| Literature DB >> 20335276 |
Joshua C Denny1, Marylyn D Ritchie, Melissa A Basford, Jill M Pulley, Lisa Bastarache, Kristin Brown-Gentry, Deede Wang, Dan R Masys, Dan M Roden, Dana C Crawford.
Abstract
MOTIVATION: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for disease-gene associations. We propose a novel method to scan phenomic data for genetic associations using International Classification of Disease (ICD9) billing codes, which are available in most EMR systems. We have developed a code translation table to automatically define 776 different disease populations and their controls using prevalent ICD9 codes derived from EMR data. As a proof of concept of this algorithm, we genotyped the first 6005 European-Americans accrued into BioVU, Vanderbilt's DNA biobank, at five single nucleotide polymorphisms (SNPs) with previously reported disease associations: atrial fibrillation, Crohn's disease, carotid artery stenosis, coronary artery disease, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis. The PheWAS software generated cases and control populations across all ICD9 code groups for each of these five SNPs, and disease-SNP associations were analyzed. The primary outcome of this study was replication of seven previously known SNP-disease associations for these SNPs.Entities:
Mesh:
Year: 2010 PMID: 20335276 PMCID: PMC2859132 DOI: 10.1093/bioinformatics/btq126
Source DB: PubMed Journal: Bioinformatics ISSN: 1367-4803 Impact factor: 6.937
Demographics of those studied
| Attribute | Value, median (interquartile range) |
|---|---|
| Age | 57 (44–68) |
| Female (%) | 55.9 |
| Total fully specified ICD9 codes | 56 (23–134) |
| Distinct fully specified ICD9 codes | 23 (11–48) |
| Distinct ICD9 three-digit codes | 17 (9–32) |
| Distinct PheWAS code groups | 17 (8–32) |
| Years of follow-up (IQR) | 4 (2–9) |
Diseases previously associated with the five SNP studied and current PheWAS ORs
| SNP | Gene/region | Disease | Cases | Previous OR | PheWAS | PheWAS OR |
|---|---|---|---|---|---|---|
| rs3135388 | DRB1*1501 | MS | 89 | 1.99 | 2.77 × 10−6 | 2.24 (1.56–3.16) |
| SLE | 141 | 2.06 | 0.51 | 1.13 (0.79–1.58) | ||
| rs17234657 | Chr. 5 | CD | 200 | 1.54 | 0.00080 | 1.57 (1.19–2.04) |
| rs2200733 | Chr. 4q25 | AF and flutter | 606 | 1.75 | 0.14 | 1.15 (0.95–1.39) |
| rs1333049 | Chr. 9p21 | CAD | 1181 | 1.20–1.47 | 0.011 | 1.13 (1.03–1.23) |
| Carotid atherosclerosis | 333 | 1.46 | 0.82 | 0.98 (0.84–1.15) | ||
| rs6457620 | Chr. 6 | RA | 392 | 2.36 | 0.0002 | 1.35 (1.15–1.58) |
aHafler et al. (2007).
bPan et al. (2009).
cWellcome Trust Case Control Consortium., 2007.
dGudbjartsson et al. (2007).
eSamani et al. (2009); Wellcome Trust Case Control Consortium., 2007.
fYe et al. (2008).
gThe code group of RA also includes other inflammatory arthritides.
Fig. 1.Phenome-wide scan for association with rs3135388. MS is replicated from prior analyses. The dashed line represents the P = 0.05; the dotted line represents the Bonferroni correction.
Fig. 2.Phenome-wide scan for association for four additional SNPs with known disease-SNP associations. The boxed diseases represent associations replicated from prior GWAS analyses. The dashed line represents the P = 0.05; the dotted line represents the Bonferroni correction.
Potential SNP–disease associations discovered through PheWAS algorithm
| SNP | Disease/syndrome | OR | ||
|---|---|---|---|---|
| rs17234657 | Non-infectious gastroenteritis and colitis | 389 | 1.42 (1.16–1.73) | 5.3 × 10−4 |
| rs3135388 | Cancer of rectum and anus | 107 | 1.76 (1.24–2.45) | 8.2 × 10−4 |
| rs2200733 | Unspecified congenital anomalies | 44 | 2.56 (1.48–4.29) | 2.6 × 10−4 |
| rs17234657 | Autonomic nervous system disorder | 100 | 0.46 (0.24–0.82) | 8.9 × 10−3 |
| rs3135388 | Diabetes mellitus | 1238 | 0.82 (0.71–0.94) | 4.3 × 10−3 |
| rs3135388 | Benign neoplasm of other parts of digestive system | 585 | 1.33 (1.12–1.57) | 9.4 × 10−4 |
| rs2200733 | Aplastic anemia | 194 | 0.49 (0.30–0.77) | 2.0 × 10−3 |
| rs6457620 | Disorders of the pituitary gland | 101 | 1.52 (1.12–2.06) | 6.3 × 10−3 |
| rs3135388 | Benign neoplasm of respiratory and intrathoracic organs | 62 | 1.96 (1.24–3.02) | 2.1 × 10−3 |
| rs3135388 | Conduct disorders | 32 | 2.08 (1.10–3.74) | 1.0 × 10−2 |
| rs3135388 | Acute renal failure | 580 | 0.74 (0.61–0.90) | 2.8 × 10−3 |
| rs17234657 | Concussion | 70 | 1.85 (1.19–2.81) | 3.9 × 10−3 |
| rs3135388 | Erythematous conditions | 206 | 1.47 (1.13–1.90) | 3.3 × 10−3 |
| rs1333049 | Phlebitis and thrombophlebitis | 188 | 1.35 (1.09–1.68) | 4.7 × 10−3 |
| rs17234657 | Chronic liver disease and cirrhosis | 421 | 0.73 (0.57–0.92) | 8.9 × 10−3 |
| RS2200733 | Anaphylactic shock and angioedema | 244 | 1.44 (1.10–1.87) | 7.0 × 10−3 |
| RS1333049 | Mononeuritis of upper limb and mononeuritis multiplex | 243 | 1.30 (1.08–1.57) | 4.9 × 10−3 |
| RS3135388 | Pulmonary heart disease | 350 | 0.71 (0.54–0.91) | 6.6 × 10−3 |
| RS2200733 | Adjustment reaction | 347 | 0.68 (0.50–0.91) | 1.0 × 10−3 |