From: The association of 9p21-3 locus with coronary atherosclerosis: a systematic review and meta-analysis
Study ID | Genotyping method | SNP: and base position | Minor allele frequency | Linkage disequilibrium (LD) (reported as D’ or r2) | Population (age/(%)male/ethnicity) | Baseline diagnosis | Outcome/prognostic marker (1) | Outcome/prognostic marker (2) | Outcome/prognostic marker (3) | Comments |
---|---|---|---|---|---|---|---|---|---|---|
Anderson, [14] | with 5′ exonuclease (Taqman) chemistry on the ABI Prism 7000 | rs2383206 | 0.48 |  | 1759 (59/64%/mixed race with 86% white) | CAD | No. diseased vessels | baseline Duke index |  | Prospective cohort |
Chen, [15] | fluorogenic 5′ nucleotidase (Taqman) assays using an ABI PRISM® 7900 HT Real-Time PCR instrument | rs2383206 (chromosomal position: 22,105,026), rs2383207 (chromosomal position: 22,105,959), rs10757278 (chromosomal position: 22,114,477), rs1333049 (chromosomal position: 22,115,503) | rs2383206 = 0.15 | D’ rs2383206 – 2383207 = 0.99 | 212 (48/58%/Chinese) | CAD | No. diseased vessels |  |  | Case control |
D’rs2383206-10757278 = 1.0 | ||||||||||
D’rs2383206 – rs1333049 = 0.99 | ||||||||||
Chen, [16] | TaqMan allelic discrimination assays | rs7865618: 22021005 | 0.38 | LD of rs7865618, rs1537378, rs1333040 with rs1333049 0.81 ≤ r2 ≤ 0.97 | 322 (59/84%/white) | CAD | ∆MLD | no. of new lesions |  | Case control |
Hoppman, [17] | TaqMan allelic discrimination assays | rs7865618: 22021005 | 0.38 | LD of rs7865618, rs1537378, rs1333040 with rs1333049 0.81 ≤ r2 ≤ 0.97 | 2028 (−−/−−%/white) | CAD/ACS | All-cause mortality | Recurrent MI | revascularization | Prospective cohort |
rs1537378: 22051614 | 0.35 | |||||||||
rs1333040: 22073404 | 0.40 | |||||||||
rs1333049: 22115503 | 0.49 | |||||||||
Peng, [18] | TaqMan single nucleotide polymorphism | rs1333049 | 0.24 | rs10757274 and rs1333049 had strong LD (r2 = 0.92) | 520 (64/78.7%/Chinese) | ACS | All-cause mortality | Recurrent MI | No. diseased vessels | Case control |
Newton-Cheh, [19] | Sequenom platform (San Diego, Calif), which resolves allele-specific single-base extension products using mass spectrometry (MALDI-TOF) | rs10757274 backup: rs2383207 | Case: 0.54 Control: 0.50 | Rs10757274 and rs2383207 are in strong linkage disequilibrium (r 2 = 0.87). | 466 (−−/--%/whites) | CAD | SCD |  |  | Retrospective case–control study of SCD†. Subgroup analysis compared 124 SCD cases with 342 controls. Both cases and controls had CAD |
Ellis, (1) [20] (CDCS) | allelespecific TaqMan genotyping probes | rs1333049 | GG: 0.22 | Â | 860 (67/69.2%/whites) | ACS | All-cause mortality | Recurrent MI | Â | Cohort study |
Ellis, (2) [20] (PMI) | allelespecific TaqMan genotyping probes | rs1333049 | GG: 0.22 | Â | 607 (62/78.6%/whites) | ACS | All-cause mortality | Recurrent MI | Â | Cohort Study |
Buysschaert, [21] | iPLEX technology on a MassARRAY | rs1333049 | 0.25 | Â | 2942 (65/67.9%/whites) | ACS | Recurrent MI | Â | Â | Prospective cohort |
rs7044859 | ||||||||||
rs1292136 | ||||||||||
rs7865618 | ||||||||||
Compact Analyser (Sequenom Inc., CA, USA). The WTCCC controls: Affymetrix platform (Affymetrix Inc., CA, USA). | ||||||||||
Patel, [22] | Centaurus (Nanogen) platform | rs10757278 | 0.24 | Â | 2334 (63/67%/whites) | CAD/ACS | No. diseased vessels | baseline Gensini score | Â | Prospective cohort |
Muehlschlegel, [23] | Golden Gate assay with an Illumina Bead Station 500G system (Illumina) | rs10116277 | 0.18 |  | 846 (−−/--%/whites) | CAD | All-cause mortality |  |  | Prospective cohort |
Dandona, [24] | Affymetrix (Santa Clara, California) 500 K and 6.0 arrays | rs1333049 | 0.19 | rs9632884 was linkage disequilibrium with rs1333049 (r2 = 0.832). | 1714 (−−/--%/whites) | CAD/ACS | No. diseased vessels | baseline Duke index | baseline Gensini Score | case control |
Liu, [25] | Golden Gate assay with an Illumina Bead Station 500 G system (Illumina, San Diego, Calif) | rs10116277 |  |  | 846 (−−/--%/whites) | CAD | Recurrent MI |  |  | Prospective cohort |
rs6475606 | ||||||||||
rs2383207: chromosom | ||||||||||
e 9 | ||||||||||
positions 21,930,588 | ||||||||||
22,366,970 | ||||||||||
Wang, [26] | TaqMan SNP allelic discrimination by means of an ABI 7900HT (Applied Biosystems, Foster City, CA, USA) | rs1333049 |  |  | 430 (−−/--%/Chinese) | CAD | ∆MLD | no. new lesions |  | case control |
Ardissino, [27] | Matrixassisted laser desorption ionization time-of-flight mass spectrometry and a Sequenome MassARRAY platform (San Diego, California) | rs1333040 | Â | Â | 1508 (41/95%/Italian) | ACS | All-cause mortality | recurrent MI | revascularization | Prospective cohort |
Wang, [28] | TaqMan SNP allelic discrimination by means of an ABI 7900HT (Applied Biosystems, Foster City, CA, USA) | rs1333049: 9p21.3 | 0.25 | Â | 620 (67/51.2%/Chinese) | CAD | No. diseased vessels | baseline Gensini score | Â | Cross sectional |
Chan, [29] |  | rs1333049 |  |  | 332 (59/84%/whites) | CAD | ∆MLD | no. new lesions |  | Prospective cohort |
Dutta, [30] | Conventional Taqman PCR (probes and assays designed by Applied Biosystems; Foster City, CA) | rs1333049 | Â | Â | 478 (75/--%/whites) | CAD | All-cause mortality | Â | Â | Propective cohort |
Kozieradzka, [31] | TaqMan SNP Genotyping Assay using the ABI 7500 Real Time PC R System (Applied Biosystems) | rs1333049 | Â | Â | 582 (62/75%/--) | CAD | All-cause mortality | Â | Â | Cohort Study |
rs4977574 | ||||||||||
rs10757278 | ||||||||||
Gioli-Pereira, [32] | Submicroliter PCR-based assay on array tape that is a continuous plastic tape used in conjunction with a flexible configuration of dispensing, pipetting, sealing and detection modules manufactured by Douglas Global Array | rs10757274, rs2383206, rs10757278, rs1333049 | rs10757274: 0.51, | Â | 611 (60/84.9%/Brazilian) | CAD | All-cause mortality | No. diseased vessels | Â | Prospective cohort |
rs2383206: 0.59, | ||||||||||
rs10757278: 0.51, | ||||||||||
rs1333049: 0.48 | ||||||||||
Virani, (1) [33] | TaqMan assays | rs1333049, | CC: 0.27, | all 4 SNPs from our analyses (rs1333049, rs2383206, rs10757278, and rs10757274) have been shown to be in strong linkage disequilibrium (LD), | 2067 (63/74%/whites) | ACS | All-cause mortality | recurrent MI | revascularization | Prospective cohort |
CG: 0.50, | ||||||||||
rs2383206, | ||||||||||
GG: 0.23; | ||||||||||
CABG group: | ||||||||||
rs10757278, rs10757274 | ||||||||||
Virani, (2) [33] | TaqMan assays | rs1333049, | CC: 0.30, | all 4 SNPs from our analyses (rs1333049, rs2383206, rs10757278, and rs10757274) have been shown to be in strong linkage disequilibrium (LD), | 1176 (65/79%/whites) | CAD | All-cause mortality | recurrent MI | revascularization | Prospective cohort |
rs2383206, | ||||||||||
rs10757278, rs10757274 | CG: 0.50, | |||||||||
GG: 0.21; | ||||||||||
Lill, [34] | Â | rs2383206 | Â | Â | 452 (58/78%/--) | CAD | All-cause mortality | Â | Â | Cohort Study |