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A template for mutational data analysis of the CFTR gene

  • Giampiero Ferraguti , Silvia Pierandrei , Sabina Maria Bruno , Fabrizio Ceci , Roberto Strom and Marco Lucarelli EMAIL logo
Published/Copyright: June 14, 2011
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Clinical Chemistry and Laboratory Medicine
From the journal Clinical Chemistry and Laboratory Medicine Volume 49 Issue 9

Abstract

Background: Automated DNA sequencing produces large amounts of data that need to be analyzed by appropriate software. Personalization of software can be a difficult and time-consuming task, especially if a large number of mutations have to be analyzed.

Methods: The Applied BioSystems SeqScape software, based on the KB basecaller algorithm, is a versatile tool that can be used for mutational analysis and for data quality assessment of sequences belonging to any gene of interest. Using this software we analyzed over 1400 sequences of CFTR exons and adjacent intronic zones, representing over 500,000 bases.

Results: We present an up to date specific template and a linked set of instructions for automated labeling of all point mutations and polymorphisms of the CFTR gene, whose mutations cause cystic fibrosis (the most common genetic disease among Caucasian individuals). We also describe our refined software settings for mutational analysis, in order to keep to a minimum the need of manual validation.

Conclusions: The use of our template greatly simplifies the mutational analysis of the CFTR gene, reducing human intervention. In our opinion, it might not only be useful to researchers that already perform CFTR mutational analysis by sequencing methods but it should also improve the approach in those laboratories that already use ABI PRISM instrumentation for a limited mutational analysis of the CFTR gene. Similar mutational templates can also be used for other disease causing genes, thus improving molecular genetics protocols.

Keywords: automated sequence analysis; CFTR mutational analysis; cystic fibrosis; SeqScape software
Corresponding author: Marco Lucarelli, Sez. Biochimica Clinica, Dip. Biotecnologie Cellulari ed Ematologia c/o Azienda Policlinico Umberto I, Sapienza Università di Roma, Viale Regina Elena 324 00161, Rome, Italy Phone: +39-06-49970458, Fax: +39-06-4464698
Received: 2011-3-5
Accepted: 2011-4-2
Published Online: 2011-06-14
Published in Print: 2011-09-01

©2011 by Walter de Gruyter Berlin Boston

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https://doi.org/10.1515/CCLM.2011.604
Keywords for this article
automated sequence analysis; CFTR mutational analysis; cystic fibrosis; SeqScape software

Articles in the same Issue

  1. Editorial
  2. Athlete's biological passport: to test or not to test?
  3. Review
  4. Prognostic value of cystatin C in acute coronary syndromes: enhancer of atherosclerosis and promising therapeutic target
  5. Opinion Papers
  6. The function of oxalic acid in the human metabolism
  7. Current limitations of the Athlete's Biological Passport use in sports
  8. Limits and pitfalls of Athlete's Biological Passport
  9. The Athlete Biological Passport from the perspective of an anti-doping organization
  10. Perspectives
  11. Genetics of infectious diseases: hidden etiologies and common pathways
  12. Guidelines and Recommendations
  13. IFCC primary reference procedures for the measurement of catalytic activity concentrations of enzymes at 37 °C. Part 9: Reference procedure for the measurement of catalytic concentration of alkaline phosphatase
  14. Genetics and Molecular Diagnostics
  15. A template for mutational data analysis of the CFTR gene
  16. High resolution melting analysis to genotype the most common variants in the HFE gene
  17. General Clinical Chemistry and Laboratory Medicine
  18. Bayesian analysis of an international ELISA comparability study
  19. Inflammatory markers in preeclamptic patients
  20. Pre-analytical effects of different lithium heparin plasma separation tubes in the routine clinical chemistry laboratory
  21. Pre-acquisition system assessment of the Sysmex® Coagulation System CS-2100i and comparison with end-user verification; a model for the regional introduction of new analysers and methods
  22. Evaluation of a commercially available rapid urinary porphobilinogen test
  23. Reference Values and Biological Variations
  24. Reference intervals and age and gender dependency for arterial blood gases and electrolytes in adults
  25. Within-subject biological variation of glucose and HbA1c in healthy persons and in type 1 diabetes patients
  26. Determinants of oxidative stress related to gender: relevance of age and smoking habit
  27. Soluble ST2 is not independently associated with androgen and estrogen status in healthy males and females
  28. Infectious Diseases
  29. Development of candidate reference reagent for HIV-1 RNA and comparison analysis for different HIV-1 RNA quantitative assay
  30. Prognostic value of serum angiotensin-converting enzyme activity for outcome of community-acquired pneumonia
  31. The evaluation of colloidal gold immunochromatographic assay (GICA) for rapid diagnosis of influenza A disease
  32. Cardiovascular Disease
  33. N-terminal pro-B-type natriuretic peptide in early and advanced phases of obesity
  34. Vaspin plasma concentrations and mRNA expressions in patients with stable and unstable angina pectoris
  35. Prospective study of first stroke in relation to plasma homocysteine and MTHFR 677C>T and 1298A>C genotypes and haplotypes – evidence for an association with hemorrhagic stroke
  36. Letters to the Editor
  37. Evaluation of the analytical performance of the Beckman Coulter AU680 automated analytical system based on quality specifications for allowable performance derived from biological variation
  38. Collagen peptides, interstitial remodelling and sudden cardiac death in hypertrophic cardiomyopathy
  39. Erratum
  40. Modified phosphatidylserine-dependent antiprothrombin ELISA enables identification of patients negative for other antiphospholipid antibodies and also detects low avidity antibodies
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