Table 1 Assessment of the genotyping methodology in the included studies : Genomic analyses of early peri-implant bone healing in humans: a systematic review

author: Siddharth Shanbhag, Vivek Shanbhag, Andreas Stavropoulos | publisher: drg. Andreas Tjandra, Sp. Perio, FISID

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)

Table 1 Assessment of the genotyping methodology in the included studies

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