ABCMdb

PMID: 12089190

Wang X, Myers A, Saiki RK, Cutting GR
Development and evaluation of a PCR-based, line probe assay for the detection of 58 alleles in the cystic fibrosis transmembrane conductance regulator (CFTR) gene.
Clin Chem. 2002 Jul;48(7):1121-3., [PubMed]

Sentences

No. Mutations Sentence Comment

68 ABCC7 p.Gly551Asp ABCC7 p.Arg117His ABCC7 p.Ala455Glu ABCC7 p.Trp1282* ABCC7 p.Arg553* ABCC7 p.Arg334Trp ABCC7 p.Arg347Pro ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Arg1162* ABCC7 p.Gly85Glu ABCC7 p.Arg560Thr ABCC7 p.Ser1255* ABCC7 p.Phe508Cys ABCC7 p.Ile506Val ABCC7 p.Gly480Cys ABCC7 p.Ile507Val ABCC7 p.Ala559Thr Amplicon Size, bp Mutations (polymorphisms) Exon 13 598 2307 insA Intron 8, exon 09 548 A455E, 5T (7/9 T polymorphism) Exon 10 482 G480C, ⌬I507, ⌬F508 (F508C, I507V, I506V polymorphisms) Intron 10, exon 11 433 1717-1G3A, G542X, G551D, R553X, A559T, R560T Exon 19 420 R1162X, 3659delC Exon 21 397 N1303K Exon 20 359 S1255X, W1282X Exon 07 328 1078delT, R334W, R347P Exon 04, intron 4 288 R117H, 621ϩ1G3T Intron 14b 248 2789ϩ5G3A Intron 19 237 3849ϩ10kbC3T Exon 03 210 G85E, 405ϩ3A3C Intron 5 166 711ϩ1G3T Intron 16 139 3120ϩ1G3A Clinical Chemistry 48, No. Login to comment 75 ABCC7 p.Arg117His Sample 2 demonstrated simultaneous detection of three alleles; 5T, R117H, and 3659delC, consistent with the previously determined genotype. Login to comment 76 ABCC7 p.Phe508Cys Sample 6 was correctly genotyped as a compound heterozygote for the common CF mutation ⌬F508 and the polymorphism F508C. Login to comment 77 ABCC7 p.Arg1162* Sample 28 demonstrated the detection of a homozygote for the R1162X mutation. Login to comment 80 ABCC7 p.Ala455Glu ABCC7 p.Gly480Cys The signal intensities of the wild-type alleles for A455E, G480C, I507/F508, and 2307insA probes were decreased when 12.5 ng of DNA was used, but could still be distinguished from background even at 6.25 ng of DNA. Login to comment 82 ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Ser549Asn During the evaluation phase, a sample that was previously genotyped as a compound heterozygote, S549N/ R553X, hybridized as expected with the R553X wild-type and mutant probes. Login to comment 83 ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Ser549Asn However, the presence of the R553X and S549N mutations precluded hybridization to the G551D wild-type probe (data not shown). Login to comment 84 ABCC7 p.Gly551Asp ABCC7 p.Arg553* Thus, although the assay correctly identified the R553X mutation in a heterozygous state, the lack of hybridization with the G551D wild-type probe (absence of signal in the wild-type allele) indicated the need for additional analysis to determine the genotype of the sample. Login to comment 88 ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Arg117His ABCC7 p.Arg117His ABCC7 p.Ala455Glu ABCC7 p.Trp1282* ABCC7 p.Arg553* ABCC7 p.Arg334Trp ABCC7 p.Arg347Pro ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Gly542* ABCC7 p.Gly542* ABCC7 p.Arg1162* ABCC7 p.Arg1162* ABCC7 p.Gly85Glu ABCC7 p.Arg560Thr ABCC7 p.Ser1255* ABCC7 p.Phe508Cys ABCC7 p.Ile506Val ABCC7 p.Gly480Cys ABCC7 p.Ile507Val ABCC7 p.Ala559Thr The genotypes of each sample are as follows: lane 1, ϩ/ϩ (ϩ is the wild type); lane 2, 5T, R117H/3659delC; lane 3, G542X/ϩ; lane 4, I506V/ϩ; lane 5, I507V/ϩ; lane 6, F508C/⌬F508; lane 7, G85E/⌬F508; lane 8, 405ϩ3A3C/3120ϩ1G3C; lane 9, R117H/ϩ; lane 10, 621ϩ1G3T/⌬F508; lane 11, 711ϩ1G3T/⌬F508; lane 12, 1078delT/ϩ; lane 13, R334W/⌬F508; lane 14, R347P/⌬F508; lane 15, A455E/ϩ; lane 16, G480C/⌬F508; lane 17, ⌬I507/ϩ; lane 18, ⌬F508/ϩ; lane 19, 1717-1G3A/ϩ; lane 20, G542X/ϩ; lane 21, G551D/⌬F508; lane 22, R553X/ϩ; lane 23, R560T/⌬F508; lane 24, G551D/A559T; lane 25, 2307insA/ϩ; lane 26, 2789ϩ5G3A/⌬F508; lane 27, 3120ϩ1G3A/⌬F508; lane 28, R1162X/R1162X; lane 29, 3659delC/⌬F508; lane 30, 3849ϩ10kbC3T/⌬F508; lane 31, S1255X/⌬F508; lane 32, W1282X/G542X; lane 33, N1303K/ϩ. Login to comment 89 ABCC7 p.Ile506Val 1122 Technical Briefs I506V/⌬F508 genotype showed a similar result. Login to comment 91 ABCC7 p.Ile506Val However, the other allele did not hybridize with the ⌬F508 probe because it did not contain that mutant sequence, nor did it hybridize with the wild-type probe because the A3G transition (data not shown), which gives rise to the I506V polymorphism, prevents hybridization to that sequence. Login to comment 98 ABCC7 p.Phe508Cys ABCC7 p.Ile506Val ABCC7 p.Ile507Val On the other hand, the ⌬F508 mutation is the most common CF allele, and three polymorphisms (I506V, I507V, and F508C) can interfere with hybridization of the wild-type oligonucleotide sequence. Login to comment 99 ABCC7 p.Phe508Cys ABCC7 p.Ile506Val ABCC7 p.Ile507Val Thus, the presence of oligonucleotides corresponding to the three polymorphisms in the Research Prototype Cystic Fibrosis Assay-31 test avoids misdiagnosis of ⌬F508/I506V, I507V, or F508C compound heterozygotes. Login to comment