ABCMdb

PMID: 18470946

Berwouts S, Gordon JT, Rundell CA, Barton DE, Dequeker E
Evaluation and use of a synthetic quality control material, included in the European external quality assessment scheme for cystic fibrosis.
Hum Mutat. 2008 Aug;29(8):1063-70., [PubMed]

Sentences

No. Mutations Sentence Comment

55 ABCC7 p.Phe508Cys ABCC7 p.Phe508Cys For example, true homozygous I507del (c.1519_1521delATC, p.Ile507del) must be distinguished from heterozygous I507del (c.1519_1521delATC, p.Ile507del) with F508C (c.1522T4G, p.Phe508Cys) in trans. Login to comment 59 ABCC7 p.Arg117His ABCC7 p.Arg117His These samples, derived from CF patients, CF mutation carriers, and noncarriers, represented the mutations: 1717-1G4A (c.1585-1G4A), 3272-26A4G (c.3140-26A4G), F508del (c.1521_1523delCTT, p.Phe508del), and R117H (c.350G4A, p.Arg117His). Login to comment 72 ABCC7 p.Arg117His ABCC7 p.Arg553* ABCC7 p.Arg347His The MMQCI-CF-P1 control distributed to EQA participants contained six homozygous mutations and one polymorphism: R553X (c.1657C4T, p.Arg553X), I507del (c.1519_1521delATC, p.Ile507del), R117 H (c.350G4A, p.Arg117His), 394delTT (c.262_263delTT, p.Leu88fs), 2183AA4G (c.2051_2052delAAinsG, p.Lys684fs), R347 H (c.1040G4A, p.Arg347His), and 5 T (c.1210-12T[5]). Login to comment 78 ABCC7 p.Arg553* Since MMQCI-CF-P1 is not fully compatible with the ElucigeneTM (Tepnel Molecular Diagnostics, Abingdon, United Kingdom) CF kits due to insufficient intronic DNA sequence being included in the MMQCI`s synthetic constructs of exon 11, a missed R553X (c.1657C4T, p.Arg553X) mutation was not counted as an error by users of this method. Login to comment 84 ABCC7 p.Arg117His Further, although reflex 5 T (c.1210-12T[5]) testing is required clinically when R117 H (c.350G4A, p.Arg117His) is detected in carriers [Grody et al., 2001b], not all laboratories performed or reported a reflex test for the polymorphic tract in intron 8 (polyT), again probably due to the synthetic nature of the sample. Login to comment 135 ABCC7 p.Arg347Pro ABCC7 p.Arg347Pro ABCC7 p.Arg347His Mutations 2183AA4G (c.2051_2052delAAinsG, p.Lys684fs) and R347 H (c.1040G4A, p.Arg347His) cross-react with 2184delA (c.2052delA, p.Lys684fs) and R347P (c.1040G4C, p.Arg347Pro), respectively, in many CFTR detection methods. Login to comment 136 ABCC7 p.Arg347Pro ABCC7 p.Arg347Pro ABCC7 p.Arg347His This explains why seven laboratories made genotype errors (missing 2183AA4G (c.2051_2052delAAinsG, p.Lys684fs) and R347 H (c.1040G4A, p.Arg347His)) and/or reported mutations not present in the QCS (2184delA (c.2052delA, p.Lys684fs) and R347P (c.1040G4C, p.Arg347Pro)); they encountered difficulties in interpreting typical cross-reaction patterns that are explained in the manual of the assays. Login to comment 142 ABCC7 p.Arg553* ABCC7 p.Arg553* ABCC7 p.Arg553* A total of three laboratories, using INNO-LiPA assay (Innogenetics NV, Gent, Belgium), reported a very weak signal for wild-type R553X (c.1657C4T, p.Arg553X) apart from a signal for mutant R553X (c.1657C4T, p.Arg553X), which indicates a heterozygous R553X (c.1657C4T, p.Arg553X) mutation. Login to comment 143 ABCC7 p.Arg553* ABCC7 p.Gly542* ABCC7 p.Gln552* Two of the laboratories that saw this weak signal for wild-type R553X (c.1657C4T, p.Arg553X) also reported weak mutant signals for Q552X (c.1654C4T, p.Gln552X) or G542X (c.1624G4T, p.Gly542X), possibly indicating DNA overload. Login to comment 144 ABCC7 p.Arg553* ABCC7 p.Gln552* The Q552X (c.1654C4T, p.Gln552X) wild-type and mutant signal should disappear when R553X (c.1657C4T, p.Arg553X) homozygous is present, using INNO-LiPA. Login to comment 151 ABCC7 p.Arg117His ABCC7 p.Arg117His ABCC7 p.Arg117His Similarly, one laboratory reported a weak signal for wild-type R117 H (c.350G4A, p.Arg117His) and normal signal for mutant R117 H (c.350G4A, p.Arg117His) instead of mutant R117 H (c.350G4A, p.Arg117His) homozygote. Login to comment 152 ABCC7 p.Ala455Glu Finally, some laboratories using the INNO-LiPA assay obtained a very faint hybridization signal for the A445E (c.1364C4A, p.Ala455Glu) mutant probe, but a normal signal for the wild-type probe. Login to comment 153 ABCC7 p.Arg117His ABCC7 p.Arg117His ABCC7 p.Ala455Glu ABCC7 p.Ala455Glu ABCC7 p.Arg553* ABCC7 p.Gly542* These very faint signals for wild-type R553X (c.1657C4T, p.Arg553X), wild-type R117H (c.350G4A, p.Arg117His), mutant G542X (c.1624G4T, p.Gly542X), and mutant A455E (c.1364C4A, p.Ala455Glu) signal were often not visible to the assessors on the copies of the raw data. Login to comment 157 ABCC7 p.Ala455Glu ABCC7 p.Ala455Glu ABCC7 p.Ala455Glu ABCC7 p.Ala455Glu ABCC7 p.Trp1282* 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.Arg553* ABCC7 p.Arg347Pro ABCC7 p.Arg347Pro ABCC7 p.Arg347Pro ABCC7 p.Arg347His ABCC7 p.Gly542* ABCC7 p.Gly542* ABCC7 p.Gln552* ABCC7 p.Gln552* ErrorTypes for the QCS in More Detail, for the LaboratoriesThat Used Only One Detection AssayÃ Genotype error Genotype Detection assay Number of labs Expected Reported Comment OLA-CFASR v2.0 1 R117 H hom ^ Correct on raw data INNO-LiPA CFTR36 1 R117 H hom R117 H het No signal for wt R117 H visible on copy of the raw data, could be very weak on original raw data INNO-LiPA CFTR36 1 R553X hom R553X het No signal for wt R553X visible on copy of the raw data, could be very weak on original raw dataI507del hom I507del/F508del Sequencing 2 R347 H hom ^ No complete raw data received Sequencing 1 I507del hom ^ No raw data received Additional mutation(s) reported Detection assay Number of labs Additional mutation(s) Comment OLA-CFASR v3.0 US 1 2184delAa hom Software called it INNO-LiPA CFTR36 3 A455E het (3labs), F508del (1lab) No signal for mut A455E visible on copy of the raw data, could be very weak on original raw data ARMS-ElucigeneTM CF29 3 2184delAa (3labs), R347P (3labs), 1717-1G4A (3labs), 3849110kbC4T (2labs) Cross reaction with 2183AA4Gb and R347 H and no full compatibility of MMQCI-CF-P1and ARMS method: no control bands visible ARMS-ElucigeneTM CF29 1CF-HT 1 2184delAa , R347P Cross reaction with 2183AA4Gb and R347H Sequencing 1 W1282X het, N1303 K het No raw data received ASPE-CFTR 4014 Tag-It 1 71111G4T het No raw data received Genotype error 1 additional mutation(s) reported Genotype Detection assay Number of labs Expected Reported Comment Additional mutation(s) Comment OLA-CFASR v3.0 EU 1 R117 H hom ^ No raw data received; probably 2183AA4Gb missed, but 2184delAa reported due to cross reaction 2184delAa hom No raw data received, probably due to cross-reaction with 2183AA4Gb 394delTTc hom 394delTTc het 2183AA4Gb hom ^ INNO-LiPA CFTR36 1 R553X hom I507del hom R553X het I507del/ F508del No signal for wt R553X visible on copy of the raw data, could be very weak on original raw data G542X het A455E het No signal for mut G542X and mut A455E visible on copy of the raw data, could be very weak on original raw data INNO-LiPA CFTR36 1 Italian regional 1 R553X hom R553X het No signal for wt R553X visible on copy of the raw data, could be very weak on original raw data Q552X het Misinterpretation: wt and mut signal for Q552X not visible, but this is a normal reaction pattern when R553X is hom present; the lab reported R553X het ARMS-ElucigeneTM CF29 1 I507del hom ^ No full compatibility of MMQCI- CF-P1 and ARMS method: no control bands R347P Cross-reaction with R347H2183AA4Gb hom ^ ÃIf the zygosity is not mentioned in the table, the laboratory did not report it. Login to comment 169 ABCC7 p.Arg553* ABCC7 p.Arg553* Further, this version of the QCS did not contain sufficient sequence for the ElucigeneTM CF29 to detect R553X (c.1657C4T, p.Arg553X), but the revised ElucigeneTM CF29 v2 can now detect R553X (c.1657C4T, p.Arg553X) in the QCS. Login to comment 188 ABCC7 p.Arg553* However, the lack of control bands for ARMS and the inability of ElucigeneTM CF29 to detect R553X (c.1657C4T, p.Arg553X) in the QCS are due to an incompatibility of the control with the detection methods. Login to comment 191 ABCC7 p.Arg117His ABCC7 p.Ala455Glu ABCC7 p.Ala455Glu ABCC7 p.Arg553* ABCC7 p.Gly542* For example, reporting the weak bands for wild-type R553X (c.1657C4T, p.Arg553X) and R117 H (c.350G4A, p.Arg117His), mutant G542X (c.1624G4T, p.Gly542X) and A455E (c.1364C4A, p.Ala455Glu) seen by some of the laboratories using the INNO-LiPA assay could be explained in this respect. Login to comment