ABCMdb

PMID: 25077647

Lyon E, Schrijver I, Weck KE, Ferreira-Gonzalez A, Richards CS, Palomaki GE
Molecular genetic testing for cystic fibrosis: laboratory performance on the College of American Pathologists external proficiency surveys.
Genet Med. 2015 Mar;17(3):219-25. doi: 10.1038/gim.2014.93. Epub 2014 Jul 31., [PubMed]

Sentences

No. Mutations Sentence Comment

39 ABCC7 p.Val520Phe One sample with a "non-ACMG" mutation, V520F, was sent as a challenge in three surveys: MGL5-2009A (which also included a sample with the non-ACMG mutation 3905insT), MGL2-2010B, and MGL5-2010B. Login to comment 40 ABCC7 p.Arg347His Two other surveys included samples with non-ACMG mutations: MGL2-2011B contained a sample with E60X (in combination with F508del), and MGL5- 2011B included a sample with R347H. Login to comment 44 ABCC7 p.Arg117His Also excluded were challenges for the IVS8 polyT polymorphism for samples that did not contain the R117H mutation. Login to comment 45 ABCC7 p.Arg117His ABCC7 p.Arg117His The ACOG/ACMG recommendations suggest testing for IVS8 5T only when the R117H mutation is discovered because the polyT modifies the clinical severity of this mutation.5,6,9 Three sample challenges included the R117H mutation and the associated IVS8 polyT polymorphism. Login to comment 87 ABCC7 p.Gly551Asp ABCC7 p.Arg117His ABCC7 p.Trp1282* ABCC7 p.Arg553* ABCC7 p.Arg347Pro ABCC7 p.Asn1303Lys ABCC7 p.Gly542* ABCC7 p.Arg560Thr These included 621+1, F508del, A455A, 1717-1, R117H, I507del, 3659delC, G85E, G542X, G551D, R553X, R347P, W1282X, N1303K, and R560T. Login to comment 106 ABCC7 p.Ala455Glu The lowest analytical sensitivity (91.1%) for a single challenge was recorded for a 2003 compound heterozygous sample (621+1G>T/A455E). Login to comment 108 ABCC7 p.Gly542* Two other genotypes were also associated with relatively low analytical sensitivities (Figure 2): a heterozygous I507del challenge (2004) and a homozygous G542X sample (2009). Login to comment 110 ABCC7 p.Gly542* ABCC7 p.Gly542* ABCC7 p.Gly542* The most common incorrect responses for the homozygous G542X challenge included reporting heterozygosity for G542X and incomplete entries (not reporting the second allele, rather than entering G542X in both allele fields). Login to comment 111 ABCC7 p.Arg553* ABCC7 p.Arg347Pro ABCC7 p.Arg347His Given the previously discussed issues with the potential problems with missing data and the known problems with some methods for distinguishing the Table 1ߒ Results from external proficiency testing for CFTR mutations: common types of genotyping errors Sample switch ߓ Two genotypes and associated clinical interpretations are correct, but results are reversed from the original challenge ߓ ߓ Samples actually reversed before testing ߓ ߓ Testing correct but genotypes reversed during reporting False-positive genotypes ߓ Genotype reported as homozygous instead of heterozygous ߓ ߓ Data entry error ߓ ߓ Methodology cannot distinguish zygosity and reported incorrectly ߓ Wrong mutation (examples) ߓ ߓ R347H reported when R347P was challenged ߓ ߓ R553X homozygosity reported instead of compound heterozygosity ߓ ߓ I507del reported for a F508del challenge ߓ ߓ I507del/F508del for I507del False-negative genotype ߓ Reported a homozygous genotype as heterozygous Table 2ߒ Results from external proficiency testing for CFTR mutations: analytic sensitivity and specificity for US and international clinical laboratories Time period (survey) Total alleles True positive False negative Analytical sensitivity (95% CI) True negative False positive Analytical specificity (95% CI) 2003-2013 (All) 10,952 3,941 49 98.8 (98.4-99.1) 6,932 30 99.6 (99.4-99.7) 2008-2013 (All) 5,521 2,525 19 99.3 (98.8-99.5) 2,965 12 99.6 (99.3-99.8) 2008-2013 (MGL2) 2,444 737 8 98.9 (97.8-99.5) 1,696 3 99.8 (99.4-99.9) 2008-2013 (MGL5) 3,077 1,788 11 99.4 (98.9-99.7) 1,269 9 99.3 (98.6-99.7) 2008-2013 (international) 770 288 12 96.0 (92.9-97.8) 470 0 100 (99.9-100) CI, confidence interval. Login to comment 118 ABCC7 p.Ala455Glu ABCC7 p.Gly542* ABCC7 p.Gly542* 90 95 A (621 + 1G>T/A455E) (G542X/G542X) (I507 wild type or negative?) Login to comment 120 ABCC7 p.Arg117His The 5T variant in intron 8 was evaluated only for the three sample challenges that contained the R117H mutation. Login to comment 121 ABCC7 p.Arg117His In three different surveys, a compound heterozygous sample (R117H/ F508del) was distributed. Login to comment 139 ABCC7 p.Gly542* The homozygous G542X challenge in the 2009 survey was closely examined to determine whether the interpretation matched the given result. Login to comment 140 ABCC7 p.Gly542* In all cases for which G542X was not entered in both allele fields, the interpretation was consistent with a result of one mutation or no mutations detected. Login to comment 149 ABCC7 p.Arg117His ABCC7 p.Arg117His The IVS8 5T variant modifies the severity of the R117H mutation when on the same chromosome (in cis), but by itself it is considered a mild mutation not associated with classic CF.9 The R117H mutation and reflex testing for the IVS8 polyT were challenged in three surveys. Login to comment 153 ABCC7 p.Arg117His ABCC7 p.Arg117His Given the ACMG/ACOG recommendations to reflex R117H samples to test for the 5T variant, laboratories should perform this test for challenges in which the R117H mutation is detected. Login to comment 154 ABCC7 p.Arg117His One possible explanation for not reporting intron 8 polyT status is that laboratories may send samples with the R117H mutation to a referral laboratory to detect the 5T variant; reporting of outside laboratory results is a practice that is prohibited in PT testing. Login to comment 182 ABCC7 p.Gly542* For example, the G542X homozygous genotype and the I507del heterozygous genotype were difficult challenges (Figure 2), but both of these genotypes are rare, especially in the context of population-based screening. Login to comment