Identification of Close Relatives in the HUGO Pan-Asian SNP Database

The HUGO Pan-Asian SNP Consortium has recently released a genome-wide dataset, which consists of 1,719 DNA samples collected from 71 Asian populations. For studies of human population genetics such as genetic structure and migration history, this provided the most comprehensive large-scale survey of genetic variation to date in East and Southeast Asia. However, although considered in the analysis, close relatives were not clearly reported in the original paper. Here we performed a systematic analysis of genetic relationships among individuals from the Pan-Asian SNP (PASNP) database and identified 3 pairs of monozygotic twins or duplicate samples, 100 pairs of first-degree and 161 second-degree of relationships. Three standardized subsets with different levels of unrelated individuals were suggested here for future applications of the samples in most types of population-genetics studies (denoted by PASNP1716, PASNP1640 and PASNP1583 respectively) based on the relationships inferred in this study. In addition, we provided gender information for PASNP samples, which were not included in the original dataset, based on analysis of X chromosome data

Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia

Positive Coexistence of Steady States for a Diffusive Ratio-Dependent Predator-Prey Model with an Infected Prey

We examine a diffusive ratio-dependent predator-prey system with disease in the prey under homogeneous Dirichlet boundary conditions with a hostile environment at its boundary. We investigate the positive coexistence of three interacting species (susceptible prey, infected prey, and predator) and provide nonexistence conditions of positive solutions to the system. In addition, the global stability of the trivial and semitrivial solutions to the system is studied. Furthermore, the biological interpretation based on the result is also presented. The methods are employed from a comparison argument for the elliptic problem as well as the fixed-point theory as applied to a positive cone on a Banach space

Predation-induced dispersal toward fitness for predator invasion in predator–prey models

In this paper, we consider a predator–prey model with nonuniform predator dispersal, called predation-induced dispersal (PID), which represents predator motility depending on the maximal predation rate and the predator death rate in a spatially heterogeneous region. We study the local stability of the semitrivial steady state when predators are absent for models with PID and linear dispersal. We then investigate the local/global bifurcation from the semitrivial steady state of these models. Finally, we compare the results of the model with PID to the results of the model with linear dispersal. We conclude that the nonuniform dispersal of predators obeying PID increases fitness for predator invasion when rare; thus, predators with PID can invade a region with an increased probability even in cases wherein predators dispersed linearly cannot invade a certain region. Based on the results, we provide an ecological interpretation with the simulations

Atypical dermoscopic findings in patients diagnosed with lichen planus by histological examination

Background/Objectives: Lichen planus (LP) is an inflammatory skin disorder characterized by discrete, violaceous, polygonal papules. The dermoscopic features of common inflammatory dermatoses are not well studied. Although previous studies have demonstrated the typical patterns of LP, we found some atypical dermoscopic findings without Wickham striae in patients who had been diagnosed with LP by histopathologic examination. Our aim was to assess the atypical dermoscopic patterns associated with LP. Methods: We analyzed the dermoscopic features of seven LP lesions with atypical dermoscopic findings from seven patients who had been clinically and histopathologically diagnosed with LP. Results: Dermoscopically, five of the seven patients showed the pigmented pattern. We observed the following diverse pigment patterns: dots/globules, diffuse peppering, perifollicular, and linear. We also observed vascular and erosive patterns of variant LP. Conclusion: In this study, we emphasize the role of dermoscopy for identification of the clinical status of LP and its correlation to the results of histopathologic examinations. In addition to the typical dermoscopic patterns, dermoscopic recognition of variation in the morphology of LP could aid in the diagnosis of LP prior to histopathologic evaluation

Identification of Survival-Specific Genes in Clear Cell Renal Cell Carcinoma Using a Customized Next-Generation Sequencing Gene Panel

Purpose: Although mutations are associated with carcinogenesis, little is known about survival-specific genes in clear cell renal cell carcinoma (ccRCC). We developed a customized next-generation sequencing (NGS) gene panel with 156 genes. The purpose of this study was to investigate whether the survival-specific genes we found were present in Korean ccRCC patients, and their association with clinicopathological findings. Materials and Methods: DNA was extracted from the formalin-fixed, paraffin-embedded tissue of 22 ccRCC patients. NGS was performed using our survival-specific gene panel with an Illumina MiSeq. We analyzed NGS data and the correlations between mutations and clinicopathological findings and also compared them with data from the Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) and Renal Cell Cancer-European Union (RECA-EU). Results: We found a total of 100 mutations in 37 of the 156 genes (23.7%) in 22 ccRCC patients. Of the 37 mutated genes, 11 were identified as clinicopathologically significant. Six were novel survival-specific genes (ADAMTS10, CARD6, NLRP2, OBSCN, SECISBP2L, and USP40), and five were top-ranked mutated genes (AKAP9, ARID1A, BAP1, KDM5C, and SETD2). Only CARD6 was validated as an overall survival-specific gene in this Korean study (p = 0.04, r = −0.441), TCGA-KIRC cohort (p = 0.0003), RECA-EU (p = 0.0005). The 10 remaining gene mutations were associated with clinicopathological findings; disease-free survival, mortality, nuclear grade, sarcomatoid component, N-stage, sex, and tumor size. Conclusions: We discovered 11 survival-specific genes in ccRCC using data from TCGA-KIRC, RECA-EU, and Korean patients. We are the first to find a correlation between CARD6 and overall survival in ccRCC. The 11 genes, including CARD6, NLRP2, OBSCN, and USP40, could be useful diagnostic, prognostic, and therapeutic markers in ccRCC

Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion

Although the Austronesian expansion had a major impact on the languages of Island Southeast Asia, controversy still exists over the genetic impact of this expansion. The coexistence of both Asian and Papuan genetic ancestry in Eastern Indonesia provides a unique opportunity to address this issue. Here, we estimate recombination breakpoints in admixed genomes based on genome-wide SNP data and date the genetic admixture between populations of Asian vs. Papuan ancestry in Eastern Indonesia. Analyses of two genome-wide datasets indicate an eastward progression of the Asian admixture signal in Eastern Indonesia beginning about 4,000-3,000 y ago, which is in excellent agreement with inferences based on Austronesian languages. The average rate of spread of Asian genes in Eastern Indonesia was about 0.9 km/y. Our results indicate that the Austronesian expansion had a strong genetic as well as linguistic impact on Island Southeast Asia, and they significantly advance our understanding of the biological origins of human populations in the Asia-Pacific regionclose222