ABCMdb

PMID: 15371903

Sugarman EA, Rohlfs EM, Silverman LM, Allitto BA
CFTR mutation distribution among U.S. Hispanic and African American individuals: evaluation in cystic fibrosis patient and carrier screening populations.
Genet Med. 2004 Sep-Oct;6(5):392-9., [PubMed]

Sentences

No. Mutations Sentence Comment

4 ABCC7 p.Ser549Asn ABCC7 p.Arg1066Cys ABCC7 p.Trp1089* 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. Login to comment 6 ABCC7 p.Ala559Thr Together, A559T and 711ϩ5GϾA were observed at a detection rate of 3.71% in CF patients and 6.38% in carriers. Login to comment 7 ABCC7 p.Arg117His ABCC7 p.Leu206Trp ABCC7 p.Asp1152His 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. Login to comment 33 ABCC7 p.Asp1270Asn ABCC7 p.Ile148Thr Specimens positive for D1270N (see later) or I148T in the absence of 3199del6 were reclassified as negative for the purpose of this analysis. Login to comment 34 ABCC7 p.Ile148Thr Specimens identified as I148T positive before the start of 3199del6 reflex testing are included in the analysis because their disease causing status is unknown. Login to comment 35 ABCC7 p.Gly551Asp ABCC7 p.Arg117His ABCC7 p.Pro574His ABCC7 p.Ala455Glu ABCC7 p.Trp1282* ABCC7 p.Arg553* ABCC7 p.Arg334Trp ABCC7 p.Arg347Pro ABCC7 p.Arg347His ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Arg1162* ABCC7 p.Asp1270Asn ABCC7 p.Ser1251Asn ABCC7 p.Arg352Gln ABCC7 p.Ile148Thr ABCC7 p.Leu206Trp ABCC7 p.Gln493* ABCC7 p.Val520Phe ABCC7 p.Ser549Arg ABCC7 p.Gly85Glu ABCC7 p.Ser549Asn ABCC7 p.Arg560Thr ABCC7 p.Thr338Ile ABCC7 p.Arg1158* ABCC7 p.Ser549Ile ABCC7 p.Met1101Lys ABCC7 p.Arg1066Cys ABCC7 p.Tyr1092* ABCC7 p.Ser1255* ABCC7 p.Gln552* ABCC7 p.Asp1152His ABCC7 p.Arg1283Met ABCC7 p.Lys710* ABCC7 p.Arg117Cys ABCC7 p.Gly91Arg ABCC7 p.Gln890* ABCC7 p.Trp1089* ABCC7 p.Gly480Cys ABCC7 p.Ser1196* ABCC7 p.Glu60* ABCC7 p.Gly178Arg ABCC7 p.Thr360Lys ABCC7 p.Tyr563Asp ABCC7 p.Gln1238* ABCC7 p.Cys524* ABCC7 p.Gln359Lys ABCC7 p.Ser364Pro ABCC7 p.Gly330* ABCC7 p.Ala559Thr 87 mutation panel The following mutations were included in the panel: ⌬F508, ⌬F311, ⌬I507, A455E, A559T, C524X, D1152H, D1270N, E60X, G178R, G330X, G480C, G542X, G551D, G85E, G91R, I148T, K710X, L206W, M1101K, N1303K, P574H, Q1238X, Q359K/T360K, Q493X, Q552X, Q890X, R1066C, R1158X, R1162X, R117C, R117H, R1283M, R334W, R347H, R347P, R352Q, R553X, R560T, S1196X, S1251N, S1255X, S364P, S549I, S549N, S549R, T338I, V520F, W1089X, W1282X, Y1092X, Y563D, 1078delT, 1161delC, 1609delCA, 1677delTA, 1717-1GϾA, 1812-1GϾA, 1898ϩ1GϾA, 1898ϩ5GϾT, 1949del84, 2043delG, 2143delT, 2183delAAϾG, 2184delA, 2307insA, 2789ϩ5GϾA, 2869insG, 3120ϩ1GϾA, 3120GϾA, 3659delC, 3662delA, 3791delC, 3821delT, 3849ϩ10kbCϾT, 3849ϩ4AϾG, 3905insT, 394delTT, 405ϩ1GϾA, 405ϩ3AϾC, 444delA, 574delA, 621ϩ1GϾT, 711ϩ1GϾT, 711ϩ5GϾA, 712-1GϾT, 3876delA CFTR mutation analysis Genomic DNA was extracted from peripheral blood lymphocytes, buccal cell swabs, or bloodspots by Qiagen QIAmp 96 DNA Blood Kit. Specimens were tested for 87 mutations by a pooled allele-specific oligonucleotide (ASO) hybridization method as previously described.16,17 Two multiplex chain reactions (PCR) were used to amplify 19 regions of the CFTR gene. Login to comment 43 ABCC7 p.Asp1270Asn ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp ABCC7 p.Arg74Trp D1270N/R74W analysis A subset of 192 D1270N-positive samples derived from this sample set as well as samples received for a variety of indications and ethnicities were analyzed for the R74W sequence change using LightCycler (Roche) amplification and melting curve analysis. Login to comment 56 ABCC7 p.Arg334Trp ABCC7 p.Gly542* ABCC7 p.Arg1066Cys ABCC7 p.Trp1089* Among 318 CF patient chromosomes, 30 mutations were identified with ⌬F508, G542X, R334W, 3120ϩ1GϾA, W1089X, 3876delA, and R1066C representing 52.52% of the total. Login to comment 63 ABCC7 p.Arg117His ABCC7 p.Arg553* ABCC7 p.Arg334Trp ABCC7 p.Gly542* ABCC7 p.Ile148Thr ABCC7 p.Leu206Trp ABCC7 p.Arg1066Cys ABCC7 p.Asp1152His The most prevalent mutations were as follows: ⌬F508, D1152H, R117H, G542X, L206W, I148T (3199del6 status unknown), ⌬I507, R1066C, R553X, 3849ϩ10kbCϾT, and R334W representing 83.72% of the total identified. Login to comment 69 ABCC7 p.Arg334Trp ABCC7 p.Gly542* ABCC7 p.Arg1066Cys ABCC7 p.Trp1089* ABCC7 p.Trp1089* With the exception of W1089X, the next 6 most frequent mutations in the patient population (G542X, R334W, 3120ϩ1GϾA, 3876delA, W1089X, and R1066C) were all seen in the carrier population at frequencies of 1.4% to 4.2%. Login to comment 70 ABCC7 p.Trp1089* The W1089X mutation, which accounted for 2.2% detection among CF patients, was not seen in the carrier population. Login to comment 71 ABCC7 p.Arg117His ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Leu206Trp ABCC7 p.Asp1152His In the carrier screening group, 4 mutations, D1152H, R117H, ⌬I507, and L206W, had frequencies of 3.8% 1 CFTR mutation distribution among Hispanic CF patients and carrier screening referrals CFTR Mutation Identified CF Patients Carrier Screening Referrals # of CF Chromosomes % Detection # of Carrier Screen Referrals % of Positive Carriers ⌬F508a 118 37.11c 136 47.39 G542Xa 11 3.46 12 4.18 R334Wa 11 3.46 6 2.09 3120 ϩ 1G Ͼ Aa 7 2.20 5 1.74 3876delAb 7 2.20 4 1.39 W1089Xb 7 2.20 R1066Cb 6 1.89 9 3.14 3849 ϩ 10kbC Ͼ Ta 3 0.94 6 2.09 R1162Xa 2 0.63 5 1.74 G85Ea 2 0.63 3 1.05 S549Nb 2 0.63 2 0.70 711 ϩ 1G Ͼ Ta 2 0.63 1 0.35 2789 ϩ 5G Ͼ Aa 2 0.63 1 0.35 1949del84b 2 0.63 1 0.35 R117Ha 1 0.31 14 4.88 ⌬I507a 1 0.31 11 3.83 R553Xa 1 0.31 7 2.44 ⌬F311b 1 0.31 1 0.35 1078delTa 1 0.31 1 0.35 621 ϩ 1G Ͼ Ta 1 0.31 1 0.35 3659delCa 1 0.31 1 0.35 Q890Xb 1 0.31 1 0.35 G551Da 1 0.31 1812 - 1G Ͼ Ab 1 0.31 I148T ϩ 3199del6a 1 0.31 A559Tb 1 0.31 1717 - 1G Ͼ Aa 1 0.31 3905insTb 1 0.31 3821delTb 1 0.31 G178Rb 1 0.31 D1152Hb 18 6.27 L206Wb 11 3.83 I148T (3199del6 status unknown)a 10 3.48 N1303Ka 4 1.39 W1282Xa 4 1.39 R117Cb 4 1.39 R352Qb 2 0.70 712 - 1G Ͼ Tb 2 0.70 Y1092Xb 1 0.35 444delAb 1 0.35 S549Rb 1 0.35 1609delCAb 1 0.35 Negative for mutations analyzed 120 37.74 15046 Total 318 62.20d 15333 100.00 a Mutation included in the ACMG/ACOG Recommended Core Mutation Panel for general population CF carrier screening.4,5 b Mutation not included in the ACMG/ACOG Recommended Core Mutation Panel for general population CF carrier screening. Login to comment 76 ABCC7 p.Ala559Thr The most frequent mutations (⌬F508, 3120ϩ1GϾA, 2307insA, and A559T) have been previously reported to be frequent in the African American population19 and represent 46.77% of the total. Login to comment 84 ABCC7 p.Arg553* ABCC7 p.Ala559Thr After ⌬F508, the next most-frequent mutations were 3120ϩ1GϾA (8.8%), 2307insA (4.17%), A559T (2.78%), and R553X (1.39%). Login to comment 86 ABCC7 p.Gly551Asp ABCC7 p.Gly542* An additional 4 mutations (G551D, 1717-1GϾA, G542X, 711ϩ5GϾA) were detected twice (0.93% each), whereas 12 other mutations were identified on one chromosome each. Login to comment 87 ABCC7 p.Ser1255* ABCC7 p.Gly480Cys ABCC7 p.Gly330* Five of the twelve mutations identified once are considered to be "African American" mutations (3791delC, G330X, G480C, 444delA, and S1255X).19 African American CF carrier screening population Among the 8,973 African American individuals referred for carrier screening, 23 different mutations were identified among 94 (1/95) carriers (Table 2). Login to comment 88 ABCC7 p.Arg117His ABCC7 p.Ala559Thr The most frequent mutations were ⌬F508 (52.1%), 3120ϩ1GϾA (9.6%), A559T (6.38%), and R117H (5.32%). Login to comment 91 ABCC7 p.Arg117His ABCC7 p.Asp1152His These include mutations known to be associated with variable phenotypic expression such as R117H,21,22 D1152H,23-25 and 3849ϩ10kbCϾT.27,28 Assuming Ϸ74% detection for the mutations analyzed and an observed carrier frequency of 1/95, an adjustment to 100% detection would result in a carrier frequency of 1/76, which is not significantly different than the expected 1/613 based on the disease incidence (P ϭ 0.1779). Login to comment 92 ABCC7 p.Asp1270Asn ABCC7 p.Asp1270Asn Reclassification of specimens positive for the D1270N sequence change Mutation analysis for all samples included D1270N. Login to comment 93 ABCC7 p.Asp1270Asn Comparison of D1270N chromosomes between African American CF patients and carrier screening referrals revealed a Ͼ 100-fold increase among carriers (2 CF patient chromosomes: 228 CF carrier alleles). Login to comment 94 ABCC7 p.Asp1270Asn ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp ABCC7 p.Arg74Trp To investigate a potential modifying effect of R74W on the D1270N phenotype, we analyzed 192 D1270N-positive individuals for the presence of R74W.29 Patients were of varying ethnicities (46.4% African American, 29.2% Hispanic, 11.9% Caucasian, 12.5% Other/Mix/Not Provided) and indications (Table 4). Login to comment 95 ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp Two individuals with the indication of carrier testing were homozygous for both D1270N and R74W. Login to comment 97 ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp Six individuals carried the genotype of a severe CF mutation (i.e., ⌬F508), one copy of D1270N and one copy of R74W. Login to comment 99 ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp Among those samples (n ϭ 167) received for carrier testing, 169 D1270N alleles and 159 R74W alleles were detected. Login to comment 100 ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp While we were unable to determine phase, overall 94% of individuals with a D1270N allele also carried an R74W allele. Login to comment 101 ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp In this data set there is no apparent correlation between D1270N, R74W, and phenotype. Login to comment 102 ABCC7 p.Asp1270Asn The D1270N sequence change was therefore not included in analysis of data for the larger study and has subsequently been removed from our CF test. Login to comment 108 ABCC7 p.Gly542* ABCC7 p.Trp1089* In the current study, 42 different mutations were identified among the Hispanic individuals (patients and carriers) tested and the most common mutations included those previously reported to be common among Hispanics, 3876delA,32 W1089X,17 as well as mutations considered frequent in African Americans (3120ϩ1GϾA)19 and panethnic (e.g., G542X, ⌬I507) populations.33 Although regional variation in overall detection rates may occur, these data provide general guidance when developing a panethnic mutation panel and information useful for genetic counseling purposes. Login to comment 112 ABCC7 p.Arg117His ABCC7 p.Leu206Trp ABCC7 p.Asp1152His In both the Hispanic and African American populations, mutations associated with a variable clinical phenotype such as R117H, D1152H, and L206W were more common in the carrier screening population than the affected population. Login to comment 115 ABCC7 p.Trp1089* The lack of detection in the carrier screening population of mutations identified among patients (e.g., 2307delA, W1089X) is not unexpected given the inherent variability in estimates of low-frequency mutations. Login to comment 116 ABCC7 p.Asp1270Asn From direct comparison of patient and carrier screening populations tested for the same mutation panel, we also identified a Ͼ 100-fold increase in the number of D1270N chromosomes among African American carriers as compared with African American CF patients. Login to comment 117 ABCC7 p.Asp1270Asn D1270N has been identified in individuals with cystic fibrosis24,33,35,36 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 R117H15 and I148T38,39 sequence changes, each of which has a cis-acting modifier influencing phenotype (5T21 and 3199del6,40 respectively). Login to comment 118 ABCC7 p.Asp1270Asn ABCC7 p.Asp1270Asn ABCC7 p.Asp1270Asn ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp ABCC7 p.Arg74Trp ABCC7 p.Arg74Trp There have been similar reports that R74W may be a potential modifier for the clinical phenotype of D1270N.29 The ⌬F508/ D1270N-R74W genotype has been reported in a girl with CF symptoms,41 in 2 CF patients, 3 CBAVD patients,24 and a 27-year-old man with CBAVD, elevated sweat chlorides, recurrent respiratory infection, and rhinitis.35 Our study of 192 D1270N-positive specimens was not suggestive of a role for R74W as a modifying allele, and a definitive explanation for the variable D1270N frequencies remains unknown. Login to comment 119 ABCC7 p.Ser549Asn ABCC7 p.Arg1066Cys In the Hispanic population, our findings support the inclusion, minimally, of 3876delA, R1066C, S549N, and 1949del84 in a mutation panel. Login to comment 120 ABCC7 p.Trp1089* Although not yet identified among our carrier screening population, the W1089X mutation with a 2.2% frequency among CF patients would also be valuable. Login to comment 122 ABCC7 p.Ala559Thr Similar recommendations have been made by other groups to add mutations that would increase detection in the Hispanic popula- tin.13,18,32 In the African American population, the A559T mutation was the 4th most common mutation among CF patient chromosomes (2.78%) and the third most frequent among CF carriers (6.38%) and as such would warrant inclusion, with 711ϩ5GϾA (0.93%), in any screening program serving an African American population. Login to comment 125 ABCC7 p.Asp1270Asn Table 4 Indications for 192 D1270N-positive patient samples Indication No. of Specimens Carrier testing-no family history 153 Carrier testing-family history 9 Carrier testing-abnormal fetal ultrasound findings 5 Known affected-CF diagnosis 3 Infertility 5 Suspected diagnosis (CF or pancreatitis) 15 Indication not provided 2 With 14% of our carrier screening referrals being from Hispanic and African American individuals, and another 12% from individuals with ethnicities other than the ACMG/ACOG recommended Caucasian or Ashkenazi Jewish, it is evident that clinicians are offering or making CF carrier screening available to a diverse population, many of whom choose testing. Login to comment 128 ABCC7 p.Asp1270Asn ABCC7 p.Arg74Trp We appreciate the assistance of Michelle Blalock, of the University of Virginia, for R74W analysis of D1270N-positive specimens and Stephen Lake for support with statistical calculations. Login to comment