Optimizing Multiplex PCR for a Set of Malay Ancestry Informative Marker-Single Nucleotide Polymorphisms (AIM-SNPs) and Preliminary Analysis of Genotypes Between Malay and non-Malay Population.

Background: Inference of genetic ancestry is of great interest in many fields and one of the markers in these analyses is ancestry informative marker single nucleotide polymorphisms (AIMSNPs). The Malay population is an ethnic group located mainly in South East Asia and comprises the largest ethnicity in Malaysia. Objectives: To determine Malay ancestry, Yahya et al, 2017 selected 37,487 SNPs from the genotyping data collected by the Malaysian Node of the Human Variome Project and Singapore Genome Variation Project and referenced them against the data from the International HapMap Project Phase 3. The SNPs determined to be informative for ancestry were compiled into AIM-SNP panels, and from these a few SNPs were selected for optimization in preparation for single base extension reaction multiplexing. Methodology: The chosen AIMSNPs were optimized and validated on Malay and non-Malay populations. Genotyping was carried out on participants of self-reported Malay and non-Malay ancestry respectively and the data were compared for Malay and non-Malay population to investigate for significant differences in the genotype between Malay and non-Malay participants. Findings: The results showed great similarities between the Malay and non-Malay population, which may arise from many factors, and further optimization of more SNPs and genotyping is required to definitively conclude the validity of the AIM-SNP panels for Malay population Conclusion: Knowledge of ancestry is important to minimise spurious association. This pilot study gives a brief account of the optimization process and offers an insight into how this may be done in South East Asian populations.

Pigmented Villonodular Synovitis of the Temporomandibular Joint with Skull Base Extension: A Retrospective Case Series

Background: Pigmented villonodular synovitis (PVNS) of the temporomandibular joint (TMJ) with skull base extension is a rare entity. Here, we summarize the clinical features, treatments, and outcomes of PVNS of the TMJ with skull base extension in a large case series. Methods: We reviewed the clinical information relating to patients diagnosed with PVNS of the TMJ with skull base extension information of patients in our center between 2011 and 2020. Results: We reviewed 10 patients (4 males and 6 females). All cases had presented with a unilateral lesion extending the middle skull base. PVNS of the TMJ with skull base extension occurred on the left side in 6 patients (60%) and on the right side in 4 patients (40%). Of the 10 patients, pain and mass were the most prevalent symptoms. All patients received surgery and no recurrence was seen after 35.90±25.35 months follow-up. Conclusion: Despite destructive biological behavior, surgery can achieve an excellent outcome for patients with PVNS of the TMJ with skull base extension. An en bloc resection may prevent recurrence and provide long-term relief. Radiotherapy may be reserved for subtotal excision and recurrent lesions but require further investigation.

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay

Multilocus variable-number tandem repeat analysis (MLVA) is widely used for genotyping of Bordetella pertussis, the causative bacteria for pertussis. However, MLVA genotyping is losing its discriminate power because prevalence of the epidemic MT27 strain (MLVA-27) is increasing worldwide. To address this, we developed a single nucleotide polymorphism (SNP) genotyping method for MT27 based on multiplexed single-base extension (SBE) assay. A total of 237 MT27 isolates collected in Japan during 1999–2018 were genotyped and classified into ten SNP genotypes (SG1 to SG10) with a Simpson’s diversity index (DI) of 0.79 (95% CI 0.76–0.82). Temporal trends showed a marked increase in the genotypic diversity in the 2010s: Simpson’s DI was zero in 1999–2004, 0.16 in 2005–2009, 0.83 in 2010–2014, and 0.76 in 2015–2018. This indicates that the SNP genotyping is applicable to the recently circulating MT27 strain. Additionally, almost all outbreak-associated MT27 isolates were classified into the same SNP genotypes for each outbreak. Multiplexed SBE assay allows for rapid and simple genotyping, indicating that the SNP genotyping can potentially be a useful tool for subtyping the B. pertussis MT27 strain in routine surveillance and outbreak investigations.

A New Extensible Continuum Manipulator Using Flexible Parallel Mechanism and Rigid Motion Transmission

An extensible continuum manipulator (ECM) has specific advantages over its non-extensible counterparts. For instance, in certain applications, such as minimally invasive surgery or pipe inspection, the base motion might be limited or disallowed. The additional extensibility provides the robot with more dexterous manipulation and a larger workspace. Existing continuum robot designs achieve extensibility mainly through artificial muscle/pneumatic, extensible backbone, concentric tube, and base extension, etc. This paper proposes a new way to achieve this additional motion degree of freedom by taking advantage of the rigid coupling hybrid mechanism concept and a flexible parallel mechanism. More specifically, a rack and pinion set is used to transmit the motion of the i-th subsegment to drive the (i+1)-th subsegment. A six-chain flexible parallel mechanism is used to generate the desired spatial bending and one extension mobility for each subsegment. This way, the new manipulator can achieve tail-like spatial bending and worm-like extension at the same time. Simplified kinematic analyses are conducted to estimate the workspace and the motion non-uniformity. A proof-of-concept prototype was integrated to verify the mechanism’s mobility and to evaluate the kinematic model accuracy. The results show that the proposed mechanism achieved the desired mobilities with a maximum extension ratio of 32.2% and a maximum bending angle of 80 degrees.

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay

Multilocus variable-number tandem repeat analysis (MLVA) is widely used for genotyping of Bordetella pertussis, the causative bacteria for pertussis. However, MLVA genotyping is losing its discriminate power because prevalence of the epidemic MT27 strain (MLVA-27) is increasing worldwide. To address this, we developed a single nucleotide polymorphism (SNP) genotyping method for MT27 based on multiplexed single-base extension (SBE) assay. A total of 237 MT27 isolates collected in Japan during 1999−2018 were genotyped and classified into ten SNP genotypes (SG1 to SG10) with a Simpson’s diversity index (DI) of 0.79 (95% CI, 0.76–0.82). Temporal trends showed a marked increase in the genotypic diversity in the 2010s: Simpson’s DI was zero in 1999–2004, 0.16 in 2005–2009, 0.83 in 2010–2014, and 0.76 in 2015–2018. This indicates that the SNP genotyping is applicable to the recently circulating MT27 strain. Additionally, almost all outbreak-associated MT27 isolates were classified into the same SNP genotypes for each outbreak. Multiplexed SBE assay allows for rapid and simple genotyping, indicating that the SNP genotyping can potentially be a useful tool for subtyping the B. pertussis MT27 strain in routine surveillance and outbreak investigations.