Table 1.
Assessment of the genotyping methodology in the included studies
| Methodology | Ivanovski et al. [ 34 ] | Donos et al. [ 35 ] | Bryington et al. [ 36 ] | Thalji et al. [ 37 ] |
|---|---|---|---|---|
| Tissue harvesting | Tissue attached to implant carefully removed with a curette, preexisting hard tissue discarded | Tissue attached to implant carefully removed with a curette and homogenized | Implants removed by reverse threading and homogenized; cell lysates isolated | Implants removed by reverse threading and homogenized; cell lysates isolated |
| Sample preparation | Total RNA isolation, purification, quantity/quality analysis and biotin-labeling | Total RNA isolation, purification, quantity/quality analysis and biotin-labeling | Total RNA isolation, quantification | Total RNA isolation, purification, quantity/quality analysis and biotin-labeling |
| Array technique | Microarray hybridization (Human WG-6 V3) | Microarray hybridization (Human WG-6 V3) | RT-PCR (custom RT-PCR array for osteogenesis genes; human inflammatory cytokines and receptors PCR array) | Microarray hybridization (Affymetrix Human Gene 1.1 ST) |
| Scanning, data preparation | Bead Station 500/Bead Studio v3 software, raw probe expression values extracted | Bead Station 500/ Bead Studio v3 software, raw probe expression values extracted | RT2 SYBR Green qPCR Master Mix/7500 Real-Time PCR system | Affymetrix Gene Chip Scanner |
| Processing | Noisy data discarded | Noisy data discarded | Normalization of osteogenesis and cytokine array | Unclear |
| Clustering | GO categories (DAVID tool) | GO categories (DAVID tool) | Osteogenesis genes; cytokine-related genes | GO categories (Gene Spring) |
| Statistical analysis | Gene Spring software | Gene Spring software | RT2 Profiler software | Gene Spring software |
| Comparisons | Pair-wise comparisons between three time points (4 vs. 7 days, 7 vs. 14 days, and 4 vs. 14 days) | Pair-wise comparisons at each time point (4, 7, and 14 days) between SLA and SLActive surfaces | T-test to evaluate differences between each implant surface per time point | Two-way ANOVAs to determine differences between implant surface type and time points; pair-wise comparisons of each implant surface independently at different time points (day 7 vs. day 3) |
GO, gene ontology; DAVID, Database for Annotation, Visualization and Integrated Discovery.