Bernice A Allitto

Pan-ethnic carrier screening and prenatal diagnosis for spinal muscular atrophy: clinical laboratory analysis of >72 400 specimens

Spinal muscular atrophy (SMA) is a leading inherited cause of infant death with a reported incidence of ∼1 in 10 000 live births and is second to cystic fibrosis as a common, life-shortening autosomal recessive disorder. The American College of Medical Genetics has recommended population carrier screening for SMA, regardless of race or ethnicity, to facilitate informed reproductive options, although other organizations have cited the need for additional large-scale studies before widespread implementation. We report our data from carrier testing (n=72 453) and prenatal diagnosis (n=121) for this condition. Our analysis of large-scale population carrier screening data (n=68 471) demonstrates the technical feasibility of high throughput testing and provides mutation carrier and allele frequencies at a level of accuracy afforded by large data sets. In our United States pan-ethnic population, the calculated a priori carrier frequency of SMA is 1/54 with a detection rate of 91.2%, and the pan-ethnic disease incidence is calculated to be 1/11 000. Carrier frequency and detection rates provided for six major ethnic groups in the United States range from 1/47 and 94.8% in the Caucasian population to 1/72 and 70.5% in the African American population, respectively. This collective experience can be utilized to facilitate accurate pre- and post-test counseling in the settings of carrier screening and prenatal diagnosis for SMA.

Standards and Guidelines for CFTR Mutation Testing

One mission of the ACMG Laboratory Quality Assurance (QA) Committee is to develop standards and guidelines for clinical genetics laboratories, including cytogenetics, biochemical, and molecular genetics specialties. This document was developed under the auspices of the Molecular Subcommittee of the Laboratory QA Committee by the Cystic Fibrosis (CF) Working Group. It was placed on the “fast track” to address the preanalytical, analytical, and postanalytical quality assurance practices of laboratories currently providing testing for CF. Due to the anticipated impact of the ACMG recommendation statement endorsing carrier testing of reproductive couples, it was viewed that CF testing would increase in volume and that the number of laboratories offering CF testing would also likely increase. Therefore, this document was drafted with the premise of providing useful information gained by experienced laboratory directors who have provided such testing for many years. In many instances, “tips” are given. However, these guidelines are not to be interpreted as restrictive or the only approach but to provide a helpful guide. Certainly, appropriately trained and credentialed laboratory directors have flexibility to utilize various testing platforms and design testing strategies with considerable latitude. We felt that it was essential to include technique-specific guidelines of several current technologies commonly used in laboratories providing CF testing, since three of the four technologies discussed are available commercially and are widely utilized. We take the view that these technologies will change, and thus this document will change with future review.

Differences in SMN1 allele frequencies among ethnic groups within North America

Background: Spinal muscular atrophy (SMA) is the most common inherited lethal disease of children. Various genetic deletions involving the bi-allelic loss of SMN1 exon 7 are reported to account for 94% of affected individuals. Published literature places the carrier frequency for SMN1 mutations between 1 in 25 and 1 in 50 in the general population. Although SMA is considered to be a pan-ethnic disease, carrier frequencies for many ethnicities, including most ethnic groups in North America, are unknown. Objectives and methods: To provide an accurate assessment of SMN1 mutation carrier frequencies in African American, Ashkenazi Jewish, Asian, Caucasian, and Hispanic populations, more than 1000 specimens in each ethnic group were tested using a clinically validated, quantitative real-time polymerase chain reaction (PCR) assay that measures exon 7 copy number. Results: The observed one-copy genotype frequency was 1 in 37 (2.7%) in Caucasian, 1 in 46 (2.2%) in Ashkenazi Jew, 1 in 56 (1.8%) in Asian, 1 in 91 (1.1%) in African American, and 1 in 125 (0.8%) in Hispanic specimens. Additionally, an unusually high frequency of alleles with multiple copies of SMN1 was identified in the African American group (27% compared to 3.3–8.1%). This latter finding has clinical implications for providing accurate adjusted genetic risk assessments to the African American population. Conclusions: Differences in the frequency of SMA carriers were significant among several ethnic groups. This study provides an accurate assessment of allele frequencies and estimates of adjusted genetic risk that were previously unavailable to clinicians and patients considering testing.

Improved detection of cystic fibrosis mutations in the heterogeneous U.S. population using an expanded, pan-ethnic mutation panel

Purpose: To determine the comparative frequency of 93 CFTR mutations in U.S. individuals with a clinical diagnosis of cystic fibrosis (CF).Methods: A total of 5,840 CF chromosomes from Caucasians, Ashkenazi Jews, Hispanics, African Americans, Native Americans, Asians, and individuals of mixed race were analyzed using a pooled ASO hybridization strategy.Results: Sixty-four mutations provided a sensitivity of 70% to 95% in all ethnic groups except Asians, and at least 81% when the U.S. population was considered as a whole.Conclusions: For population-based carrier screening for CF in the heterogeneous U.S. population, which is characterized by increasing admixture, a pan-ethnic mutation panel of 50 to 70 CFTR mutations may provide a practical test that maximizes sensitivity.

The I148T CFTR allele occurs on multiple haplotypes: A complex allele is associated with cystic fibrosis

Purpose: To determine whether CFTR intragenic changes modulate the cystic fibrosis (CF) phenotype in individuals who are positive for the I148T allele.Methods: The CFTR genes from individuals who carried at least one copy of the I148T allele were analyzed for additional changes that may be acting as genetic modifiers.Results: Seven of eight individuals with a known or suspected diagnosis of CF who carried I148T in combination with a severe CF mutation also carried 3199del6. Eight apparently healthy adult individuals who were compound heterozygous for I148T and a severe CF mutation or homozygous for I148T did not carry the deletion (P = 0.0014). The I148T allele occurs on at least three haplotypes: an IVS-8 9T background, a 7T background, or a 9T + 3199del6 background. The 3199del6 allele was not identified in 386 non-CF chromosomes.Conclusions: It is concluded that I148T occurs on at least three haplotypes and the complex allele I148T + 9T + 3199del6 is associated with a classic CF phenotype.

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.

Cystic Fibrosis Carrier Testing in an Ethnically Diverse US Population

BACKGROUND The incidence of cystic fibrosis (CF) and the frequency of specific disease-causing mutations vary among populations. Affected individuals experience a range of serious clinical consequences, notably lung and pancreatic disease, which are only partially dependent on genotype. METHODS An allele-specific primer-extension reaction, liquid-phase hybridization to a bead array, and subsequent fluorescence detection were used in testing for carriers of 98 CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] mutations among 364 890 referred individuals with no family history of CF. RESULTS One in 38 individuals carried one of the 98 CFTR mutations included in this panel. Of the 87 different mutations detected, 18 were limited to a single ethnic group. African American, Hispanic, and Asian individuals accounted for 33% of the individuals tested. The mutation frequency distribution of Caucasians was significantly different from that of each of these ethnic groups (P < 1 × 10⁻¹⁰). CONCLUSIONS Carrier testing using a broad mutation panel detects differences in the distribution of mutations among ethnic groups in the US.

Cystic fibrosis and chromosome abnormalities associated with echogenic fetal bowel.

OBJECTIVE To determine the prevalence of cystic fibrosis mutations and chromosome abnormalities in the fetuses of a heterogeneous population of pregnant women referred for prenatal testing for echogenic fetal bowel. METHODS Fetal or parental samples obtained after a second-trimester sonographic finding of echogenic fetal bowel were submitted to a referral diagnostic laboratory during a 2-year period. Results of DNA testing and karyotyping on these samples were analyzed to determine the prevalence of cystic fibrosis transmembrane reductase gene mutations and chromosome abnormalities. RESULTS Of 244 cases tested, two fetuses were positive for two cystic fibrosis mutations. This rate (0.8% or two of 244) is 20 times higher than the general white population rate of one per 2500. In a third case, both parents were carriers but the fetus was not tested. Nine (8%) of 113 fetuses tested had one cystic fibrosis mutation. Of 106 fetuses for whom chromosome results were available, three (2.8%) fetuses had a chromosomal abnormality: two had trisomy 21 and one had Klinefelter syndrome. A fourth fetus carried a de novo, apparently balanced, 5;12 translocation. CONCLUSION These laboratory results are representative of a broad spectrum of clinical settings and indicate a generalized increased risk associated with this sonographic finding. Therefore, when a second-trimester sonographic diagnosis of fetal echogenic bowel is made, fetal testing for both cystic fibrosis and chromosome abnormalities is warranted.

Carrier testing for seven diseases common in the Ashkenazi Jewish population: implications for counseling and testing

Abstract Objective: To determine carrier detection rates among Ashkenazi Jews with no family history tested for the following autosomal recessive disorders: Tay-Sachs disease (TS), cystic fibrosis (CF), Gaucher’s disease (GD), Fanconi’s anemia Group C (FA-C), Bloom syndrome (BS), Canavan disease (CD), and Niemann-Pick disease type A (NP). Methods: Data from a 28-month period were collated. Samples were analyzed by PCR and dot blot hybridization with ASO probes. The number of mutations analyzed and individuals tested were disease specific: 3 and 5,754 (TS), 70 or 86 and 9,168 (CF), 5 and 5,277 (GD), 1 and 4,132 (FA-C), 1 and 2,425 (BS), 4 and 9,228 (CD), and 3 and 6,187 (NP). Results: Our experience is one of the largest to date with referrals from across the United States. Carrier rates were as expected for TS (1/27), CF (1/24), and GD (1/14); higher than previously reported for FA-C (1/66) and BS (1/80); and lower for CD (1/58) and NP (1/121). Four individuals tested for CF and ten for GD had two mutations, consistent with very mild disease. Conclusion: ACOG guidelines recommend that carrier testing for TS and CD be offered to individuals of Ashkenazi Jewish descent. Similar guidelines are expected for CF. Given the severity of NP, the increased morbidity of FA-C and BS, and the frequency of GD, consideration should be given to offering education and testing for these as well. The carrier frequencies determined here will provide accurate risk revisions for counseling.