Systematic Comparison of Computational Tools for Sanger Sequencing-Based Genome Editing Analysis.

Successful genome editing depends on the cleavage efficiency of programmable nucleases (PNs) such as the CRISPR-Cas system. Various methods have been developed to assess the efficiency of PNs, most of which estimate the occurrence of indels caused by PN-induced double-strand breaks. In these methods, PN genomic target sites are amplified through PCR, and the resulting PCR products are subsequently analyzed using Sanger sequencing, high-throughput sequencing, or mismatch detection assays. Among these methods, Sanger sequencing of PCR products followed by indel analysis using online web tools has gained popularity due to its user-friendly nature. This approach estimates indel frequencies by computationally analyzing sequencing trace data. However, the accuracy of these computational tools remains uncertain. In this study, we compared the performance of four web tools, TIDE, ICE, DECODR, and SeqScreener, using artificial sequencing templates with predetermined indels. Our results demonstrated that these tools were able to estimate indel frequency with acceptable accuracy when the indels were simple and contained only a few base changes. However, the estimated values became more variable among the tools when the sequencing templates contained more complex indels or knock-in sequences. Moreover, although these tools effectively estimated the net indel sizes, their capability to deconvolute indel sequences exhibited variability with certain limitations. These findings underscore the importance of judiciously selecting and using an appropriate tool with caution, depending on the type of genome editing being performed.

Comparison of early wound healing using modified papilla preservation technique between enamel matrix derivative and recombinant human fibroblast growth factor.

PURPOSE: Enamel matrix derivative (EMD) has demonstrated beneficial effects on wound healing following surgery. However, the effects of recombinant human fibroblast growth factor 2 (rhFGF-2) in periodontal regeneration therapy have not been extensively studied. This retrospective study was conducted to compare the wound healing outcomes of the modified papilla preservation technique (mPPT) between EMD and rhFGF-2 therapies. METHODS: A total of 79 sites were evaluated for early wound healing using the modified early wound healing index (mEHI), which included 6 items: incision, fibrin clotting, step, redness, swelling, and dehiscence. A numeric analog scale, along with postoperative images of the 6 mEHI items, was established and used for the evaluations. The inter-rater reliability of the mEHI was assessed via intraclass correlation coefficients (ICCs). After adjusting for factors influencing the mPPT, the differences in mEHI scores between the EMD and rhFGF-2 groups were statistically analyzed. Additionally, radiographic bone fill (RBF) was evaluated 6 months after surgery. RESULTS: The ICC of the mEHI was 0.575. The mEHI, redness score, and dehiscence scores were significantly higher in the rhFGF-2 group (n=33) than in the EMD group (n=46). Similar results were observed in the subgroup of patients aged 50 years or older, but not in those younger than 50 years. In the subgroup with non-contained bone defects, related results were noted, but not in the subgroup with contained bone defects. However, early wound healing did not correlate with RBF at 6 months after surgery. CONCLUSIONS: Within the limitations of this study, the findings suggest that early wound healing following the use of mPPT with rhFGF-2 is somewhat superior to that observed after mPPT with EMD. However, mEHI should be improved for use as a predictive tool for early wound healing and to reflect clinical outcomes after surgery.

Impact of COVID-19 spread on visit intervals and clinical parameters for patients with periodontitis in supportive periodontal therapy: a retrospective study.

PURPOSE: This study investigated the relationship between the number of days that hospital visits were postponed and changes in clinical parameters due to the spread of coronavirus disease 2019 (COVID-19), after the Japanese government declared a state of emergency in April 2020. METHODS: Regarding the status of postponement of appointments, we analyzed the patients who had visited the Nihon University Hospital at Matsudo for more than 1 year for supportive periodontal therapy (SPT) and classified them into low-, moderate- and high-risk subgroups according to the periodontal risk assessment (PRA). Clinical parameters for periodontal disease such as probing depth (PD), full-mouth bleeding score (FMBS), full-mouth plaque score, periodontal inflamed surface area (PISA), and periodontal epithelial surface area (PESA) were analyzed in 2 periods, from October 2019 to March 2020 and after April 2020. Correlation coefficients between days of deferral and the degree of changes in clinical parameters were calculated. RESULTS: The mean age of the 749 patients was 67.56±10.85 years, and 63.82% were female. Out of 749 patients, 33.24% deferred their SPT appointments after April 2020. The average total of postponement days was 109.49±88.84. The number of postponement days was positively correlated with changes in average PD (rs=0.474) and PESA (rs=0.443) in the high-risk subgroup of FMBS, and average PD (rs=0.293) and PESA (rs=0.253) in the high-risk subgroup of tooth number (TN). Patients belonging to the high-risk subgroups for both FMBS and TN had a positive correlation between postponement days and PISA (rs=0.56). CONCLUSIONS: The findings, the spread of COVID-19 appears to have extended the visit interval for some SPT patients. Moreover, longer visit intervals were correlated with the worsening of some clinical parameters for SPT patients with high PRA.