title: Inherited chronic obstructive pulmonary disease: new selective-sequencing workup for alpha1-antitrypsin deficiency identifies 2 previously unidentified null alleles.
abstract: BACKGROUND
  alpha(1)-Antitrypsin (alpha(1)AT) deficiency predisposes individuals to chronic obstructive pulmonary disease (COPD) and/or liver disease. Phenotyping of the protein by isoelectric focusing is often used to characterize alpha(1)AT deficiency, but this method may lead to misdiagnosis (e.g., by missing null alleles). We evaluated a workup that included direct sequencing of the relevant parts of the gene encoding alpha(1)AT, SERPINA1 [serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1], for patients with alpha(1)AT concentrations < or =1.0 g/L.
  
  
  METHODS
  During a 5-year period, we identified 66 patients with alpha(1)AT concentrations < or =1.0 g/L and amplified and sequenced exons 2, 3, and 5 of the alpha(1)AT gene in these patients. To ensure that no relevant genotypes were missed, we sequenced the same exons in 48 individuals with alpha(1)AT concentrations between 1.0 and 1.5 g/L.
  
  
  RESULTS
  Sequence analysis revealed 18 patients with combinations of disease-associated alpha(1)AT alleles: 8 homozygous for the deficient Z allele and 10 compound heterozygotes for various deficient or null alleles. We identified and named 2 new null alleles, Q0(soest) (Thr(102)-->delA, which produces a TGA stop signal at codon 112) and Q0(amersfoort) (Tyr(160)-->stop). No relevant disease-associated allele combinations were missed at a 1.0-g/L threshold.
  
  
  CONCLUSIONS
  Up to 22% of the alleles in disease-associated alpha(1)AT allele combinations may be missed by conventional methods. Genotyping by direct sequencing of samples from patients with alpha(1)AT concentrations < or =1.0 g/L detected these alleles and identified 2 new null alleles.
authors.affiliation: Department of Clinical Chemistry, Meander Medical Center, Utrechtseweg 160, Amersfoort, The Netherlands. janke.prins@hetnet.nl
authors.forename: Janke
authors.initials: J
authors.lastname: Prins
authors.forename: Brenda B
authors.initials: BB
authors.lastname: van der Meijden
authors.forename: Rob J
authors.initials: RJ
authors.lastname: Kraaijenhagen
authors.forename: Jos P M
authors.initials: JP
authors.lastname: Wielders
mesh_terms: D000483:Alleles; D002648:Child; D002675:Child, Preschool; D005260:Female; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D010375:Pedigree; D029424:Pulmonary Disease, Chronic Obstructive / Q000235:genetics*; D020539:Sequence Analysis, Protein; D000515:alpha 1-Antitrypsin / Q000235:genetics*; D019896:alpha 1-Antitrypsin Deficiency / Q000235:genetics*
chemical_list: D000515:alpha 1-Antitrypsin