Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing.
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ABSTRACT:
SUBMITTER: Huang YT
PROVIDER: S-EPMC8011154 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:OBJECTIVES:Air polishing with sodium bicarbonate powders with a grain size of 40 ?m is recommended for patient comfort. However, the efficacy of small grain size on stain removal has not been adequately studied. This study aimed to compare the stain removal efficacy of sodium bicarbonate powders with grain sizes of 65 and 40 ?m and to evaluate patient acceptance and operator opinion after using both air polishing powders. MATERIALS AND METHODS:A double-blind, randomized, split-mouth study was conducted with 35 participants with moderate to heavy dental staining on both sides of the upper teeth. Removal of dental stains on the index teeth was performed using sodium bicarbonate powders with a grain size of either 65 or 40 ?m. The time taken to completely remove all dental stains was recorded. After treatment, a questionnaire was used to evaluate patient acceptance and the operator's opinion. RESULTS:The average time for the removal of all stains by powder was 4.5 ± 3.6 min with a grain size of 65 ?m and 4.4 ± 3.8 min with a grain size of 40 ?m. The difference in the average time between the two groups was not significant (P = 0.461). The operator's opinions of the two powders were identical, and patient acceptance did not differ significantly between the two types of powders. CONCLUSIONS:The 40 ?m sodium bicarbonate powder removed dental stains as efficiently as the 65-?m powder. Powder handling and patient acceptance were comparable between grain sizes of 65 and 40 ?m.
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Project description:Background: 22q11.2 deletion syndrome (22q11.2DS) is a disorder caused when a small part of chromosome 22 is missing. Diagnosis is currently established by the identification of a heterozygous deletion at chromosome 22q11.2 through chromosomal microarray analysis or other genomic analyses. However, more accurate identification of the breakpoint contributes to a clearer understanding of the 22q11.2 deletion syndrome. Methods: In this study, we present a feasible nanopore sequencing method of 22q11.2 deletion. This DNA enrichment method-region-specific amplification (RSA)-is able to analyze the 22q11.2 deletion by specific amplification of an approximately 1-Mb region where the breakpoint might exist. RSA introduces universal primers into the target region DNA by a Y-shaped adaptor ligation and a single primer extension. The enriched products, completed by amplification with universal primers, are then processed by standard ONT ligation sequencing protocols. Results: RSA is able to deliver adequate coverage (>98%) and comparable long reads (average length >1 Kb) throughout the 22q11.2 region. The long nanopore sequencing reads, derived from three umbilical cord blood samples, have facilitated the identification of the breakpoint of the 22q11.2 deletion, as well as by Sanger sequencing. Conclusion: The Oxford Nanopore MinION sequencer can use RSA to sequence the target region 22q11.2; this method could also be used for other hard-to-sequence parts of the genome.
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