BlueCross and BlueShield of Montana Medical Policy/Codes
Genetic Testing for Alpha-1 Antitrypsin Deficiency
Chapter: Genetic Testing
Current Effective Date: October 25, 2013
Original Effective Date: November 01, 2012
Publish Date: October 25, 2013
Revised Dates: September 27, 2013

According to the 2003 joint statement on diagnosis and management of alpha-1 antitrypsin deficiency (AATD) by the American Thoracic Society/European Respiratory Society (1):

The following features should prompt suspicion by physicians that their patient may be more likely to have AATD:

* Clinical Factors

  • Early-onset emphysema (age of 45 years or less);
  • Emphysema in the absence of a recognized risk factor (smoking, occupational dust exposure, etc.);
  • Emphysema with prominent basilar hyperlucency;
  • Otherwise unexplained liver disease;
  • Necrotizing panniculitis;
  • Anti-proteinase 3-positive vasculitis (C-ANCA [anti-neutrophil cytoplasmic antibody]-positive vasculitis); or
  • Bronchiectasis without evident etiology

* Family History

  • A first-degree relative is defined as a parent, child or sibling.

The following table shows the range of serum levels of AAT by common phenotypes according to the commercial standard milligram per deciliter (mg/dL) and the purified standard micromole (uM). A level of less than 11 uM is generally considered to be associated with an increased risk of clinical disease, but this cut-off may vary according to the specific test used (1,3):

























MM=2 copies of the normal M allele sequence

MZ=heterozygous genotype that is lower risk

Most common abnormal alleles=Z and S; ZZ tends to be most severely affected

(See Description below for more information)

Description of disease

AATD is an autosomal recessive genetic disorder that results in decreased production of the alpha-1 antitrypsin (AAT) protein, or production of abnormal types of the protein that are functionally deficient. Data from screening studies have found the prevalence of AATD in the United States to be between 1 in 2,857 and 1 in 5,097 individuals respectively. AATD occurs largely in Caucasians. (1)

AAT is an acute phase glycoprotein, synthesized primarily in the liver and secreted into the bloodstream. One of the primary functions of the AAT protein is to protect the lungs from damage by the enzyme elastase. Elastase, part of the normal response to injury and inflammation, breaks down proteins but can also break down and damage lung tissue if its action is not regulated by AAT. Individuals with AAT deficiency thus have an increased risk of lung disease.

Respiratory disease tends to be more severe and occur sooner (i.e., between age 40 and 50) in individuals with AAT deficiency who smoke cigarettes and/or are exposed to occupational dust or fumes. In non-smokers and individuals without environmental exposure, onset of respiratory disease occurs more commonly in the sixth decade. Childhood-onset lung disease is rare with AATD. AATD is also associated with an increased risk of liver disease, thought to occur due to aggregation of damaged AAT in the liver cells, where the protein is produced. The most common manifestation of liver disease in childhood is jaundice. Adult-onset liver disease generally manifests as cirrhosis and fibrosis. Necrotizing panniculitis is a rare, but well-recognized complication of AAT deficiency. This dermatological condition is characterized by inflammatory and necrotizing lesions of the skin and subcutaneous tissue. (2)

The primary interventions to prevent or treat symptoms in individuals with AATD involve behavioral change, especially avoiding or quitting cigarette smoking. Smoking is the most important risk factor for the development of emphysema in AATD in individuals who are homozygous for the most severe AAT mutations. (1) In addition, individuals with AATD are advised to avoid other substances that can irritate the lungs e.g., cigarette smoke, dust and workplace chemicals, as well as substances such as alcohol that can cause liver damage. There are also general recommendations to exercise, avoid stress and have a nutritious diet. Furthermore, patients with AATD may be recommended to have earlier or more aggressive treatments for conditions such as asthma outbreaks or acute exacerbations of chronic obstructive pulmonary disease (COPD). One treatment option that is specific to AATD is alpha-1 antitrypsin augmentation. Patients generally receive injections of plasma every 3 to 4 weeks for life. There is a lack of consensus about the efficacy of this treatment.

Diagnostic testing for AAT

Several types of tests are available for patients who are suspected of having AATD. A blood test is available that quantifies the total amount of alpha-1 antitrypsin in the blood, detecting decreases in AAT protein levels, but not distinguishing among abnormal protein types. AAT is an acute phase reactant, and levels will be elevated in acute and chronic inflammatory conditions, infections and some cancers, which may cause levels to appear normal in individuals with mild to moderate AAT deficiency. In general, a serum concentration of AAT less than 15-20% of the normal value is highly suggestive of a homozygous alpha-1 antitrypsin mutation. (3)

The alpha-1 phenotype test identifies the type of circulating AAT protein in the blood by isoelectric focusing of the various AAT protein types. Patterns of protein migration in an electric field are evaluated and compared to normal patterns to determine if and what type of abnormal AAT protein may be present.

Genetic testing is also available. Production of AAT is encoded by the SERPINA1 gene which is co-dominant (each gene copy is responsible for producing half of the AAT). Although there are more than 75 sequence variants of the SERPINA1 gene (i.e., 75 possible alleles), only several are common in North America. Approximately 95% of individuals have 2 copies of the normal M allele sequence (MM) and have mean serum concentrations of AAT ranging from 20-53 umol/L. The most common abnormal forms are the Z allele and the S allele. Individuals with 2 copies of the Z allele (ZZ) tend to be most severely affected, with mean serum concentrations of AAT of 2.5 to 7 umol/L and a high risk of COPD. Individuals with genotype SS and heterozygous individuals with genotype MZ have low risk of COPD and moderately lower levels of AAT. Individuals with rarer mutations of the SERPINA1 gene or null alleles may not produce any AAT and are also at high risk. (4)

Genetic testing for AATD is most commonly done by the alpha-1 genotype test. This test uses Polymerase chain reaction (PCR) analysis, or some other type of nucleic acid-based analysis, to identify abnormal alleles of AAT DNA. Currently, genotype tests are only designed to detect the most common mutations, i.e., the S and Z alleles.

A common approach to testing for AATD is to initially perform serum quantitation. If the AAT level is found to be low, a follow-up phenotype or genotype test is ordered. (5) Another approach, as exemplified by the Mayo clinic, is to perform serum protein quantification, followed by genotype testing in individuals with clinical suspicion of AATD. If these tests are discordant, phenotype testing is then performed. (6)

Regulatory Status

An example of a U.S. Food and Drug Administration (FDA)-cleared phenotyping test is the Hydragel 18 alpha-1 antitrypsin isofocusing (Hydragel 18 A1AT) kit (Sebia Inc., GA). In 2007, this test was cleared for marketing through the 510(k) process. The test is designed for the qualitative detection and identification of the phenotypes of AAT protein.

No FDA-cleared genotyping tests were found. Thus, genotyping is offered as a laboratory-developed test. Clinical laboratories may develop and validate tests in-house (“home-brew”) and market them as a laboratory service; such tests must meet the general regulatory standards of the Clinical Laboratory Improvement Act (CLIA). The laboratory offering the service must be licensed by CLIA for high-complexity testing.


Each benefit plan, summary plan description or contract defines which services are covered, which services are excluded, and which services are subject to dollar caps or other limitations, conditions or exclusions. Members and their providers have the responsibility for consulting the member's benefit plan, summary plan description or contract to determine if there are any exclusions or other benefit limitations applicable to this service or supply.  If there is a discrepancy between a Medical Policy and a member's benefit plan, summary plan description or contract, the benefit plan, summary plan description or contract will govern.


Genetic testing for alpha-1 antitrypsin (AAT) deficiency (AATD) may be considered medically necessary when both of the following conditions are met:

  1. Patient is suspected of having AATD because of clinical factors and/or because the patient may be at high risk of having AATD due to a first-degree relative with AATD*; AND
  2. Patient has a serum AAT level in the range of severe deficiency*.

* NOTE: See Clinical Factors and Family History in Description section

Genetic testing for AATD is considered experimental, investigational and unproven in all other situations.


Literature Review

Validation of the clinical use of any genetic test focuses on 3 main principles: 1) the analytic validity of the test, which refers to the technical accuracy of the test in detecting a mutation that is present or in excluding a mutation that is absent; 2) the clinical validity of the test, which refers to the diagnostic performance of the test (sensitivity, specificity, positive and negative predictive values) in detecting clinical disease; and 3) the clinical utility of the test, i.e., how the results of the diagnostic test will be used to change management of the patient and whether these changes in management lead to clinically important improvements in health outcomes.

Analytic validity

Analytic performance of the Hydragel 18 A1AT phenotyping test is reported in an FDA decision summary document. (7) Within-run test result reproducibility was determined by testing 8 samples 15 or 18 times on a single gel. Two normal samples and 6 pathological samples with MS, SS, MZ, ZZ and MX phenotypes were included; the test was able to reproduce the corresponding phenotype correctly. Between-run gel reproducibility was determined by testing 15 samples and 3 controls 12 times on 2 lots of gels. Again, the phenotypes were reproduced correctly.

No published studies on the analytic validity of any AAT (alpha-1 antitrypsin) genotyping test conducted in the United States, other than FDA documents, were identified.

Clinical validity

In 2008, Ljujic and colleagues in Serbia published findings of a study with 27 emphysema patients. (8) Phenotyping was performed using isoelectric focusing and genotyping by denaturing gradient gel electrophoresis. Isoelectric focusing was successfully performed in 25 cases and genotyping results were available for all 27 patients. Phenotyping and genotyping were concordant for the 4 patients found to have 1 or 2 ‘Z’ alleles. However, genotyping found 2 unusual mutations and in both of these cases, phenotyping found normal variants.

The FDA decision summary for the Hydrogel phenotyping test included an evaluation of clinical sensitivity and specificity. (7) Samples were evaluated from 64 patients with the following diagnoses: congenital AATD [alpha-1 antitrypsin deficiency] (n=16), pulmonary disorder (n=15), hepatic disorder (n=8), infertility (n=1), panniculitis (n=1) and normal (n=23). The sensitivity of the phenotype test was 39/39 (100%) and the specificity was 23/25 (92%). (Note: This analysis excludes 4 individuals with indeterminate diagnoses).

Clinical utility

The clinical utility of genetic testing for AATD depends on how the results can be used to improve patient management. With AATD, this could occur in several ways, including the following:

  • Patient knowledge of AAT status could lead to behavior change that improves health outcomes. In particular, asymptomatic smokers could quit smoking which prevents or delays onset of lung disease, and symptomatic smokers could quit smoking which might prevent progression of lung disease. Knowledge of AAT status could also lead to other behavioral changes including avoiding pollutants, increasing exercise, avoiding alcohol, and avoiding smoking for those who have not started. (9)
  • A diagnosis of AATD could lead to changes in treatment which may improve patient outcomes. The only treatment specific to AATD is alpha-1 antitrypsin augmentation therapy. In addition, the intensity and/or timing of other treatments may be different for individuals with known AATD. This includes antibiotic treatments for lung infections and vaccinations (influenza, pneumococcus, hepatitis A and B, etc.). (1)

Smoking cessation

In 2003, a joint statement on diagnosis and management of AATD from the American Thoracic Society (ATS) and the European Respiratory Society (ERS) was published. (1) The authors stated that the joint statement was based on systematic reviews and an evidence-based approach to evaluating evidence. A review of smoking cessation studies in the ATS/ERS joint statement did not identify any RCTs (random controlled trials) on the impact of AATD status on smoking cessation. However, they identified an RCT on a related topic. This study which found that, at one year, individuals who received genetic susceptibility information (in this case, CYP2D6 genotype results) were significantly more likely to report a quit attempt than individuals who received counseling only; quit rates did not differ significantly in the 2 groups. (10)

The MEDLINE search identified a study by Carpenter and colleagues reporting on findings of a survey of individuals who had volunteered for genetic testing for AATD. (11) A total of 4,344 individuals completed a test kit; 331 (7.6%) respondents were rejected because their blood sample was insufficient. The remaining participants were mailed a follow-up letter with their test results and a genotype-specific brochure. Results of the testing revealed that 2,228 (56%) of the valid samples tested normal, 1,530 (38%) were found to be heterozygous carriers for AATD (MZ genotype) and 255 (6%) were found to be severely AAT deficient (SZ or ZZ genotype). A total of 729/2,228 (33%) of participants with valid blood samples identified themselves as current cigarette smokers. These smokers were sent an additional questionnaire 3 months after the initial letter. Test results among smokers were 55% normal genotype, 38% carrier and 7% severely AAT deficient. Of the 729 surveys sent to smokers, 205 (28%) were completed. Six smokers were excluded because they smoked less than 6 cigarettes per day, leaving 199 participants in the study sample. Survey responders were more likely to be older than non-respondents; there were no significant differences in response rates by genotype group. Among survey respondents, individuals with severe AATD were significantly more likely to make any self-reported quit attempt than were individuals with a normal genotype (59% vs. 33%, p<0.05). Of 8 quit behaviors listed in the survey, AAT deficient smokers reported engaging in a mean of 2.4 (standard deviation [SD]=2.3). This was significantly higher than the number of quit behaviors reported by carriers (0.7, SD=1.3) or normals (1.3, SD=2.0), p=0.04. There was not a significant difference between groups, however, in the abstinence rate at 3 months (defined as 24-hour point prevalence). This study was limited in that it lacked a control group of smokers who were not tested for AATD, and there was a low response rate to the 3-month survey.

Smoking prevention

The ATS/ERS joint statement on AATD identified 2 case-control studies that included children identified at birth as having AATD and matched to a demographically similar control group. The number of children with AATD was 61 in one study and 22 in the other. These studies reported a lower frequency of adolescent smoking in individuals identified at birth as having AATD, compared to the control individuals. (1)

Conclusions: The available studies suggest that knowledge of AATD status may lead to more quit attempts but not higher smoking cessation rates. There is also limited evidence from 2 small case-control studies that individuals who know from birth they have AATD are less likely to initiate smoking than individuals without genetic information knowledge.

Treatments for individuals with AATD

Alteration of timing or intensity of treatments for patients with AATD

The ATS/ERS joint statement on AATD (1) recommended the following interventions for individuals with emphysema who have AATD:

  • Inhaled bronchodilators;
  • Preventive vaccinations against influenza and pneumococcus;
  • Supplemental oxygen when indicated by conventional criteria, including during air travel;
  • Pulmonary rehabilitation for individuals with functional impairment;
  • Consideration of lung transplantation for selected individuals with severe functional impairment and airflow obstruction; or
  • Early antibiotic treatment for individuals with purulent acute exacerbations of COPD.

The authors noted that these are recommendations for treating patients with COPD in general and are applicable to those with pulmonary disease associated with AATD; no controlled studies specific to AATD were cited in support of the above recommendations to determine whether the timing, intensity, or compliance with these treatments is altered by knowledge of AATD status.

Apha-1 antitrypsin augmentation therapy

A 2010 Cochrane review addressed the benefits and harms of augmentation therapy with AAT in patients with AATD and lung disease. (12) The investigators searched for RCTs comparing augmentation therapy with AAT to placebo or no intervention and reporting one or more of the primary outcomes: mortality, forced expiratory volume in one second (FEV1) or adverse effects. Two RCTs were identified; both were conducted by the same research team. (13,14) The first trial, published in 1999, enrolled 58 ex-smokers with AATD (ZZ genotype). Patients were treated with AAT (250 mg/kg) or placebo 4 times a week for 3 years. The primary outcome was FEV1. The second trial, published in 2009, included 82 ex-smokers or never-smokers with the ZZ or heterozygous Z genotype. Patients were treated for 2 years with AAT (60 mg/kg) or placebo. The primary outcome was lung density measured by computed tomography (CT) scans, which the trial authors noted was an exploratory outcome; in the trial, FEV1 was reported as a secondary outcome. Adverse events were not reported in the first trial. A pooled analysis of the 2 studies did not find a significant difference in FEV1 deterioration over the course of the study in the treatment compared to the placebo group. The pooled mean difference in FEV1 (mL) was -19.92 (95% confidence interval [CI]: -40.86 to 1.02). A pooled analysis of lung density change (g/L) according to CT findings favored the treatment group. The mean difference was 1.14, 95% CI=: 0.14 to 2.14, p=0.026. Potential biases in the trials noted by the Cochrane review authors include potential financial conflicts of interest and, in the second trial, selective reporting of outcomes, which refers to the trial authors’ emphasis of the intermediate outcome CT lung density. The Cochrane review concluded that there was insufficient evidence to recommend augmentation therapy with AAT. No additional trials on AAT augmentation therapy were identified in the MEDLINE search.

Conclusions: A national guideline recommends different interventions for individuals with emphysema found to have AATD such as preventive vaccinations and early antibiotic treatment. The only AATD-specific treatment is AAT augmentation therapy, which is often prescribed for patients with documented AATD and COPD. A Cochrane review concluded that the RCT evidence was insufficient to determine whether alpha-1 antitrypsin augmentation therapy is effective for improving health outcomes in individuals with AATD. In their pooled analysis of data from 2 studies, there was significantly greater decrease in lung density among patients who received augmentation therapy; the difference in FEV1 was not statistically significant although the upper confidence interval was close to 1.

Ongoing Clinical Trials

International Study Evaluating the Safety and Efficacy of Inhaled, Human, Alpha-1 Antitrypsin (AAT) in Alpha-1 Antitrypsin Deficient Patients With Emphysema (NCT01217671): (15) This is a double-blind randomized controlled trial comparing the safety and efficacy of inhaled AAT versus placebo in adults with emphysema. Estimated enrollment is 200 patients. The primary efficacy measures are exacerbations and lung density after 1 year. Adverse events are included as secondary outcomes. The study is being conducted at sites in Canada and several European countries and is sponsored by Kameda, Ltd.

Practice Guidelines and Position Statements

In 2003, the American Thoracic Society published recommendations on the diagnosis and management of individuals with alpha-1 antitrypsin deficiency. (1)

ATS recommendations were classified as follows:

Type A: Genetic testing is recommended

Type B: Genetic testing should be discussed and could be accepted or declined

Type C: Genetic testing is not recommended i.e., should not be encouraged

Type D: Recommend against genetic testing i.e., should be discouraged

Type A recommendations for diagnostic testing in the following situations:

  • Symptomatic adults with emphysema, COPD or asthma with airflow obstruction that is not completely reversible with aggressive treatment with bronchodilators;
  • Individuals with unexplained liver disease;
  • Asymptomatic individuals with persistent obstruction on pulmonary function tests with identifiable risk factors (e.g. cigarette smoking, occupational exposure);
  • Adults with necrotizing panniculitis;
  • Siblings of an individual with known alpha-1 antitrypsin (AAT) deficiency.

Type B recommendations for diagnostic testing in the following situations:

  • Adults with bronchiectasis without evidence etiology;
  • Adolescents with persistent airflow obstruction;
  • Asymptomatic individuals with persistent airflow obstruction and no risk factors;
  • Adults with C-ANCA positive (anti-proteinase 3-positive) vasculitis;
  • Individuals with a family history of COPD or liver disease not known to be attributed to AAT deficiency;
  • Distant relatives of an individual who is homozygous for AAT deficiency;
  • Offspring or parents of an individual with homozygous AAT deficiency;
  • Siblings, offspring, parents, or distant relatives of an individual who is heterozygous for AAT deficiency;
  • Individuals at high risk of having AAT deficiency-related diseases;
  • Individuals who are not at risk themselves of having AAT deficiency but who are partners of individuals who are homozygous or heterozygous for AAT deficiency.

Type C recommendations for diagnostic testing in the following situations:

  • Adults with asthma in whom airflow obstruction is completely reversible;
  • Predispositional testing;
  • Population screening of smokers with normal spirometry.

Type D recommendations for diagnostic testing in the following situations:

  • Predispositional fetal testing;
  • Population screening of either neonates, adolescents, or adults.*

*Population screening is not recommended currently. However, a possible exception (type B recommendation) may apply in countries satisfying all 3 of the following conditions: 1) the prevalence of AAT deficiency is high (about 1/1,500, or more); 2) smoking is prevalent; and 3) adequate counseling services are available.


The literature evidence on the analytic and clinical validity of genetic testing for AATD is limited. In addition, there are few RCTs evaluating the impact of AATD testing on patient outcomes. However, national guidelines recommend specific interventions for patients with emphysema and AATD, and AAT augmentation therapy is often prescribed for patients with AATD and COPD. The available evidence suggests that knowledge of AATD status may discourage non-smokers from initiating smoking and may increase quit attempts among smokers, but it has not been shown to increase successful quitting. Evidence from small RCTs on AAT augmentation therapy are not definitive of a treatment benefit, but reports trend toward improvement in lung function. As a result, genetic testing for AATD may lead to improved outcomes by altering interventions for AATD and therefore may be considered medically necessary for individuals with suspected AATD or those at high risk for AATD due to personal or family history, who have serum levels of alpha-1 antitrypsin level in the range for homozygous disease.


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The presence or absence of procedure, service, supply, device or diagnosis codes in a Medical Policy document has no relevance for determination of benefit coverage for members or reimbursement for providers. Only the written coverage position in a medical policy should be used for such determinations.

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ICD-9 Codes
ICD-10 Codes
Procedural Codes: 81332
  1. American Thoracic Society; European Respiratory Society. American Thoracic Society/European Respiratory Society statement: standards for the diagnosis and management of individuals with alpha-1 antitrypsin deficiency. Am J Respir Crit Care Med 2003; 168(7):818-900.
  2. Schlade-Bartusiak K, Cox DW. Alpha-1 antitripsin deficiency. In Pagon RA, Bird TD, Dolan CR et al. (eds.). Gene Reviews (internet). Seattle (WA): University of Washington. Available online at: . Last accessed March 2012.
  3. Global Initiative for Chronic Obstructive Lung Disease. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease. Revised 2011. Available online at: . Last accessed March 2012.
  4. Kelly E, Greene CM, Carroll TP et al. Alpha-1 antitrypsin deficiency. Respir Med 2010; 104(6):763-72.
  5. Alpha-1 Foundation. Testing for Alpha-1. Available online at: Last accessed March 2012.
  6. Mayo Clinic: Mayo Medical Laboratories. Alpha-1 antitrypsin: A comprehensive testing algorithm. Available online at: . Last accessed March 2012.
  7. Food and Drug Administration (FDA). 510(k) substantial equivalence determination decision summary (K063498). Available online at . Last accessed March 2012.
  8. Ljujic M, Topic A, Divac A et al. Isoelectric focusing phenotyping and denaturing gradient gel electrophoresis genotyping: a comparison of two methods in detection of alpha-1-antitrypsin variants. Transl Res 2008; 151(5):255-9.
  9. Lerman C, Gold K, Audrain J et al. Incorporating biomarkers of exposure and genetic susceptibility into smoking cessation treatment: effects on smoking-related cognitions, emotions, and behavior change. Health Psychol 1997; 16(1):87-99.
  10. Audrain J, Boyd NR, Roth J et al. Genetic susceptibility testing in smoking-cessation treatment: one-year outcomes of a randomized trial. Addict Behav 1997; 22(6):741-51.
  11. Carpenter MJ, Strange C, Jones Y et al. Does genetic testing result in behavioral health change? Changes in smoking behavior following testing for alpha-1 antitrypsin deficiency. Ann Behav Med 2007; 33(1):22-8.
  12. Gøtzsche PC, Johansen HK. Intravenous alpha-1 antitrypsin augmentation therapy for treating patients with alpha-1 antitrypsin deficiency and lung disease. Cochrane Database Syst Rev 2010; (7): CD007851.
  13. Dirksen A, Dijkman JH, Madsen F et al. A randomized clinical trial of alpha1- antitrypsin augmentation therapy. Am J Respir Crit Care Med 1999; 160(5 pt 1):1468-72.
  14. Dirksen A, Piitulainen E, Parr DG et al. Exploring the role of CT densitometry: a randomized study of augmentation therapy in alpha1-antitrypsin deficiency. Eur Respir J 2009; 33(6):1345-53.
  15. International Study Evaluating the Safety and Efficacy of Inhaled, Human, Alpha-1 Antitrypsin (AAT) in Alpha-1 Antitrypsin Deficient Patients With Emphysema (NCT01217671). Sponsored by Kameda, Ltd. Last updated February 8, 2012. Available online at . Last accessed March 2012.
  16. Genetic Testing for Alpha-1 Antitrypsin Deficiency. Chicago, Illinois: Blue Cross Blue Shield Association Medical Policy Reference Manual (2013 January) Medicine 2.04.79.
July 2012  New Policy for BCBSMT: Policy created with literature search through February 2012. Genetic testing for AATD may be considered medically necessary for individuals who meet criteria and investigational otherwise.
October 2013 Policy formatting and language revised.  Policy statement unchanged.
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Genetic Testing for Alpha-1 Antitrypsin Deficiency