagnosis in additional family members.