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Table 1 Assessment of the genotyping methodology in the included studies

From: Genomic analyses of early peri-implant bone healing in humans: a systematic review

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)
  1. GO, gene ontology; DAVID, Database for Annotation, Visualization and Integrated Discovery.