Coverage Policy Manual
Policy #: 2011047
Category: Laboratory
Initiated: June 2011
Last Review: April 2022
  Genetic Test: Genotyping for 9p21 Single Nucleotide Polymorphisms to Predict Risk of Cardiovascular Disease or Aneurysm

Description:
A number of highly correlated single nucleotide polymorphisms (SNPs) found in the chromosome 9 region p21 locus (9p21) have been significantly associated with myocardial infarction (MI), particularly early onset MI, and other manifestations of cardiovascular disease (CVD). Associations with abdominal aortic aneurysm and with intracranial aneurysm have also been reported. Genotyping for 9p21 SNPs may be offered as an approach to identify patients who may be at increased risk of some of these outcomes.
 
Background
In 2007, multiple investigators nearly simultaneously reported the first common genetic variant affecting the risk of coronary heart disease (CHD; defined as inadequate circulation to cardiac muscle and surrounding tissue resulting in myocardial infarction [MI], unstable angina pectoris, coronary revascularization, or death) in Caucasians through genome-wide association studies using single nucleotide polymorphism (SNP) arrays. Additional studies identified other SNPs with similar estimates of CHD risk. These SNPs were confirmed in case-control replication studies in a variety of study populations, showing that the identified SNPs were associated with CHD and even more specifically with MI (Scheffold, 2011). All of the SNPs were found within a locus spanning a 58-kilobase region at chromosome 9p21.3 (thus the locus is sometimes represented more specifically as 9p21.3; for simplicity, 9p21 will be used for the rest of this document), are highly correlated (r2>0.8) and thus are said to be in linkage disequilibrium (the non-random association of alleles The association of any identified SNP with CHD risk was shown to be independent of traditional risk factors (Scheffold, 2011).
 
Several studies have extended the 9p21 association to other vascular diseases including ischemic stroke; thus 9p21 may be reported as being associated with cardiovascular disease (CVD; defined as CHD and cerebrovascular disease) outcomes. Associations have also been reported with abdominal aortic aneurysm (AAA) and with intracranial arterial aneurysm and other vascular diseases (Johansen, 2010).
 
 
Several genes are found at the 9p21 locus, including ANRIL, which encodes a large noncoding RNA which may have regulatory functions, and CDKN2A and CDKN2B, which encode cyclin-dependent kinase inhibitors (Johansen, 2010).  The mechanisms by which the SNPs lead to increased CHD risk have been largely unknown. Recently, Harismendy et al. identified several potential enhancer regulatory DNA sequences in the 9p21 region (Harismendy, 2011).  They reported that the SNP rs10747278, consistently associated with increased risk of CHD, occurs in one of these enhancer sequences and that the the risk allele disrupts a transcription factor binding site involved in the inflammatory response (STAT1). The interaction of STAT1 with part of the inflammatory signaling pathway, interferon-gamma, is impaired in 9p21 risk carriers. Further study of the relationship between these risk variants, 9p21 regulatory elements, the inflammatory response, and atherosclerosis pathogenesis is planned.
 
Availability
The Berkeley HeartLab offers the 9p21-EarlyMICheck™ Genotype Test, which detects the rs10757278 A>G and rs1333049 G>C SNPs within the 9p21 locus of chromosome. The information on the website (http://www.bhlinc.com/clin_test_9p21.php ) indicates that the SNPs have been shown to predict increased risk for early onset myocardial infarction, for abdominal aortic aneurysm, and for myocardial infarction / coronary heart disease in general. It is suggested that the test may help identify patients at increased risk for these conditions, allowing providers to characterize and reduce other contributing risk factors.
 
Cardiac risk genotyping panels offered by other laboratories may include and individually report 9p21 SNP results. For example, the deCODE MI™ test genotypes 9p21.3 rs10757278 in addition to 7 other SNPs from other chromosomal loci to estimate the risk of coronary heart disease and MI.
 
Regulatory Status
There is no manufactured test kit for 9p21 genotyping that has been reviewed by the Food and Drug Administration. 9p21 genotyping tests are laboratory-developed tests (LTD), offered by clinical laboratories licensed under CLIA for high-complexity testing.
 
Coding
There is no specific CPT code for this test. Effective in 2013, if the specific analyte is listed in codes 81200-81355 or 81400-81408, that CPT code would be reported along with the unlisted code 81479 for the analytes that are not listed. If none of the analytes are listed in the more specific CPT codes, unlisted code 81479 would be reported for the whole test.
 
Prior to 2013, a series of molecular diagnostic codes (83890-83912) or an unlisted code such as 84999 (unlisted chemistry procedure) would likely have been used.
  

Policy/
Coverage:
Does Not Meet Primary Coverage Criteria Or Is Investigational For Contracts Without Primary Coverage Criteria
 
Genotyping for 9p21 single nucleotide polymorphisms does not meet member benefit certificate primary coverage criteria that there be scientific evidence of effectiveness including use to identify patients who may be at increased risk of cardiovascular disease or its manifestations (e.g., MI, ischemic stroke) or those who may be at increased risk of abdominal aortic aneurysm or intracranial aneurysm.
 
For members with contracts without primary coverage criteria, genotyping for 9p21 single nucleotide polymorphisms is considered investigational including use to identify patients who may be at increased risk of cardiovascular disease or its manifestations (e.g., MI, ischemic stroke) or those who may be at increased risk of abdominal aortic aneurysm or intracranial aneurysm. Investigational services are specific contract exclusions in most member benefit certificates of coverage.

Rationale:
Meta-analyses of the Association of 9p21 with CHD/CAD
Palomaki et al. conducted the first formal systematic review of the 9p21 literature to estimate the strength of the association between established 9p21 SNP variants and heart disease and to examine clinical utility (Palomaki, 2010). This review was commissioned by the Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group (EWG). Sixteen published studies that analyzed 47 data sets, and that reported 9p21 SNP genotypes in association with outcomes of CHD (including MI) or coronary artery disease (CAD; the result of the accumulation of atheromatous plaques within the walls of the coronary arteries that supply the myocardium, and the most common cause of CHD) were included in this review. Ischemic stroke and aneurysm outcomes were excluded from this analysis; all CHD/CAD outcomes were combined. Data sets were limited to Asian and White populations.
 
Three publications were cohort studies, the rest case-control studies; level 1 and level 2 evidence, respectively, using EWG methods (Teutsch, 2009).  Five SNPs in the 9p21 locus (rs1333049, rs10757274, rs2383207, rs2891168, and rs10757278) covered all studies/data sets. First, the review demonstrated that the choice of SNP was relatively unimportant; in combining the data from 2 studies, 4 SNPs provided nearly identical odds ratios (ORs). Thus, the results from only one SNP per study were used.
 
Across all studies, consensus genotype frequencies in controls were 27%, 50%, and 23% for 0, 1, and 2 at-risk alleles, respectively. The random-effects summary OR across all studies/data sets was 1.25 (95% confidence interval [CI],1.21-1.29; p<0.001; I2=10%) for individuals with 2 at-risk SNP alleles compared to individuals with one at-risk allele. When the same analysis was restricted to individuals younger than 55 years of age, the summary OR increased to 1.35 (95% CI, 1.3-1.4). Limiting the data sets to only those with upper age cutoff levels greater than 70 years, the summary OR was 1.19 (95% CI, 1.13-1.25; P<0.001). For individuals (all data sets) with no at-risk alleles compared to individuals with one at-risk allele the summary OR was 0.80 (95% CI, 0.77-0.82; p<0.001). No differences were found between Asians and Whites.
 
Since this study, 3 additional meta-analyses of 9p21 genotyping have been published. Schunkert et al. and the CARDIoGRAM Consortium conducted a meta-analysis of 14 genome-wide association studies of CAD (Schunkert, 2011). The 9p21 association per risk allele with CAD, as measured by SNP rs4977574, was 1.29 (95% CI, 1.23–1.36; p=1.35 × 1022). In an earlier report of this analysis, the association was stronger among cases less than 50 years of age at an OR of 1.45 (p=0.0015) (Preuss, 2010). The Coronary Artery Disease Genetics Consortium meta-analyzed four large genome-wide association studies of CAD and reported an allele risk of 1.20 (95% CI, 1.16–1.25; p=1.62 × 1025) for 9p21 SNP rs4977574 and CAD. These results compare well with Palomaki et al, 2010.  
 
Recent Individual Studies
Several studies analyzing individual patient cohorts or case-control populations for association of 9p21 and CHD/CAD have been published since the Palomaki et al. review.  Most results again compare well with Palomaki et al. Scheffold et al. evaluated a population of male patients with acute MI compared to an otherwise comparable population of males without an event and reported a slightly higher allele risk for several 9p21 SNPs (Scheffold, 2011). The estimates increased when the population was limited to those cases with a family history of MI; the authors point out that the combination risk factor of family history plus 9p21 status is similar in value to those of traditional risk factors such as hypertension, diabetes mellitus, and current smoking.
 
9p21 Allele Dosage and Disease Severity, Progression
Dandona et al. reported a strong direct association between the proportion of early onset patients with angiographically-determined 3-vessel disease and increasing gene dosage of 9p21 SNP rs1333049 (OR per risk allele copy = 1.45, 95% CI 1.18-1.79; p=4.26x10-4) (Dandona, 2010).  Patel et al. also reported greater 9p21 risk allele frequency with increasing angiographically-defined CAD severity (p=0.003) (Patel, 2010).  
 
9p21 Association with Ischemic Stroke
Several studies have reported, with mixed results, on the association of 9p21 with ischemic stroke, an outcome not included in the studies discussed in the prior text. Anderson et al. conducted a meta-analysis of 8 studies, focusing on 2 9p21 SNPs s1537378 and rs10757278 (Anderson, 2010).  Inclusion of all data resulted in a high degree of heterogeneity; restriction to only those studies with sufficient information to allow stroke subtype-specific analysis (n=5) resulted in an overall OR estimate of 1.15 (95% CI 1.08 to 1.23, p=0.0001), and a large artery subtype estimate from 3 cohorts of 1.20 (95% CI 1.08 to 1.33, p=0.0006), suggesting that the risk is largely restricted to the large artery subtype. Subsequently Olsson et al. published a case-control study of the association of 9p12 and ischemic stroke in individuals aged younger than 70 years (Olsson, 2011). In this study, the low-risk allele of 9p21 SNP rs7857345 showed significant association with decreased risk of large vessel disease after adjusting for traditional risk factors.  However, not all tested 9p21 SNPs were significant.
 
9p21 Association with Aneurysm
The 9p21 locus has been associated, along with four other genetic markers, with risk for intracranial aneurysm. However, these risk factors explain only up to 5% of the familial risk, reducing enthusiasm for genetic testing for this outcome at this time. There has been a greater focus on the association of 9p21 with abdominal aortic aneurysm (AAA). Several studies report 9p21 allele-specific estimates of risk in the range of 1.2-1.8 (Thompson, 2009) (Helgadottir, 2008) (Brown, 2008) (Biros, 2010).  Biros combined the results of their study with the results of previous studies and reported a combined estimate of about 1.3 for both 9p21 SNPs rs10757278 and rs1333049 (Biros, 2010).  This is lower than other well-characterized risk factor estimates for AAA such as age, family history, and smoking (Lederle, 2000).
 
Clinical Utility
The information in the prior text addresses primarily clinical validity, or the association between 9p21 and various outcomes of interest. The clinical validity of 9p21 with CHD/CAD outcomes is well-established and consistent in multiple independent populations, with evidence of increasing severity of outcomes with increasing risk allele dosage. The clinical validity for 9p21 and ischemic stroke or AAA is less well-studied and less certain. Clinical validity provides the clinical basis for a test, but evidence of clinical utility is needed to support clinical use.
 
Clinical utility is satisfied when the evidence shows that using a test to change medical management for at least some patients significantly improves outcomes. Palomaki et al. addressed clinical utility with a reclassification analysis, asking whether or not genotyping helped reclassify individuals more accurately than traditional risk factors according to their known outcomes, which was measured by calculating the net reclassification index (NRI) with data from 3 studies/4 data sets (Palomaki, 2010). For the 4 data sets, the proportions of cases reclassified by 9p21 genotype after initial classification by traditional risk factors were 0.5%, 0.7%, 2.5%, and -0.1%; of controls, 0.3%, 4.2%, -0.1%, and 0%; corresponding NRIs were 0.8%, 4.9%, 2.5%, and -0.2%; none of the NRIs were statistically significant. In addition, the study showing the largest NRI achieved most of the risk reclassification because of reduced risk in individuals without events, which would have less chance of improving outcomes. Moreover, in two individual studies the net reclassification index actually worsened when 9p21 risk alleles were added to algorithms that also included family history as a CAD risk factor (Paynter, 2009) (Talmud, 2008).
 
Studies have also used the OR associated with an individual’s 9p21 genotype to modify a risk assessment based on traditional risk factors. For example, based on the results of Palomaki et al. an individual with a 10-year CHD risk of 10% based on traditional risk factors who has 2 9p21 at-risk alleles would have their risk estimate increased to about 14% (10% x 1.2 x.1.2) compared to an individual with no at-risk alleles (Palomaki, 2010). Davies et al. however, found that the addition of 9p21 to traditional risk factors was not significant as measured by area under the curve (AUC=0.8013 with traditional risk factors alone versus 0.8044 with traditional risk factors plus 9p21, p=0.097) (Davies, 2010). Other similar attempts to add 9p21 alone as a risk factor have not demonstrated significance in addition to traditional risk factors (Paynter, 2009) (Talmud, 2008) (Brautbar, 2009).  An improved risk calculation, if shown, would be an intermediate outcome. The expectation is that improved risk assessment might influence patient and provider decisions about preventive interventions and behavioral change. However, as Palomaki et al. note, only 37% of U.S. physicians reported regular use of a heart disease risk score (Sposito, 2009) and the evidence that such risk scores translate into net clinical benefits is minimal (Sheridan, 2008). Thus, the clinical utility of 9p21 genotyping cannot be assumed even if risk assessment is improved.
 
The EGAPP Working Group Published a Recommendation on “genomic profiling to assess cardiovascular risk to improve cardiovascular health” which included a recommendation on 9p21 profiling alone based on Palomaki et al.  In general, the EWG found “… insufficient evidence to recommend testing for the 9p21 genetic variant or 57 other variants in 28 genes . . . to assess risk for cardiovascular disease (CVD) in the general population, specifically heart disease and stroke. The EWG found that the magnitude of net health benefit from use of any of these tests alone or in combination is negligible. The EWG discourages clinical use unless further evidence supports improved clinical outcomes.  Based on the available evidence, the overall certainty of net health benefit is deemed “Low.””
 
Summary
The association of 9p21 SNP alleles with CHD/CAD outcomes (clinical validity) is well-established and consistent in multiple independent populations, with evidence of increasing severity of outcomes with increasing risk allele dosage. The clinical validity for 9p21 and ischemic stroke or abdominal aortic aneurysm is less well-studied and less certain. Despite the clinical validity evidence for CHD/CAD outcomes, however, clinical utility, i.e. that the use of the test to change medical management improves CHD/CAD health outcomes, is not established. No studies have shown that 9p21 genotyping significantly improves risk reclassification after initial classification by traditional risk factors, nor have studies shown that addition of 9p21 genotyping to traditional risk factors improves risk assessment, an intermediate outcome.
 
2012 Update
A search of the MEDLINE database was conducted through September 2012.  There was no new information identified that would prompt a change in the coverage statement. The following is a summary of the key identified literature.
 
Several studies analyzing individual patient cohorts or case-control populations for association of 9p21 and CHD/CAD have been published since the Palomaki et al. review (Scheffold, 2011; Paynter, 2010; Ripatti, 2010; Dandona, 2010; Patel, 2010; Davies, 2010; Beckie, 2011; Beckie, 2011; Dutta, 2011;  Shiffman, 2011).
 
Beckie et al. studied the allelic frequencies and haplotype structure of genetic variants on chromosome 9p21 in a cohort of black and white women with early-onset CHD (Beckie, 2011; Beckie, 2011).  The authors report interethnic diversity in the SNP risk alleles and the haplotype structure of chromosome 9p21 SNP variants, suggesting that different variants may influence CHD in whites and blacks. Shiffman also reported no association of rs10757274 and incident MI in African American men (N=228) and women (N=405) aged >65. 2 (Shiffman, 2011).
 
Wang et al. studied CAD in a Chinese Han cohort with and without type 2 diabetes (Wang, 2011). An adjusted (gender, hypertension, hyperlipidemia, smoking) analysis of the homozygous risk genotype for rs1333049 showed an increased risk of early-onset CAD among diabetic (OR: 2.367, 95% CI: 1.258–4.453, P=0.008), but not among non-diabetic patients (OR: 1.632, 95% CI: 0.995–2.654, P=0.057).
 
Dutta et al. studied CAD mortality at older ages in association with 9p21 variants, reporting a positive association with mortality but no significant association with deaths due to stroke (HR: 1.07; 95% CI: 0.81–1.41; P=0.63) (Dutta, 2011).
 
A few studies have explored the association of 9p21 variants with a variety of other conditions such as peripheral arterial disease, (Murabito, 2012) coronary artery calcification, (O’Donnell, 2011) and polypoidal choroidal vasculopathy (characterized by aneurismal dilations at the border of the choroidal vascular network) (Zhang, 2011).  While all studies reported positive associations, the strength of the associations was modest and none suggested clinical use.
 
2013 Update
A literature search was conducted using MEDLINE database through September 2013. There wss no new information identified that would prompt a change in the coverage statement. The following is a summary of the key identified literature.
 
Two meta-analyses were identified. Zhou et al. conducted a meta-analysis of 7 case-control studies (n=7,123 total) and found associations between early-onset CAD and rs2383207 (OR: 0.79, 95% CI: 0.71-0.88, p<0.0001), rs10757278 (OR: 1.28, 95% CI: 1.15-1.42, p<0.00001), rs10757274 (OR: 1.17, 95% CI: 1.08-1.33, p=0.02), and rs2383206 (OR: 1.17, 95% CI: 1.10-1.25, p<0.00001) (Zhou, 2012). In a meta-analysis of 21 studies that included patients with information on CAD, MI status and 9p21 genotype (n=33,673), Chan et al. also found associations with CAD and the 9p21 locus and reported an OR of 1.15 (95% CI: 1.04 to 1.26) for heterozygous carriers and an OR of 1.23 (95% CI: 1.08 to 1.39) for homozygous carriers. However, when underlying CAD was present in both case subjects (n=17,791) and control subjects (n=15,882), the prevalence of MI was not significantly associated with the 9p21 risk allele (OR: 0.99, 95% CI: 0.95 to 1.03) (Chan, 2013).
 
Ongoing Clinical Trials
A search of online ClinicalTrials.gov registry in March 2013 identified 2 small pilot randomized trials addressing 9p21 genetic risk information. The impact of incorporating 9p21 genetic risk information into coronary heart disease counseling will be evaluated in NCT01766271. In NCT01658137, investigators will examine whether a high fruit and vegetable diet will interact with the 9p21 risk allele to alter the risk of myocardial infarction.
 
Summary
A number of highly correlated single nucleotide polymorphisms (SNPs) found in the chromosome 9 region p21 locus (9p21) have been associated with coronary artery/heart disease (CAD/CHD), intracranial aneurysms, and abdominal aortic aneurysms. Genotyping for 9p21 SNPs may identify patients who are at increased risk for these conditions or their manifestations. However, no studies have shown that 9p21 genotyping significantly improves risk reclassification after initial classification by traditional risk factors, nor have studies shown that addition of 9p21 genotyping to traditional risk factors improves risk assessment.
   
2014 Update
A literature search conducted through March 2014 did not reveal any new information that would prompt a change in the coverage statement. The key identified literature is summarized below.
 
Analytic Validity
 
A literature search conducted through March 2014 did not reveal any new information that would prompt a change in the coverage statement. The key identified literature is summarized below.Figure 1
 
Published literature describing the development of the Centaurus Assay reported 100% concordance with a gold standard (Kutyavin, 2006). Real time PCR based methods are generally considered to have high accuracy.
 
9p21 Polymorphisms and Coronary Heart Disease
 
Zhou et al. conducted a meta-analysis of 7 case-control studies (n=7,123 total) and found associations between early-onset CAD and rs2383207 (OR: 0.79, 95% CI: 0.71-0.88, p<0.0001), rs10757278 (OR: 1.28, 95% CI: 1.15-1.42, p<0.00001), rs10757274 (OR: 1.17, 95% CI: 1.08-1.33, p=0.02), and rs2383206 (OR: 1.17, 95% CI: 1.10-1.25, p<0.00001) (Zhou, 2012). In a meta-analysis of 21 studies that included patients with information on CAD, MI status and 9p21 genotype (n=33,673), Chan et al. also found associations with CAD and the 9p21 locus and reported an OR of 1.15 (95% CI: 1.04 to 1.26) for heterozygous carriers and an OR of 1.23 (95% CI: 1.08 to 1.39) for homozygous carriers. However, when underlying CAD was present in both case subjects (n=17,791) and control subjects (n=15,882), the prevalence of MI was not significantly associated with the 9p21 risk allele (OR: 0.99, 95% CI: 0.95 to 1.03) (Chan, 2013). In a meta-analysis of 21 case-control studies evaluating the association between 9p21 SNPs and CHD in an East Asian population, including 25,945 cases and 31,777 controls, Dong et al. found a significant association between the allele rs1333049 and CHD (OR 1.30, 95% CI 1.25-1.35, P<0.001) (Dong, 2013).
 
 Figure 1
Individual Studies: 9p21 Allele Dosage and Disease Severity, Progression, and Risk of Death. In a retrospective analysis of a cohort of 589 patients who underwent percutaneous coronary intervention for ST-elevation myocardial infarction, Szpacowicz et al. evaluated the association of the 9p21 SNPs rs1333049, rs10757278, and rs4977574 with 5-year all-cause mortality (Szpakowicz, 2013). In the cohort as a whole, there was no significant association between genotype and mortality. However, among the subgroup of 238 patients with high risk of death at 6 months-post admission (GRACE risk score 155), heterozygotes and high-risk homozygotes had significantly higher 5-year mortality than low-risk homozygotes (32.4% vs 12.3%, P=0.008, adjusted for Bonferroni’s correction).
 
9p21 Polymorphisms and Ischemic Stroke
 
Chou et al. conducted a retrospective analysis of neuropathology and genotyping on 755 deceased participants from two longitudinal cohort studies on memory and aging (Chou, 2013). The authors evaluated the association between macro- and microscopic infarcts on neuropathology and 74 SNPs associated with well-established ischemic stroke risk factors and those previously found to be associated with clinical stroke in GWAS. A 9p21 SNP at the CDKN2A/B locus (rs2383207) was significantly associated with the presence of macroscopic infarct on pathology (OR 1.26; 95% CI 1.02-1.55, P=0.0314).
 
Dichgans et al (Dichgans, 2014) analyzed data from the CARDIOGRAM/C4D consortium study described above (Schunkert, 2011; Preuss, 2010) in conjunction with data from the METASTROKE consortium (Traylor, 2012) to evaluate whether CAD and ischemic stroke share genetic risk in respect to common genetic variants. The authors found that the 9p21 locus was significantly associated with both CAD and the phenotype of large artery stroke (PLAS =3.85 x 10-6; Spearman’s rho coefficient for large artery stroke/CAS = 0.85, P=2.9E-35).
 
9p21 Polymorphisms and Aneurysms
 
The 9p21 locus has been associated with risk of both intracranial and abdominal aortic aneurysms. In 2013, Alg et al. reported results from a systematic review and meta-analysis of all genetic association studies of sporadic intracranial aneurysm to identify genetic risk factors for intracranial aneurysm (Alg, 2013). The authors included 66 cohort or case-control studies of intracranial aneurysms that examined a total of 41 SNPs, not limited to the 9p21 locus, in 29 genes. Among polymorphisms with the strongest associations with intracranial aneurysm were the 9p21 SNPs rs10757278 (odds ratio [OR] 1.29, 95% confidence interval [CI] 1.21-1.38) and rs1333040 (OR 1.24; 95% CI 1.20–1.29).
 
Association of 9p21 with Other Conditions
 
A few studies have explored the association of 9p21 variants with a variety of other conditions such as peripheral arterial disease, (Murabito, 2012) coronary artery calcification, (O’Donnell, 2011), aortic calcification (van Setten, 2013, polypoidal choroidal vasculopathy (characterized by aneurismal dilations at the border of the choroidal vascular network), (Zhang, 2011) and arterial stiffness in hypertensive individuals (Cesana, 2013). In contrast, Folsom et al. found no association between SNPs at the 9p21 locus with arterial elasticity and retinal microvascular diameter (Folsom, 2013).
 
While some studies reported positive associations, the strength of the associations was modest and none suggested clinical use.
In summary the clinical validity of 9p21 with CHD/CAD outcomes is well-established and consistent in multiple independent populations, with evidence of increasing severity of outcomes with increasing risk allele dosage. The magnitude of increased risk is modest, with odds ratios for cardiovascular disease generally in the 1-2 range. The clinical validity for 9p21 and ischemic stroke or AAA is less well-studied and less certain.
 
Clinical Utility of 9p21 and Coronary Heart Disease
 
Gransbo et al. evaluated the incremental impact of a 9p21 SNP (rs497757) on CVD risk prediction (Gransbo, 2013). The authors used data from the Malmo Diet and Cancer study, a prospective, population-based cohort study that included 28,449 individuals, with the primary outcome of incident CVD. The net reclassification index (NRI) was calculated when the presence of the rs4977574 SNP was added to a prediction model that used traditional risk factors (age, sex, hypertension, lipid-lowering therapy, diabetes, smoking, and body mass index). While there was a significant association between the rs4977574 SNP and incident CVD, the addition of the 9p21 genotype did little to improve risk prediction in additive multivariate models. Although statistically significant, the NRI was small (1.2%, P=0.043).
 
Clinical Utility of 9p21 and Other Cardiovascular Disease
 
Downing et al. evaluated the impact of adding 9p21 polymorphism (rs10757269) in a risk-factor-based model predicting peripheral artery disease (Downing, 2014). Among 393 subjects in the prospective Genetic Determinants of Peripheral Artery Disease study who met study inclusion criteria, the rs10757269 allele was associated with the presence of peripheral artery disease (defined as ankle–brachial index < 0.9) after controlling for traditional cardiovascular risk factors and other biomarkers (OR 1.92; 95% CI, 1.29–2.85). The addition of 9p21 genotype to a previously-validated peripheral artery disease risk model (including age, sex, race, smoking history, body mass index, hypertension stage, diabetes status, and history of cardiovascular disease, congestion heart failure, and CAD) lead to improved risk classification (net reclassification index 33.5%, P=0.001).
 
In summary the clinical utility of 9p21 mutation testing has not been established. The contribution of 9p21 to overall cardiovascular risk, above that of traditional risk factors, is small and not likely to be clinically important. Studies of risk reclassification do not report that 9p21 testing results in substantial numbers of patients being reclassified to clinically relevant categories.
 
2015 Update
A literature search conducted through March 2015 did not reveal any new information that would prompt a change in the coverage statement. The key identified literature is summarized below.
 
Szpacowicz and colleagues evaluated the association of the 9p21 SNPs rs1333049, rs10757278, and rs4977574 with 5-year all-cause mortality in a cohort of 589 patients who underwent percutaneous coronary intervention for ST-elevation MI (Szpacowicz, 2014). Results were published in 2014, after retraction of a previous publication due to reporting of an incorrect allele being associated with mortality. In the cohort as a whole, there was no significant association between genotype and mortality. Among the subgroup of 238 patients with high risk of death (GRACE risk score 155), the heterozygotes or homozygotes with a high risk genotype had higher risk of mortality (for rs10757278: HR 2.2, 95% CI 1.15 to 4.2; for rs4977574: HR 2.7, 95% Ci 1.3 to 5.4; for rs1333049, HR 2.3, 95% Ci 1.2 to 4.5).
 
In 2014 Ni and colleagues reported results of a meta-analysis of genetic association studies between 9p21 polymorphisms and ischemic stroke, which included 21 studies with 34,128 patients and 153,428 controls (Ni, 2014). The rs10757278 polymorphism was significantly associated with increased overall ischemic stroke risk (per-allele OR for ischemic stroke: 1.11; 95% CI 1.07 to 1.15; P<10-5) and increased large-vessel stroke risk (per-allele OR for large vessel stroke: 1.15; 95% CI 1.10 to 1.19), but not with small vessel, cardioembolic, or other types of stroke.
 
Individual Studies
Since the publication of the previous meta-analyses, a number of individual studies have evaluated the association between 9p21 polymorphisms and ischemic stroke. For example, in a retrospective study evaluating the association between macro- and microscopic infarcts on neuropathology, Chou et al reported that the 9p21 SNP at the CDKN2A/B locus (rs2383207) was significantly associated with the presence of macroscopic infarct on pathology (OR=1.26; 95% CI, 1.02 to 1.55; p=0.031).
 
Other studies have focused on particular population subsets, with mixed findings. Yue and colleagues reported significant associations between the SNPs rs2383207, rs3731245, and rs1537378 were significantly associated with cerebral infarction in a Chinese Han population (ORs 1.18, 95 % CI 1.01 to 1.37; OR 1.29, 95% CI 1.06 to 1.56; and OR 1.30, 95% CI 1.05 to 1.60, respectively) (Yue, 2014).
 
Wei and colleagues reported slightly higher risk of AAA associated with homozygosity for the rs10757278 and rs1333040 risk alleles in a Chinese Han population, after controlling for other AAA risk factors (OR 2.31, 95% CI 1.22 to 4.36; and OR 2.14, 95% CI 1.13 to 4.05, respectively) (Wei, 2014).
 
In summary the clinical utility of 9p21 mutation testing has not been established. The contribution of 9p21 genotyping to overall cardiovascular risk assessment, above that of traditional risk factors, is small and not likely to be clinically important. Studies of risk reclassification do not report that 9p21 testing results in substantial numbers of patients being reclassified to clinically relevant categories. No studies were identified that evaluate whether the use of 9p21 genotyping is associated with changes in patient management, improvements in clinical outcomes, or both.
 
The association of single nucleotide polymorphisms (SNPs) at the 9p21 locus with coronary artery/heart disease (CAD/CHD) incidence and outcomes (clinical validity) is well-established and consistent in multiple independent populations, with evidence of increasing severity of outcomes with increasing risk allele dosage. The clinical validity for the association of 9p21 polymorphisms and with ischemic stroke, aneurysms, or other vascular disorders is less well-studied and less certain evidence that 9p21 polymorphisms are associated with for CAD/CHD outcomes, the clinical utility of 9p21 genotyping has not been established. Studies have not conclusively demonstrated have shown that 9p21 genotyping significantly improves risk reclassification after initial classification by traditional risk factors that the addition of 9p21 genotyping to traditional risk factors improves risk assessment. No studies were identified that evaluate whether the use of 9p21 genotyping is associated with changes in patient management, improvements in clinical outcomes, or both. Thus, 9p21 genotyping for all applications is investigational.
 
Practice Guidelines and Position Statements
In 2013, the American College of Cardiology (ACC) Foundation and the American Heart Association (AHA) Task Force on Practice Guidelines issued guidelines on the assessment of cardiovascular risk, which did not address assessment of 9p21 polymorphisms (Goff, 2013).
 
2016 Update
A literature search conducted through March 2016 did not reveal any new information that would prompt a change in the coverage statement.
 
2017 Update
A literature review conducted using the MEDLINE database did not reveal any new literature that would prompt a change in the coverage statement.
 
2018 Update
Annual policy review completed with a literature search using the MEDLINE database through March 2018. No new literature was identified that would prompt a change in the coverage statement.
 
2019 Update
A literature search was conducted through March 2019.  There was no new information identified that would prompt a change in the coverage statement.  
 
2020 Update
A literature search was conducted through March 2020.  There was no new information identified that would prompt a change in the coverage statement.  
 
2021 Update
Annual policy review completed with a literature search using the MEDLINE database through March 2021. No new literature was identified that would prompt a change in the coverage statement.
 
2022 Update
Annual policy review completed with a literature search using the MEDLINE database through March 2022. No new literature was identified that would prompt a change in the coverage statement.

CPT/HCPCS:
81479Unlisted molecular pathology procedure
84999Unlisted chemistry procedure

References: Alg VS, Sofat R, Houlden H et al.(2013) Genetic risk factors for intracranial aneurysms: a meta-analysis in more than 116,000 individuals. Neurology 2013; 80(23):2154-65.

Anderson CD, Biffi A, Rost NS et al.(2010) Chromosome 9p21 in ischemic stroke: population structure and meta-analysis. Stroke 2010; 41(6):1123-31.

Beckie TM, Beckstead JW, Groer MW.(2011) The association between variants on chromosome 9p21 and inflammatory biomarkers in ethnically diverse women with coronary heart disease: a pilot study. Biol Res Nurs 2011; 13(3):306-19.

Beckie TM, Groer MW, Beckstead JW.(2011) The relationship between polymorphisms on chromosome 9p21 and age of onset of coronary heart disease in black and white women. Genet Test Mol Biomarkers 2011; 15(6):435-42.

Bendjilali N, Nelson J, Weinsheimer S, et al.(2014) Common variants on 9p21.3 are associated with brain arteriovenous malformations with accompanying arterial aneurysms. J Neurol Neurosurg Psychiatry. Nov 2014;85(11):1280-1283. PMID 24777168

Biros E, Cooper M, Palmer LJ et al.(2010) Association of an allele on chromosome 9 and abdominal aortic aneurysm. Atherosclerosis 2010; 212(2):539-42.

Bown MJ, Braund PS, Thompson J et al.(2008) Association between the coronary artery disease risk locus on chromosome 9p21.3 and abdominal aortic aneurysm. Circ Cardiovasc Genet 2008; 1(1):39-42.

Brautbar A, Ballantyne CM, Lawson K et al.(2009) Impact of adding a single allele in the 9p21 locus to traditional risk factors on reclassification of coronary heart disease risk and implications for lipid-modifying therapy in the Atherosclerosis Risk in Communities study. Circ Cardiovasc Genet 2009; 2(3):279-85.

Cesana F, Nava S, Menni C et al.(2013) Does the 9p region affect arterial stiffness? Results from a cohort of hypertensive individuals. Blood Press 2013; 22(5):302-6.

Chan K, Patel RS, Newcombe P et al.(2013) Association between the chromosome 9p21 locus and angiographic coronary artery disease burden: a collaborative meta-analysis. J Am Coll Cardiol 2013; 61(9):957-70.

Chou SH, Shulman JM, Keenan BT et al.(2013) Genetic susceptibility for ischemic infarction and arteriolosclerosis based on neuropathologic evaluations. Cerebrovasc Dis 2013; 36(3):181-8.

Coronary Artery Disease (C4D) Genetics Consortium.(2011) A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease. Nat Genet 2011; 43(4):339-44.

Dandona S, Stewart AF, Chen L et al.(2010) Gene dosage of the common variant 9p21 predicts severity of coronary artery disease. J Am Coll Cardiol 2010; 56(6):479-86.

Dandona S, Stewart AF, Chen L et al.(2010) Gene dosage of the common variant 9p21 predicts severity of coronary artery disease. J Am Coll Cardiol 2010; 56(6):479-86.

Davies RW, Dandona S, Stewart AF et al.(2010) Improved prediction of cardiovascular disease based on a panel of single nucleotide polymorphisms identified through genome-wide association studies. Circ Cardiovasc Genet 2010; 3(5):468-74.

Davies RW, Dandona S, Stewart AF et al.(2010) Improved prediction of cardiovascular disease based on a panel of single nucleotide polymorphisms identified through genome-wide association studies. Circ Cardiovasc Genet 2010; 3(5):468-74.

Dichgans M, Malik R, Konig IR et al.(2014) Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. Stroke 2014; 45(1):24-36.

Dong L, Wang H, Wang DW et al.(2013) Association of chromosome 9p21 genetic variants with risk of coronary heart disease in the East Asian population: a meta-analysis. Ann Hum Genet 2013; 77(3):183-90.

Downing KP, Nead KT, Kojima Y et al.(2014) The combination of 9p21.3 genotype and biomarker profile improves a peripheral artery disease risk prediction model. Vasc Med 2014; 19(1):3-8.

Dutta A, Henley W, Lang IA et al.(2011) The coronary artery disease-associated 9p21 variant and later life 20-year survival to cohort extinction. Circ Cardiovasc Genet 2011; 4(5):542-8.

Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. Recommendations from the EGAPP Working Group:(2010) genomic profiling to assess cardiovascular risk to improve cardiovascular health. Genet Med 2010; 12(12):839-43.

Folsom AR, Pankow JS, Li X et al.(2013) No association of 9p21 with arterial elasticity and retinal microvascular findings. Atherosclerosis 2013; 230(2):301-3.

Goff DC, Jr., Lloyd-Jones DM, Bennett G, et al.(2014) 2013 ACC/AHA guideline on the assessment of cardiovascular risk: a report of the American College of Cardiology/American Heart Association Task Force on Practice Guidelines. J Am Coll Cardiol. Jul 1 2014;63(25 Pt B):2935-2959. PMID 24239921

Gransbo K, Almgren P, Sjogren M et al.(2013) Chromosome 9p21 genetic variation explains 13% of cardiovascular disease incidence but does not improve risk prediction. J Intern Med 2013; 274(3):233-40.

Harismendy O, Notani D, Song X et al.(2011) 9p21 DNA variants associated with coronary artery disease impair interferon-gamma signalling response. Nature 2011; 470(7333):264-8.

Helgadottir A, Thorleifsson G, Magnusson KP et al.(2008) The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm. Nat Genet 2008; 40(2):217-24.

Helgadottir A, Thorleifsson G, Manolescu A et al.(2007) A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 2007; 316(5830):1491-3.

Johansen CT, Lanktree MB, Hegele RA.(2010) Translating genomic analyses into improved management of coronary artery disease. Future Cardiol 2010; 6(4):507-21.

Kutyavin IV, Milesi D, Belousov Y et al.(2006) novel endonuclease IV post-PCR genotyping system. Nucleic Acids Res 2006; 34(19):e128.

Lederle FA, Johnson GR, Wilson SE et al.(2000) The aneurysm detection and management study screening program: validation cohort and final results. Arch Intern Med 2000; 160(10):1425-30.

Lian J, Ba Y, Dai D, et al.(2014) A replication study and a meta-analysis of the association between the CDKN2A rs1333049 polymorphism and coronary heart disease. J Atheroscler Thromb. 2014;21(11):1109-1120. PMID 24930384

McPherson R, Pertsemlidis A, Kavaslar N et al.(2007) A common allele on chromosome 9 associated with coronary heart disease. Science 2007; 316(5830):1488-91.

Murabito JM, White CC, Kavousi M et al.(2012) Association between chromosome 9p21 variants and the ankle-brachial index identified by a meta-analysis of 21 genome-wide association studies. Circ Cardiovasc Genet 2012; 5(1):100.

Ni X, Zhang J.(2014) Association between 9p21 genomic markers and ischemic stroke risk: evidence based on 21 studies. PLoS One. 2014;9(3):e90255. PMID 24625579

O'Donnell CJ, Kavousi M, Smith AV et al.(2011) Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction. Circulation 2011; 124(25):2855-64.

Olsson S, Jood K, Blomstrand C et al.(2011) Genetic variation on chromosome 9p21 shows association with the ischaemic stroke subtype large-vessel disease in a Swedish sample aged
Palomaki GE, Melillo S, Bradley LA.(2010) Association between 9p21 genomic markers and heart disease: a meta-analysis. JAMA 2010; 303(7):648-56.

Patel RS, Su S, Neeland IJ et al.(2010) The chromosome 9p21 risk locus is associated with angiographic severity and progression of coronary artery disease. Eur Heart J 2010; 31(24):3017-23.

Patel RS, Su S, Neeland IJ et al.(2010) The chromosome 9p21 risk locus is associated with angiographic severity and progression of coronary artery disease. Eur Heart J 2010; 31(24):3017-23.

Paynter NP, Chasman DI, Buring JE et al.(2009) Cardiovascular disease risk prediction with and without knowledge of genetic variation at chromosome 9p21.3. Ann Intern Med 2009; 150(2):65-72.

Paynter NP, Chasman DI, Pare G et al.(2010) Association between a literature-based genetic risk score and cardiovascular events in women. JAMA 2010; 303(7):631-7.

Paynter NP, Chasman DI, Pare G et al.(2010) Association between a literature-based genetic risk score and cardiovascular events in women. JAMA 2010; 303(7):631-7.

Preuss M, Konig IR, Thompson JR et al.(2010) Design of the Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Study: A Genome-wide association meta-analysis involving more than 22 000 cases and 60 000 controls. Circ Cardiovasc Genet 2010; 3(5):475-83.

Ripatti S, Tikkanen E, Orho-Melander M et al.(2010) A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses. Lancet 2010; 376(9750):1393-400.

Ripatti S, Tikkanen E, Orho-Melander M et al.(2010) A multilocus genetic risk score for coronary heart disease: case-control and prospective cohort analyses. Lancet 2010; 376(9750):1393-400.

Samani NJ, Erdmann J, Hall AS et al.(2007) Genomewide association analysis of coronary artery disease. N Engl J Med 2007; 357(5):443-53.

Scheffold T, Kullmann S, Huge A et al.(2011) Six sequence variants on chromosome 9p21.3 are associated with a positive family history of myocardial infarction: a multicenter registry. BMC Cardiovasc Disord 2011; 11:9.

Scheffold T, Kullmann S, Huge A et al.(2011) Six sequence variants on chromosome 9p21.3 are associated with a positive family history of myocardial infarction: a multicenter registry. BMC Cardiovasc Disord 2011; 11:9.

Schunkert H, Konig IR, Kathiresan S et al.(2011) Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. Nat Genet 2011; 43(4):333-8.

Sheridan SL, Crespo E.(2008) Does the routine use of global coronary heart disease risk scores translate into clinical benefits or harms? A systematic review of the literature. BMC Health Serv Res 2008; 8:60.

Shiffman D, O'Meara ES, Rowland CM et al.(2011) The contribution of a 9p21.3 variant, a KIF6 variant, and C-reactive protein to predicting risk of myocardial infarction in a prospective study. BMC Cardiovasc Disord 2011; 11:10.

Sposito AC, Ramires JA, Jukema JW et al.(2009) Physicians' attitudes and adherence to use of risk scores for primary prevention of cardiovascular disease: cross-sectional survey in three world regions. Curr Med Res Opin 2009; 25(5):1171-8.

Sturiale CL, Fontanella MM, Gatto I, et al.(2014) Association between polymorphisms rs1333040 and rs7865618 of chromosome 9p21 and sporadic brain arteriovenous malformations. Cerebrovasc Dis. 2014;37(4):290-295. PMID 24820060

Szpakowicz A, Kiliszek M, Pepinski W, et al.(2014) Polymorphism of 9p21.3 locus is associated with 5-year survival in high-risk patients with myocardial infarction. PLoS One. 2014;9(8):e104635. PMID 25105296

Szpakowicz A, Pepinski W, Waszkiewicz E et al.(2013) Polymorphism of 9p21.3 locus is associated with 5-year survival in high-risk patients with myocardial infarction. PLoS One 2013; 8(9):e72333.

Talmud PJ, Cooper JA, Palmen J et al.(2008) Chromosome 9p21.3 coronary heart disease locus genotype and prospective risk of CHD in healthy middle-aged men. Clin Chem 2008; 54(3):467-74.

Teutsch SM, Bradley LA, Palomaki GE et al.(2009) The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Initiative: methods of the EGAPP Working Group. Genet Med 2009; 11(1):3-14.

Thompson AR, Golledge J, Cooper JA et al.(2009) Sequence variant on 9p21 is associated with the presence of abdominal aortic aneurysm disease but does not have an impact on aneurysmal expansion. Eur J Hum Genet 2009; 17(3):391-4.

Traylor M, Farrall M, Holliday EG et al.(2012) Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE collaboration): a meta-analysis of genome-wide association studies. Lancet Neurol 2012; 11(11):951-62.

van Setten J, Isgum I, Smolonska J et al.(2013) Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction. Atherosclerosis 2013; 228(2):400-5.

Wang W, Peng WH, Lu L et al.(2011) Polymorphism on chromosome 9p21.3 contributes to early-onset and severity of coronary artery disease in non-diabetic and type 2 diabetic patients. Chin Med J 2011; 124(1):66-71.

Wei Y, Xiong J, Zuo S, et al.(2014) Association of polymorphisms on chromosome 9p21.3 region with increased susceptibility of abdominal aortic aneurysm in a Chinese Han population. J Vasc Surg. Apr 2014;59(4):879-885. PMID 24365123

Wellcome Trust Case Control Consortium:(2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447(7145):661-78.

Yue X, Tian L, Fan X, et al.(2015) Chromosome 9p21.3 Variants Are Associated with Cerebral Infarction in Chinese Population. J Mol Neurosci. Feb 11 2015. PMID 25665551

Zhang X, Wen F, Zuo C et al.(2011) Association of genetic variation on chromosome 9p21 with polypoidal choroidal vasculopathy and neovascular age-related macular degeneration. Investig Ophthalmol Vis Sci 2011; 52(11):8063-7.

Zhou LT, Qin L, Zheng DC et al.(2012) Meta-analysis of genetic association of chromosome 9p21 with early-onset coronary artery disease. Gene 2012; 510(2):185-8.


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