ABCMdb

PMID: 9781062

Dequeker E, Cassiman JJ
Evaluation of CFTR gene mutation testing methods in 136 diagnostic laboratories: report of a large European external quality assessment.
Eur J Hum Genet. 1998 Mar-Apr;6(2):165-75., [PubMed]

Sentences

No. Mutations Sentence Comment

2 ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Asn1303Lys These samples carried the following CFTR genotypes: dF508/N1303K; dI507/wild; dF508/G551D; dF508/621 + 1 GtoT; R553X/wild and 1717-1 GtoA/wild. Login to comment 30 ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Asn1303Lys This collection of samples contained the most frequently found CFTR mutations in Europe: dF508/N1303K, dI507/wild, dF508/G551D, dF508/621 + 1 GtoT, R553X/wild, and 1717-1 GtoA/wild. Login to comment 80 ABCC7 p.Asn1303Lys Sample CF96-1 (dF508/N1303K) This was correctly typed in 134 of 136 laboratories, ie 99%. Login to comment 82 ABCC7 p.Asn1303Lys Two laboratories did not detect the N1303K mutation, although their routine testing strategy included this mutation. Login to comment 83 ABCC7 p.Asn1303Lys The first indicated a wild type for allele 2 instead of N1303K. Login to comment 84 ABCC7 p.Asn1303Lys The raw data of the reverse dot blot (Inno Lipa CF2) showed that the hybridisation with either wild-type and mutant-type of N1303K failed. Login to comment 89 ABCC7 p.Asn1303Lys Although the correct dF508/N1303K could have been derived from their raw data, the laboratory concluded differently. Login to comment 98 ABCC7 p.Asn1303Lys Another laboratory found, based on a home-made line probe assay, the genotype dI507/N1303K for sample CF96-2. Login to comment 104 ABCC7 p.Gly551Asp Sample CF96-3 (dF508/G551D) This was correctly typed in 131 of 136 laboratories, ie 96%. Login to comment 105 ABCC7 p.Gly551Asp ABCC7 p.Arg553* One of these laboratories could not distinguish the G551D from the R553X mutation. Login to comment 106 ABCC7 p.Arg553* They tested for the presence of R553X by digestion of a multiplex PCR product (exons 9, 10 and 11) with Hinc II. Login to comment 107 ABCC7 p.Gly551Asp ABCC7 p.Arg553* On the data sheet, they indicated that R553X could only be distinguished from G551D in homozygotes but not in heterozygotes. Login to comment 108 ABCC7 p.Gly551Asp ABCC7 p.Arg553* From the laboratories which typed incorrectly, two reported R553X instead of G551D, based on restriction endonuclease digestions of PCR products with BgtN I and Hinc II, or Msp I. Login to comment 109 ABCC7 p.Gly551Asp ABCC7 p.Arg553* Two other laboratories reported dF508/R553X and G551D as the genotype for CF96-3. Login to comment 120 ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Asn1303Lys The fourth laboratory used restriction enzyme analysis to check for 621 + 1 GtoT but did not provide raw data or Table 3 Schematic overview of the results of the quality control trial Total sample Allele A Allele B Both Not Correct Correct alleles correctly incorrectly Testing labsa assignment Testing labsa assignment assigned assignedb n n n n n n Sample Allele A Allele B (% of total) (% of testing labs) (% of total) (% of testing labsa) (% of testing labsa) (% of all labs) CF96-1 dF508 N1303K 136 (100) 136 (100) 122 (90) 120 (98) 120 (98) 134 (99) CF96-2 dI507 wild 119 (87) 101 (85) 136 (100) 131 (96) 96 (81) 113 (83) CF96-3 dF508 G551D 136 (100) 136 (100) 127 (93) 123 (97) 123 (97) 131 (96) CF96-4 dF508 621+1 136 (100) 135 (99) 62 (46) 54 (87) 53 (85) 129 (95) GtoT CF96-5 R553X wild 123 (90) 119 (93) 136 (100) 134 (99) 117 (95) 130 (96) CF96-6 1717-1 wild 106 (78) 101 (92) 136 (100) 133 (98) 98 (92) 129 (95) GtoA a'Testing labs`: the labs that effectively tested for the particular mutation. Login to comment 124 ABCC7 p.Arg553* ABCC7 p.Arg553* Two laboratories reported dF508/R553X and the third the genotype dF508/R553X-3849 + 4AtoG. Login to comment 128 ABCC7 p.Arg553* Samples CF96-5 (R553X/wild) This was correctly typed in 130 laboratories, ie 95.6% and incorrectly by the other six laboratories. Login to comment 129 ABCC7 p.Arg553* Two laboratories wrote G553X instead of R553X for allele 1 on the data sheet, and apologised for the typing error afterwards. Login to comment 130 ABCC7 p.Arg553* Two other laboratories reported the genotype wild/ wild, although testing for mutation R553X was performed. Login to comment 132 ABCC7 p.Arg553* Although a very weak signal for the R553X mutation could be observed on the raw data, they interpreted the sample as wild type. Login to comment 134 ABCC7 p.Arg553* One laboratory reported the genotype R553X/621 + 1 GtoT, which can only be explained if two samples were pooled. Login to comment 135 ABCC7 p.Arg553* The last laboratory reported genotype R553X/3849 + 10 kb LtoT, but they required larger amounts of DNA to confirm their results in a new test. Login to comment 144 ABCC7 p.Ser549Arg A fifth laboratory reported the presence of S549R instead of 1717-1 GtoA, based on the results of DGGE with GC-clamps, and confirmation by sequencing. Login to comment 155 ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Gly551Asp ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Asn1303Lys ABCC7 p.Asn1303Lys ABCC7 p.Asn1303Lys ABCC7 p.Asn1303Lys ABCC7 p.Ser549Arg Table 6 Detailed genotyping results of the DNA samples included in the quality control trial No. of Sample Allele 1 Allele 2 laboratories Method used CF96-1 dF508 N1303K 119 dF508/N1303K dF508 - 13 dF508 or dI507 N1303K 1 dF508 or dI507 - 1 dF508 wild 1 Inno-Lipa CF2 dF508 dF508 1 Heteroduplex Analysis/ARMS CF96-2 dI507 wild 93 dI507/wild - wild 17 dI507 or dF508 wild 3 dF508 wild 17 13 ´ Heteroduplex analysis 1 ´ allele specific PCR 1 ´ GeneScan analysis 1 ´ ASO reverse dot blot wild wild 1 administration error (Inno-Lipa CF2) dI507 N1303K 1 home-made line probe assay dI507 dF508 4 3 ´ Inno-Lipa CF2 1 ´ method not specified CF96-3 dF508 G551D 120 dF508/G551D dF508 - 7 dF508 G551D or R553X 1 dF508/dI507 G551D 2 broken tube 1 dF580 R553X 2 Restriction enzyme analysis dF508 R553X and G551D 2 1 ´ Restriction enzyme analysis 1 ´ RFLP dF508 2183AAtoG 1 ASO dot blot CF96-4 dF508 621+1 GtoT 53 dF508/621+1GtoT dF508 - 73 dF508 or dI507 621+1 GtoT 1 dF508 or dI507 - 1 wild 621+1 GtoT 1 dF508 wild 4 1 ´ SSCP 1 ´ RFLP 1 ´ home-made reverse dot blot 1 ´ Restriction enzyme analysis dF508 R553X 2 1 ´ SSCP 1 ´ Reverse dot blot dF508 R553X/3849+4 AtoG 1 1 ´ Restriction/enzyme analysis CF96-5 R553X wild 115 R553X/wild - wild 8 R553X or G551D wild 2 No amplification 5 G553X wild 2 administration error wild wild 2 1 ´ ARMS 1 ´ Restriction enzyme analysis R553X 621+1 GtoT 1 RFLP R553X 3849+10kb LtoT 1 Restriction enzyme analysis/ sequencing CF96-6 1717-1 GtoA wild 99 1717-1 GtoA/wild - wild 30 1717-1 GtoA 1717-1 GtoA 3 3 ´ Inno-Lipa CF2 W1717 wild 1 SSCP wild wild 1 Restriction enzyme analysis S549R wild 1 DGGE 1717+1 GtoA wild 1 ARMS administration error almost half of all laboratories. 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