title: Linkage analysis of alpha 1-antitrypsin deficiency: lessons for complex diseases.
abstract: OBJECTIVE
  Severe alpha 1-antitrypsin (A1AT) deficiency is the one proven genetic risk factor for chronic obstructive pulmonary disease (COPD). Familial aggregation has been demonstrated for COPD among individuals who do not have A1AT deficiency, but linkage analysis of COPD has not been reported. To investigate the optimal phenotype definitions and analytical methods for the linkage analysis of COPD, we examined a set of 28 A1AT- deficient families containing 155 individuals. We have used the protease inhibitor (PI) type as a genetic marker rather than a disease gene, and we have performed linkage analysis between PI type and serum A1AT level and spirometry-related phenotypes.
  
  
  METHODS
  Linkage analysis was performed on the quantitative phenotypes forced expiratory volume at 1 s (FEV(1) as % predicted), the ratio of FEV(1) to forced vital capacity (FEV(1)/FVC as % predicted), and serum A1AT level using the variance component approach in SOLAR, the generalized estimating equation approach in RELPAL, and the model-based classical lod score method in LINKAGE. Linkage analysis with qualitative A1AT and spirometry phenotypes was performed using a model-based method (LINKAGE) and a model-free method (GENEHUNTER). Adjustments for smoking effects were investigated under each method.
  
  
  RESULTS
  All of the methods demonstrated linkage of PI type to serum A1AT level. Interestingly, however, the other quantitative phenotypes provided only weak evidence for linkage of PI type to lung disease. Better evidence for linkage of lung disease to PI type was found using a moderate or a mild threshold for the definition of airflow obstruction.
  
  
  CONCLUSIONS
  For linkage analysis of spirometry phenotypes in A1AT deficiency, qualitative phenotypes provided stronger evidence for linkage than quantitative phenotypes. Possible contributors to the stronger evidence for linkage to qualitative spirometry phenotypes include the ascertainment scheme and the nonnormality of the pulmonary function data in PI Z subjects. This study provides guidelines for studies of the genetics of COPD unrelated to A1AT deficiency.
authors.affiliation: Channing Laboratory, Brigham and Women's Hospital, Boston, Mass. 02114, USA. ed.silverman@channing.harvard.edu
authors.forename: E K
authors.initials: EK
authors.lastname: Silverman
authors.forename: J D
authors.initials: JD
authors.lastname: Mosley
authors.forename: D C
authors.initials: DC
authors.lastname: Rao
authors.forename: L J
authors.initials: LJ
authors.lastname: Palmer
authors.forename: M A
authors.initials: MA
authors.lastname: Province
authors.forename: R C
authors.initials: RC
authors.lastname: Elston
authors.forename: S T
authors.initials: ST
authors.lastname: Weiss
authors.forename: E J
authors.initials: EJ
authors.lastname: Campbell
mesh_terms: D005260:Female; D005541:Forced Expiratory Volume; D008040:Genetic Linkage; D005838:Genotype; D006801:Humans; D008297:Male; D010375:Pedigree; D010641:Phenotype; D029424:Pulmonary Disease, Chronic Obstructive / Q000097:blood / Q000235:genetics*; D012129:Respiratory Function Tests; D015842:Serine Proteinase Inhibitors / Q000235:genetics* / Q000378:metabolism; D013147:Spirometry; D011795:Surveys and Questionnaires; D000515:alpha 1-Antitrypsin / Q000235:genetics* / Q000378:metabolism; D019896:alpha 1-Antitrypsin Deficiency / Q000097:blood / Q000235:genetics*
chemical_list: D015842:Serine Proteinase Inhibitors; D000515:alpha 1-Antitrypsin