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In dairy cattle, the prevalence of genomic testing is now widespread, and commonly both sires and many offspring in the form of children, grandchildren, and great-grandchildren, are genotyped. Calling phases from genotypes is useful for several reasons, in particular for construction of haplotypes and imputation of missing genotypes. In this paper, we present a new computationally efficient method to call phases of grandfathers and great-grandfathers when enough genotyped offspring are present. The method consists of first identifying sharedhaplotypes between ancestor and offspring, followed by phasing segments based on homozygote genotypes in offspring, and finally merging haplotype segments to call entire ancestral haplotypes. The implementation is based on using bit vectors and fast binary computations. Results show that the method is effective in finding shared haplotypes to be used for phasing.

Additional file 1. Figure S1. Supine blood pressure according to ��1-antitrypsin deficiency genotype. Figure S2. Ankle-brachial index according to ��1-antitrypsin deficiency genotype. Figure S3. Risk of cardiovascular disease according to ��1-antitrypsin deficiency genotype by step-up logistic regression. Figure S4. Risk of cardiovascular disease according to ��1-antitrypsin deficiency genotype, stratified by sex, age, smoking status and COPD. Figure S5. Binscatter plots of systolic blood pressure, ischemic heart disease, ischemic cerebrovascular disease, or hypertension versus plasma ��1-antitrypsin partitioned into 20 bins. Figure S6. Exclusion sensitivity plot. Figure S7. Systolic blood pressure according to ��1-antitrypsin deficiency genotype, stratified by study population.

Nanna Korsbæk,1,2 Eskild M Landt,1 Morten Dahl1,2 1Department of Clinical Biochemistry, Zealand University Hospital, Køge, Denmark; 2Department of Clinical Medicine, University of Copenhagen, Copenhagen, DenmarkCorrespondence: Morten DahlDepartment of Clinical Biochemistry, Zealand University Hospital, Lykkebækvej 1, Køge, DK-4600, DenmarkTel +4547325545Email modah@regionsjaelland.dkRationale: Individuals exposed to second-hand smoking may be more susceptible to asthma and chronic obstructive pulmonary disease (COPD). We investigated the risk of respiratory symptoms, asthma, and COPD in adults exposed to second-hand smoking at different stages of life in the general population.Methods: We identified individuals who had been exposed to second-hand smoking in childhood only, adulthood only, or lifelong in a cohort of 20,421 adults from the Danish General Suburban Population Study and recorded respiratory symptoms, lung function, asthma, and COPD as outcomes.Results: Among 20,421 adults from the general population, 2,551 (12%) had been lifelong exposed to second-hand smoking, 459 (2%) had been exposed in adulthood only, and 13,998 (69%) had been exposed in childhood only; the mean ages of the three groups were 54 years, 55 years, and 57 years, respectably, compared with 56 years in non-exposed individuals (P< 0.001). Equivalent values for the prevalence of current smoking were 25%, 20%, and 18% versus 12% (P< 0.001). After adjustment for age, smoking, and sex, the odds ratios for wheezing, severe dyspnoea, cough on exertion, and asthma increased as a function of second-hand smoke exposure (Ps≤ 0.004); individuals who had been exposed to second-hand smoking lifelong, in adulthood only, or in childhood only versus non-exposed had increased odds ratios for wheezing of 1.62 (95% CI=1.41– 1.87), 1.50 (1.15– 1.94), and 1.16 (1.04– 1.30). Corresponding values were 2.08 (1.52– 2.85), 2.05 (1.22-3-44), and 1.23 (0.95– 1.59) for severe dyspnoea, 1.56 (1.33– 1.83), 1.53 (1.15– 2.02), and 1.19 (1.05– 1.35) for cough on exertion, 1.36 (1.14– 1.63), 1.49 (1.09– 2.05), and 1.13 (0.99– 1.30) for asthma, and 1.24 (1.03– 1.48), 1.25 (0.90– 1.74), and 1.09 (0.96– 1.24) for COPD. The population attributable fractions of asthma and COPD due to lifelong second-hand smoke exposure were 4.3% and 2.9%.Conclusion: Individuals exposed to lifelong second-hand smoking have increased risks of respiratory symptoms, asthma, and COPD, and may account for 4.3% and 2.9% of people with asthma and COPD in the general population.Keywords: atopy, chronic obstructive pulmonary disease, passive smoking, pulmonary function, wheezing