scholarly journals Common sequence variants affect molecular function more than rare variants?

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Yannick Mahlich ◽  
Jonas Reeb ◽  
Maximilian Hecht ◽  
Maria Schelling ◽  
Tjaart Andries Petrus De Beer ◽  
...  
2010 ◽  
Vol 43 (9) ◽  
pp. 754-758 ◽  
Author(s):  
Hirschfeldova Katerina ◽  
Sedova Michaela ◽  
Vrablik Michal ◽  
Svobodova Helena ◽  
Zvarova Jana ◽  
...  

2009 ◽  
Vol 55 (4) ◽  
pp. 739-747 ◽  
Author(s):  
János Márki-Zay ◽  
Christoph L Klein ◽  
David Gancberg ◽  
Heinz G Schimmel ◽  
László Dux

Abstract Background: Depending on the method used, rare sequence variants adjacent to the single nucleotide polymorphism (SNP) of interest may cause unusual or erroneous genotyping results. Because such rare variants are known for many genes commonly tested in diagnostic laboratories, we organized a proficiency study to assess their influence on the accuracy of reported laboratory results. Methods: Four external quality control materials were processed and sent to 283 laboratories through 3 EQA organizers for analysis of the prothrombin 20210G>A mutation. Two of these quality control materials contained sequence variants introduced by site-directed mutagenesis. Results: One hundred eighty-nine laboratories participated in the study. When samples gave a usual result with the method applied, the error rate was 5.1%. Detailed analysis showed that more than 70% of the failures were reported from only 9 laboratories. Allele-specific amplification-based PCR had a much higher error rate than other methods (18.3% vs 2.9%). The variants 20209C>T and [20175T>G; 20179_20180delAC] resulted in unusual genotyping results in 67 and 85 laboratories, respectively. Eighty-three (54.6%) of these unusual results were not recognized, 32 (21.1%) were attributed to technical issues, and only 37 (24.3%) were recognized as another sequence variant. Conclusions: Our findings revealed that some of the participating laboratories were not able to recognize and correctly interpret unusual genotyping results caused by rare SNPs. Our study indicates that the majority of the failures could be avoided by improved training and careful selection and validation of the methods applied.


2008 ◽  
Vol 100 (18) ◽  
pp. 1326-1330 ◽  
Author(s):  
Pengyuan Liu ◽  
Haris G. Vikis ◽  
Daolong Wang ◽  
Yan Lu ◽  
Yian Wang ◽  
...  

2021 ◽  
Vol 8 ◽  
Author(s):  
Francesco Demetrio Lofaro ◽  
Dario Pasquale Mucciolo ◽  
Vittoria Murro ◽  
Laura Pavese ◽  
Daniela Quaglino ◽  
...  

Pseudoxanthoma elasticum (PXE) is a rare autosomal recessive disease clinically characterised by early cutaneous alterations, and by late clinically relevant ocular, and cardiovascular manifestations. ABCC6 genetic tests are used to confirm clinical PXE diagnosis, but this strategy may be rather challenging when only one ABCC6 pathogenic variant is found. A next-generation sequencing approach focusing on 362 genes related to the calcification process and/or to inherited retinal diseases was performed on a patient with clinical PXE diagnosis (skin papules and laxity, angioid streaks, and atrophy) who was carrier of only one ABCC6 rare sequence variant. Beside ABCC6, several rare sequence variants were detected which can contribute either to the occurrence of calcification (GGCX and SERPINF1 genes) and/or to ophthalmological manifestations (ABCA4, AGBL5, CLUAP1, and KCNV2 genes). This wide-spectrum analysis approach facilitates the identification of rare variants possibly involved in PXE, thus avoiding invasive skin biopsy as well as expensive and time-consuming diagnostic odyssey and allows to broaden and to deepen the knowledge on this complex rare disease and to improve patients' counselling, also with a future perspective of personalised medicine.


2015 ◽  
Vol 35 (6) ◽  
pp. 1526-1531 ◽  
Author(s):  
Eythor Bjornsson ◽  
Daniel F. Gudbjartsson ◽  
Anna Helgadottir ◽  
Thorarinn Gudnason ◽  
Tomas Gudbjartsson ◽  
...  

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