Lawrence M. Silverman

A Novel Mutation in the Cystic Fibrosis Gene in Patients with Pulmonary Disease but Normal Sweat Chloride Concentrations

BACKGROUNDnMany patients with chronic pulmonary disease similar to that seen in cystic fibrosis have normal (or nondiagnostic) sweat chloride values. It has been difficult to make the diagnosis of cystic fibrosis in these patients because no associated mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene has been identified.nnnMETHODSnWe evaluated 23 patients with pulmonary disease characteristic of cystic fibrosis but with sweat chloride concentrations in the normal range. Mutations in the CFTR gene were sought by direct sequencing of polymerase chain reaction-amplified nasal epithelial messenger RNA and by testing the functioning of affected epithelium.nnnRESULTSnA cytidine phosphate guanosine dinucleotide C-to-T point mutation in intron 19 of the CFTR gene, termed 3849 + 10 kb C to T, was identified in 13 patients from eight unrelated families. This mutation was found in patients from three different ethnic groups with three different extended haplotypes. The mutation leads to the creation of a partially active splice site in intron 19 and to the insertion into most CFTR transcripts of a new 84-base-pair exon, containing an in-frame stop codon, between exons 19 and 20. Normally spliced transcripts were also detected at a level approximately 8 percent of that found in normal subjects. This mutation is associated with abnormal nasal epithelial and sweat acinar epithelial function.nnnCONCLUSIONSnWe have identified a point mutation in intron 19 of CFTR and abnormal epithelial function in patients who have cystic fibrosis-like lung disease but normal sweat chloride values. The identification of this mutation indicates that this syndrome is a form of cystic fibrosis. Screening for the mutation should prove diagnostically useful in this population of patients.

Genetic Modifiers of Liver Disease in Cystic Fibrosis

CONTEXTnA subset (approximately 3%-5%) of patients with cystic fibrosis (CF) develops severe liver disease with portal hypertension.nnnOBJECTIVEnTo assess whether any of 9 polymorphisms in 5 candidate genes (alpha(1)-antitrypsin or alpha(1)-antiprotease [SERPINA1], angiotensin-converting enzyme [ACE], glutathione S-transferase [GSTP1], mannose-binding lectin 2 [MBL2], and transforming growth factor beta1 [TGFB1]) are associated with severe liver disease in patients with CF.nnnDESIGN, SETTING, AND PARTICIPANTSnTwo-stage case-control study enrolling patients with CF and severe liver disease with portal hypertension (CFLD) from 63 CF centers in the United States as well as 32 in Canada and 18 outside of North America, with the University of North Carolina at Chapel Hill as the coordinating site. In the initial study, 124 patients with CFLD (enrolled January 1999-December 2004) and 843 control patients without CFLD were studied by genotyping 9 polymorphisms in 5 genes previously studied as modifiers of liver disease in CF. In the second stage, the SERPINA1 Z allele and TGFB1 codon 10 genotype were tested in an additional 136 patients with CFLD (enrolled January 2005-February 2007) and 1088 with no CFLD.nnnMAIN OUTCOME MEASURESnDifferences in distribution of genotypes in patients with CFLD vs patients without CFLD.nnnRESULTSnThe initial study showed CFLD to be associated with the SERPINA1 Z allele (odds ratio [OR], 4.72; 95% confidence interval [CI], 2.31-9.61; P = 3.3 x 10(-6)) and with TGFB1 codon 10 CC genotype (OR, 1.53; 95% CI, 1.16-2.03; P = 2.8 x 10(-3)). In the replication study, CFLD was associated with the SERPINA1 Z allele (OR, 3.42; 95% CI, 1.54-7.59; P = 1.4 x 10(-3)) but not with TGFB1 codon 10. A combined analysis of the initial and replication studies by logistic regression showed CFLD to be associated with SERPINA1 Z allele (OR, 5.04; 95% CI, 2.88-8.83; P = 1.5 x 10(-8)).nnnCONCLUSIONSnThe SERPINA1 Z allele is a risk factor for liver disease in CF. Patients who carry the Z allele are at greater risk (OR, approximately 5) of developing severe liver disease with portal hypertension.

Clinical laboratory reports in molecular pathology

CONTEXTnMolecular pathology is a rapidly growing area of laboratory medicine in which DNA and RNA are analyzed. The recent introduction of array technology has added another layer of complexity involving massive parallel analysis of multiple genes, transcripts, or proteins.nnnOBJECTIVEnAs molecular technologies are increasingly implemented in clinical settings, it is important to bring uniformity to the way that test results are reported.nnnDATA SOURCESnThe College of American Pathologists Molecular Pathology Resource Committee members summarize elements that are already common to virtually all molecular pathology reports, as set forth in the College of American Pathologists checklists used in the laboratory accreditation process. Consensus recommendations are proposed to improve report format and content, and areas of controversy are discussed. Resources are cited that promote use of proper gene nomenclature and that describe methods for reporting mutations, translocations, microsatellite instability, and other genetic alterations related to inherited disease, cancer, identity testing, microbiology, and pharmacogenetics.nnnCONCLUSIONSnThese resources and recommendations provide a framework for composing patient reports to convey molecular test results and their clinical significance to members of the health care team.

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

Purpose: We reviewed CFTR mutation distribution among Hispanic and African American individuals referred for CF carrier screening and compared mutation frequencies to those derived from CF patient samples.Methods: Results from CFTR mutation analyses received from January 2001 through September 2003, were analyzed for four populations: Hispanic individuals with a CF diagnosis (n = 159) or carrier screening indication (n = 15,333) and African American individuals with a CF diagnosis (n = 108) or carrier screening indication (n = 8,973). All samples were tested for the same 87 mutation panel.Results: In the Hispanic population, 42 mutations were identified: 30 in the patient population (77.5% detection rate) and 33 among carrier screening referrals. Five mutations not included in the ACMG/ACOG carrier screening panel (3876delA, W1089X, R1066C, S549N, 1949del84) accounted for 7.55% detection in patients and 5.58% among carriers. Among African American referrals, 33 different mutations were identified: 21 in the patient population (74.4% detection) and 23 in the carrier screening population. Together, A559T and 711+5G>A were observed at a detection rate of 3.71% in CF patients and 6.38% in carriers. The mutation distribution seen in both the carrier screening populations reflected an increased frequency of mutations with variable expression such as D1152H, R117H, and L206W.Conclusions: A detailed analysis of CFTR mutation distribution in the Hispanic and African American patient and carrier screening populations demonstrates that a diverse group of mutations is most appropriate for diagnostic and carrier screening in these populations. To best serve the increasingly diverse U.S. population, ethnic-specific mutations should be included in mutation panels.

Developing a sustainable process to provide quality control materials for genetic testing

Purpose: To provide a summary of the outcomes of two working conferences organized by the Centers for Disease Control and Prevention (CDC), to develop recommendations for practical, sustainable mechanisms to make quality control (QC) materials available to the genetic testing community.Methods: Participants were selected to include experts in genetic testing and molecular diagnostics from professional organizations, government agencies, industry, laboratories, academic institutions, cell repositories, and proficiency testing (PT)/external Quality Assessment (EQA) programs. Current efforts to develop QC materials for genetic tests were reviewed; key issues and areas of need were identified; and workgroups were formed to address each area of need and to formulate recommendations and next steps.Results: Recommendations were developed toward establishing a sustainable process to improve the availability of appropriate QC materials for genetic testing, with an emphasis on molecular genetic testing as an initial step.Conclusions: Improving the availability of appropriate QC materials is of critical importance for assuring the quality of genetic testing, enhancing performance evaluation and PT/EQA programs, and facilitating new test development. To meet the needs of the rapidly expanding capacity of genetic testing in clinical and public health settings, a comprehensive, coordinated program should be developed. A Genetic Testing Quality Control Materials Program has therefore been established by CDC in March 2005 to serve these needs.

Detection of immunoglobulin heavy chain gene rearrangements in classic hodgkin lymphoma using commercially available BIOMED-2 primers.

Context Classic Hodgkin lymphoma (cHL) is regarded as a clonal B-cell neoplasm. The BIOMED-2 group recently validated a set of immunoglobulin heavy chain (IGH) multiplex primers with high sensitivity in B-cell non-Hodgkin lymphomas. We postulated that after using these primers, a higher proportion of the cHLs would have detectable rearrangements without microdissection. Design Forty-two patients with cHL were selected. The densities of Reed-Sternberg cells/10 high-power field and CD30+ cells/10 high-power field were classified as low, intermediate, or high. The quantities of background CD20+ B cells were classified as low or high. DNA from formalin-fixed, paraffin-embedded sections was used to perform polymerase chain reactions with the InVivoScribe IGH Gene Clonality Assay for ABI detection. Dominant peaks were considered to be monoclonal if they were >3× the height of the polyclonal background, and borderline monoclonal if between 2 and 3×. Result Overall, 10/42 (24%) of the cHL samples were monoclonal, and 7/42 (17%) were borderline monoclonal. Higher densities of CD30+ cells and lower background B cells were statistically correlated with clonality. Conclusions The BIOMED-2 primers demonstrate IGH gene clonality in 24% to 40% of cHLs without microdissection. In a subset of the cHL, the IGH gene rearrangement analysis might be useful for diagnosis, but can lead to confusion between cHLs and non-Hodgkin lymphomas if used as a discriminative criterion.

Consensus Characterization of 16 FMR1 Reference Materials: A Consortium Study

Fragile X syndrome, which is caused by expansion of a (CGG)(n) repeat in the FMR1 gene, occurs in approximately 1:3500 males and causes mental retardation/behavioral problems. Smaller (CGG)(n) repeat expansions in FMR1, premutations, are associated with premature ovarian failure and fragile X-associated tremor/ataxia syndrome. An FMR1-sizing assay is technically challenging because of high GC content of the (CGG)(n) repeat, the size limitations of conventional PCR, and a lack of reference materials available for test development/validation and routine quality control. The Centers for Disease Control and Prevention and the Association for Molecular Pathology, together with the genetic testing community, have addressed the need for characterized fragile X mutation reference materials by developing characterized DNA samples from 16 cell lines with repeat lengths representing important phenotypic classes and diagnostic cutoffs. The alleles in these materials were characterized by consensus analysis in nine clinical laboratories. The information generated from this study is available on the Centers for Disease Control and Prevention and Coriell Cell Repositories websites. DNA purified from these cell lines is available to the genetics community through the Coriell Cell Repositories. The public availability of these reference materials should help support accurate clinical fragile X syndrome testing.

Elevated Prevalence of 35-44 FMR1 Trinucleotide Repeats in Women With Diminished Ovarian Reserve

Introduction: Fragile X premutations are associated with primary ovarian insufficiency when the patient presents with amenorrhea, but the fragile X mental retardation 1 (FMR1) CGG repeat count among cycling women with low ovarian reserve (diminished ovarian reserve [DOR]) is not yet established. Patients and Methods: Sixty-two infertile DOR patients were recruited from 4 US private and academic fertility centers. Results: The prevalence of 35-44 FMR1 CGG repeats was 14.5%. Compared with the general female population estimate from the literature, infertile women with DOR were more likely to have 35-44 FMR1 CGG repeats (14.5% and 3.9%, respectively, P = .0003). Similar findings were noted by 5-repeat bandwidth: 35-39 CGG repeats (9.7% DOR vs 3.2% comparison, P = .012) or 40-44 CGG repeats (4.8% DOR vs 0.7% comparison, P = .024). Conclusions: These data suggest that CGG repeats of 35-44 may be markedly overrepresented in women with DOR, whereas the current FMR1 reference range indicates that there is no clinical phenotype with <45 CGG repeats.

Evaluation of high resolution gel β2-transferrin for detection of cerebrospinal fluid leak

Abstract Background: Cerebrospinal fluid (CSF) leaks are potentially life-threatening conditions that can be diagnosed by detection of β2-transferrin using protein electrophoresis. Another less commonly available test is β-trace protein quantitation using immunoassay. The objectives of this study were to evaluate a new immunofixation-based β2-transferrin test for detection of CSF leaks and to compare it to an existing agarose gel electrophoresis test and β-trace protein immunoassay. Methods: For method comparison, 63 consecutive samples from physician-ordered β2-transferrin tests were analyzed using two different electrophoresis methods, agarose gel fractionation followed by acid-violet staining, and high resolution agarose gel electrophoresis followed by β2-transferrin immunofixation. A subset of samples (16/63) were analyzed for β-trace protein. Results were compared against patient chart data for the presence of a CSF leak. Additional studies were performed to assess the stability, detection limit, and analytical specificity of the β2-transferrin immunofixation test. Results: The β2-transferrin immunofixation test had a sensitivity of 100% (40/40) and specificity of 71% (12/17) for detection of CSF leaks. By comparison, the agarose gel test had a sensitivity of 87% (35/40) and specificity of 94% (16/17). β-trace protein had a sensitivity of 100% (10/10) and specificity of 86% (5/6). Serum and saliva could be differentiated from CSF by the β2-transferrin immunofixation test based on their migration patterns. However, whole blood samples appeared positive for β2-transferrin at a threshold of ∼4 g/L hemoglobin. At a cut-off of 3 mg/L, β-trace protein was increased in 10/10 cases with documented CSF leak and in 1/6 patients without CSF leak. Conclusions: Both the new immunofixation test for β2-transferrin and the β-trace protein were effective at detecting CSF leaks. Users of the β2-transferrin immunofixation test should be cautioned against interpreting samples with blood contamination.

HFE Genotyping Using Multiplex Allele-Specific Polymerase Chain Reaction and Capillary Electrophoresis

CONTEXTnHereditary hemochromatosis is recognized as one of the most common autosomal recessive disorders, with a prevalence of 1 in 200 to 400 in the white population. Early detection and treatment are completely effective in preventing pathology. It is anticipated that testing for hereditary hemochromatosis will increase, as will the need for a technology that can handle the demand.nnnOBJECTIVEnTo describe a high-throughput, single-tube, allele-specific multiplex polymerase chain reaction assay for identifying the 2 mutations in the HFE gene associated with hereditary hemochromatosis.nnnDESIGNnFluorescence-labeled polymerase chain reaction products from a multiplex polymerase chain reaction are analyzed by automated capillary electrophoresis.nnnDATA ANALYSISnThe assay was validated by analysis of 25 blinded samples, and results were concordant with an established laboratory assay.nnnCONCLUSIONnThe assay described offers a significant improvement over manual laboratory assays in throughput, reduced technologist time, and cost.