Comparison of structural variant callers for massive whole-genome sequence data.

BACKGROUND: Detecting structural variations (SVs) at the population level using next-generation sequencing (NGS) requires substantial computational resources and processing time. Here, we compared the performances of 11 SV callers: Delly, Manta, GridSS, Wham, Sniffles, Lumpy, SvABA, Canvas, CNVnator, MELT, and INSurVeyor. These SV callers have been recently published and have been widely employed for processing massive whole-genome sequencing datasets. We evaluated the accuracy, sequence depth, running time, and memory usage of the SV callers. RESULTS: Notably, several callers exhibited better calling performance for deletions than for duplications, inversions, and insertions. Among the SV callers, Manta identified deletion SVs with better performance and efficient computing resources, and both Manta and MELT demonstrated relatively good precision regarding calling insertions. We confirmed that the copy number variation callers, Canvas and CNVnator, exhibited better performance in identifying long duplications as they employ the read-depth approach. Finally, we also verified the genotypes inferred from each SV caller using a phased long-read assembly dataset, and Manta showed the highest concordance in terms of the deletions and insertions. CONCLUSIONS: Our findings provide a comprehensive understanding of the accuracy and computational efficiency of SV callers, thereby facilitating integrative analysis of SV profiles in diverse large-scale genomic datasets.

Cntnap2-dependent molecular networks in autism spectrum disorder revealed through an integrative multi-omics analysis.

Autism spectrum disorder (ASD) is a major neurodevelopmental disorder in which patients present with core symptoms of social communication impairment, restricted interest, and repetitive behaviors. Although various studies have been performed to identify ASD-related mechanisms, ASD pathology is still poorly understood. CNTNAP2 genetic variants have been found that represent ASD genetic risk factors, and disruption of Cntnap2 expression has been associated with ASD phenotypes in mice. In this study, we performed an integrative multi-omics analysis by combining quantitative proteometabolomic data obtained with Cntnap2 knockout (KO) mice with multi-omics data obtained from ASD patients and forebrain organoids to elucidate Cntnap2-dependent molecular networks in ASD. To this end, a mass spectrometry-based proteometabolomic analysis of the medial prefrontal cortex in Cntnap2 KO mice led to the identification of Cntnap2-associated molecular features, and these features were assessed in combination with multi-omics data obtained on the prefrontal cortex in ASD patients to identify bona fide ASD cellular processes. Furthermore, a reanalysis of single-cell RNA sequencing data obtained from forebrain organoids derived from patients with CNTNAP2-associated ASD revealed that the aforementioned identified ASD processes were mainly linked to excitatory neurons. On the basis of these data, we constructed Cntnap2-associated ASD network models showing mitochondrial dysfunction, axonal impairment, and synaptic activity. Our results may shed light on the Cntnap2-dependent molecular networks in ASD.

Predictors of surgical outcomes for limited palatal muscle resection in patients with obstructive sleep apnea.

OBJECTIVE: Limited palatal muscle resection (LPMR) is a modified palatal surgical technique to correct retropalatal obstruction without complications. This study aims to determine the associated factors affecting the success and cure rate of LPMR in patients with obstructive sleep apnea (OSA), thus guiding patient selection and improving surgical outcome. METHODS: Thirty-five OSA patients underwent LPMR were enrolled. All patients received routine physical examination, preoperative drug-induced sleep endoscopy (DISE), and polysomnography (PSG). Clinical, polysomnographic, cephalometric variables, and DISE findings were evaluated. These measurements were compared between the surgical success and failure group based on the results of preoperative and postoperative PSG. Furthermore, we compared the cured and non-cured groups in the surgical success group. RESULTS: Among 35 patients, the overall success rate was 57 % with a cure rate of 31.4 %. Patients with Friedman stage II had a significantly higher success rate (p = 0.032). According to DISE results, tongue base obstruction affected the surgical outcome (p < 0.001). The success rate was 100 % in the no tongue base obstruction during DISE, 72.2 % in the partial obstruction, and 9.1 % in the total obstruction. Tonsil size is also helpful in predicting surgical success rate (p = 0.041). Furthermore, patients with mild AHI were more likely to be surgical cures. when compared with patients with severe AHI (p = 0.044). CONCLUSION: Patients with larger tonsil size and no tongue base obstruction during DISE may have a higher chance of surgical success with LPMR. The lower AHI may be predictors of surgical cure after LPMR.

Immunomodulatory Effect of Adipose Stem Cell-Derived Extra-Cellular Vesicles on Cytokine Expression and Regulatory T Cells in Patients with Asthma.

Although mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) are as effective as MSCs in the suppression of allergic airway inflammation, few studies have evaluated the immunomodulatory capacity of MSC-derived EVs in patients with asthma. Thus, we assessed the effects of adipose stem cell (ASC)-derived EVs on cytokine expression and regulatory T cells (Tregs) in peripheral blood mononuclear cells (PBMCs) of asthmatic patients. PBMCs (1 × 106 cells/mL) were isolated from asthmatic patient and healthy controls and co-cultured with 1 µg/mL of ASC-derived EVs. Th (T helper) 1-, Th2-, and Treg-related cytokine expression, fluorescence-activated cell sorting analysis of CD4+CD25+FOXP3+ T cells, and co-stimulatory molecules were analyzed before and after ASC-derived EV treatment. The expression levels of IL-4 and costimulatory molecules such as CD83 and CD86 were significantly higher in PBMCs of asthmatic patients than in control PBMCs. However, ASC-derived EV treatment significantly decreased the levels of interleukin (IL)-4 and co-stimulatory molecules such as CD83 and CD86 in the phytohemagglutinin (PHA)-stimulated PBMC of asthmatic patients. Furthermore, ASC-derived EVs remarkably increased the transforming growth factor-ß (TGF-ß) levels and expression of Tregs in the PBMC of asthmatic patients. ASC-derived EVs induce Treg expansion and have immunomodulatory effects by downregulating IL-4 and upregulating TGF-ß in PBMCs of asthmatic patients.

Integrative single-cell transcriptome analysis provides new insights into post-COVID-19 pulmonary fibrosis and potential therapeutic targets.

The global COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 virus has resulted in a significant number of patients experiencing persistent symptoms, including post-COVID pulmonary fibrosis (PCPF). This study aimed to identify novel therapeutic targets for PCPF using single-cell RNA-sequencing data from lung tissues of COVID-19 patients, idiopathic pulmonary fibrosis (IPF) patients, and a rat transforming growth factor beta-1-induced fibrosis model treated with antifibrotic drugs. Patients with COVID-19 had lower alveolar macrophage counts than healthy controls, whereas patients with COVID-19 and IPF presented with elevated monocyte-derived macrophage counts. A comparative transcriptome analysis showed that macrophages play a crucial role in IPF and COVID-19 development and progression, and fibrosis- and inflammation-associated genes were upregulated in both conditions. Functional enrichment analysis revealed the upregulation of inflammation and proteolysis and the downregulation of ribosome biogenesis. Cholesterol efflux and glycolysis were augmented in both macrophage types. The study suggests that antifibrotic drugs may reverse critical lung fibrosis mediators in COVID-19. The results help clarify the molecular mechanisms underlying pulmonary fibrosis in patients with severe COVID-19 and IPF and highlight the potential efficacy of antifibrotic drugs in COVID-19 therapy. Collectively, all these findings may have significant implications for the development of new treatment strategies for PCPF.

Regulation of stomatal development by stomatal lineage miRNAs.

Stomata in the plant epidermis play a critical role in growth and survival by controlling gas exchange, transpiration, and immunity to pathogens. Plants modulate stomatal cell fate and patterning through key transcriptional factors and signaling pathways. MicroRNAs (miRNAs) are known to contribute to developmental plasticity in multicellular organisms; however, no miRNAs appear to target the known regulators of stomatal development. It remains unclear as to whether miRNAs are involved in stomatal development. Here, we report highly dynamic, developmentally stage-specific miRNA expression profiles from stomatal lineage cells. We demonstrate that stomatal lineage miRNAs positively and negatively regulate stomatal formation and patterning to avoid clustered stomata. Target prediction of stomatal lineage miRNAs implicates potential cellular processes in stomatal development. We show that miR399-mediated PHO2 regulation, involved in phosphate homeostasis, contributes to the control of stomatal development. Our study demonstrates that miRNAs constitute a critical component in the regulatory mechanisms controlling stomatal development.

BMP4 signaling plays critical roles in self-renewal of R2i mouse embryonic stem cells.

Mouse embryonic stem cells (mESCs) can be maintained in a pluripotent state under R2i culture conditions that inhibit the TGF-ß and ERK signaling pathways. BMP4 is another member of the TGF-ß family that plays a crucial role in maintaining the pluripotency state of mESCs. It has been reported that inhibition of BMP4 caused the death of R2i-grown cells. In this study, we used the loss-of-function approach to investigate the role of BMP4 signaling in mESC self-renewal. Inhibition of this pathway with Noggin and dorsomorphin, two bone morphogenetic protein (BMP) antagonists, elicited a quick death of the R2i-grown cells. We showed that the canonical pathway of BMP4 (BMP/SMAD) was dispensable for self-renewal and maintaining pluripotency of these cells. Transcriptome analysis of the BMPi-treated cells revealed that the p53 signaling and two adhesion (AD) and apoptotic mitochondrial change (MT) pathways could be involved in the cell death of the BMPi-treated cells. According to our results, inhibition of BMP4 signaling caused a decrease in cell adhesion and ECM detachment, which triggered anoikis in the R2i-grown cells. Altogether, these findings demonstrate that endogenous BMP signaling is required for the survival of mESCs under the R2i condition.

ORESARA 15, a PLATZ transcription factor, controls root meristem size through auxin and cytokinin signalling-related pathways.

An optimal size of post-embryonic root apical meristem (RAM) is achieved by a balance between cell division and differentiation. Despite extensive research, molecular mechanisms underlying the coordination of cell division and differentiation are still fragmentary. Here, we report that ORESARA 15 (ORE15), an Arabidopsis PLANT A/T-RICH SEQUENCE-AND ZINC-BINDING PROTEIN (PLATZ) transcription factor preferentially expressed in the RAM, determines RAM size. Primary root length, RAM size, cell division rate, and stem cell niche activity were reduced in an ore15 loss-of-function mutant but enhanced in an activation-tagged line overexpressing ORE15, compared with wild type. ORE15 forms mutually positive and negative feedback loops with auxin and cytokinin signalling, respectively. Collectively, our findings imply that ORE15 controls RAM size by mediating the antagonistic interaction between auxin and cytokinin signalling-related pathways.

High Precision Classification of Resting and Eating Behaviors of Cattle by Using a Collar-Fitted Triaxial Accelerometer Sensor.

Cattle are less active than humans. Hence, it was hypothesized in this study that transmitting acceleration signals at a 1 min sampling interval to reduce storage load has the potential to improve the performance of motion sensors without affecting the precision of behavior classification. The behavior classification performance in terms of precision, sensitivity, and the F1-score of the 1 min serial datasets segmented in 3, 4, and 5 min window sizes based on nine algorithms were determined. The collar-fitted triaxial accelerometer sensor was attached on the right side of the neck of the two fattening Korean steers (age: 20 months) and the steers were observed for 6 h on day one, 10 h on day two, and 7 h on day three. The acceleration signals and visual observations were time synchronized and analyzed based on the objectives. The resting behavior was most correctly classified using the combination of a 4 min window size and the long short-term memory (LSTM) algorithm which resulted in 89% high precision, 81% high sensitivity, and 85% high F1-score. High classification performance (79% precision, 88% sensitivity, and 83% F1-score) was also obtained in classifying the eating behavior using the same classification method (4 min window size and an LSTM algorithm). The most poorly classified behavior was the active behavior. This study showed that the collar-fitted triaxial sensor measuring 1 min serial signals could be used as a tool for detecting the resting and eating behaviors of cattle in high precision by segmenting the acceleration signals in a 4 min window size and by using the LSTM classification algorithm.

Time-evolving genetic networks reveal a NAC troika that negatively regulates leaf senescence in Arabidopsis.

Senescence is controlled by time-evolving networks that describe the temporal transition of interactions among senescence regulators. Here, we present time-evolving networks for NAM/ATAF/CUC (NAC) transcription factors in Arabidopsis during leaf aging. The most evident characteristic of these time-dependent networks was a shift from positive to negative regulation among NACs at a presenescent stage. ANAC017, ANAC082, and ANAC090, referred to as a "NAC troika," govern the positive-to-negative regulatory shift. Knockout of the NAC troika accelerated senescence and the induction of other NACs, whereas overexpression of the NAC troika had the opposite effects. Transcriptome and molecular analyses revealed shared suppression of senescence-promoting processes by the NAC troika, including salicylic acid (SA) and reactive oxygen species (ROS) responses, but with predominant regulation of SA and ROS responses by ANAC090 and ANAC017, respectively. Our time-evolving networks provide a unique regulatory module of presenescent repressors that direct the timely induction of senescence-promoting processes at the presenescent stage of leaf aging.

Relationship between allergic rhinitis and nasal surgery success in patients with obstructive sleep apnea.

OBJECTIVES: Nasal obstruction is common in patients with obstructive sleep apnea (OSA). Nonetheless, the effectiveness of isolated nasal surgery in treatment of OSA remains controversial. This study is to evaluate the subjective and objective outcome after isolated nasal surgery in patients with OSA and to determine the associated factors related to the success rate of isolated nasal surgery. METHODS: The study population consisted of 35 patients with nasal obstruction who had been diagnosed with OSA and were undergoing septoplasty and inferior turbinate reduction to correct nasal pathologies. Preoperative drug-induced sleep endoscopy was performed to evaluate the obstruction site. Patients were assessed before and after nasal surgery using subjective outcomes measures, including the Visual Analog Scale and Epworth Sleepiness Scale, as well as by overnight polysomnography. RESULTS: All patients experienced improved nasal breathing postoperatively. At 6 months postoperatively, patients exhibited significant symptomatic improvement in snoring, sleep apnea, morning headache, tiredness, and daytime sleepiness. Postoperative polysomnography revealed significant improvement in the apnea-hypopnea index, respiratory disturbance index, and percentage of time with oxygen saturation < 90%. Although the overall success rate of nasal surgery alone was 14.3%, the criteria for success were met in 50% of patients with allergic rhinitis. Furthermore, the success rate was significantly higher in patients with moderate to severe nasal obstruction than in patients with mild nasal obstruction. CONCLUSION: Among patients with OSA, those with allergic rhinitis and severe nasal obstruction are likely to have a better surgical outcome following isolated nasal surgery.

Antagonistic Roles of PhyA and PhyB in Far-Red Light-Dependent Leaf Senescence in Arabidopsis thaliana.

Leaf senescence is regulated by diverse developmental and environmental factors to maximize plant fitness. The red to far-red light ratio (R:FR) detected by plant phytochromes is reduced under vegetation shade, thus initiating leaf senescence. However, the role of phytochromes in promoting leaf senescence under FR-enriched conditions is not fully understood. In this study, we investigated the role of phyA and phyB in regulating leaf senescence under FR in Arabidopsis thaliana (Arabidopsis). FR enrichment and intermittent FR pulses promoted the senescence of Arabidopsis leaves. Additionally, phyA and phyB mutants showed enhanced and repressed senescence phenotypes in FR, respectively, indicating that phyA and phyB antagonistically regulate FR-dependent leaf senescence. Transcriptomic analysis using phyA and phyB mutants in FR identified differentially expressed genes (DEGs) involved in leaf senescence-related processes, such as responses to light, phytohormones, temperature, photosynthesis and defense, showing opposite expression patterns in phyA and phyB mutants. These contrasting expression profiles of DEGs support the antagonism between phyA and phyB in FR-dependent leaf senescence. Among the genes showing antagonistic regulation, we confirmed that the expression of WRKY6, which encodes a senescence-associated transcription factor, was negatively and positively regulated by phyA and phyB, respectively. The wrky6 mutant showed a repressed senescence phenotype compared with the wild type in FR, indicating that WRKY6 plays a positive role in FR-dependent leaf senescence. Our results imply that antagonism between phyA and phyB is involved in fine-tuning leaf senescence under varying FR conditions in Arabidopsis.

Gut-Specific Delivery of T-Helper 17 Cells Reduces Obesity and Insulin Resistance in Mice.

BACKGROUND & AIMS: Obesity and metabolic syndrome have been associated with alterations to the intestinal microbiota. However, few studies examined the effects of obesity on the intestinal immune system. We investigated changes in subsets of intestinal CD4+ T-helper (TH) cells with obesity and the effects of gut-tropic TH17 cells in mice on a high-fat diet (HFD). METHODS: We isolated immune cells from small intestine and adipose tissue of C57BL/6 mice fed a normal chow diet or a HFD for 10 weeks and analyzed the cells by flow cytometry. Mice fed a vitamin A-deficient HFD were compared with mice fed a vitamin A-sufficient HFD. Obese RAG1-deficient mice were given injections of only regulatory T cells or a combination of regulatory T cells and TH17 cells (wild type or deficient in integrin ß7 subunit or interleukin 17 [IL17]). Mice were examined for weight gain, fat mass, fatty liver, glucose tolerance, and insulin resistance. Fecal samples were collected before and after T cell transfer and analyzed for microbiota composition by metagenomic DNA sequencing and quantitative polymerase chain reaction. RESULTS: Mice placed on a HFD became obese, which affected the distribution of small intestinal CD4+ TH cells. Intestinal tissues from obese mice had significant reductions in the proportion of TH17 cells but increased proportion of TH1 cells, compared with intestinal tissues from nonobese mice. Depletion of vitamin A in obese mice further reduced the proportion of TH17 cells in small intestine; this reduction correlated with more weight gain and worsening of glucose intolerance and insulin resistance. Adoptive transfer of in vitro-differentiated gut-tropic TH17 cells to obese mice reduced these metabolic defects, which required the integrin ß7 subunit and IL17. Delivery of TH17 cells to intestines of mice led to expansion of commensal microbes associated with leanness. CONCLUSIONS: In mice, intestinal TH17 cells contribute to development of a microbiota that maintains metabolic homeostasis, via IL17. Gut-homing TH17 cells might be used to reduce metabolic disorders in obese individuals.

Leukocyte-specific protein 1 regulates T-cell migration in rheumatoid arthritis.

Copy number variations (CNVs) have been implicated in human diseases. However, it remains unclear how they affect immune dysfunction and autoimmune diseases, including rheumatoid arthritis (RA). Here, we identified a novel leukocyte-specific protein 1 (LSP1) deletion variant for RA susceptibility located in 11p15.5. We replicated that the copy number of LSP1 gene is significantly lower in patients with RA, which correlates positively with LSP1 protein expression levels. Differentially expressed genes in Lsp1-deficient primary T cells represent cell motility and immune and cytokine responses. Functional assays demonstrated that LSP1, induced by T-cell receptor activation, negatively regulates T-cell migration by reducing ERK activation in vitro. In mice with T-cell-dependent chronic inflammation, loss of Lsp1 promotes migration of T cells into the target tissues as well as draining lymph nodes, exacerbating disease severity. Moreover, patients with RA show diminished expression of LSP1 in peripheral T cells with increased migratory capacity, suggesting that the defect in LSP1 signaling lowers the threshold for T-cell activation. To our knowledge, our work is the first to demonstrate how CNVs result in immune dysfunction and a disease phenotype. Particularly, our data highlight the importance of LSP1 CNVs and LSP1 insufficiency in the pathogenesis of RA and provide previously unidentified insights into the mechanisms underlying T-cell migration toward the inflamed synovium in RA.

Radiologic Factors Affecting Ankle Pain Before and After Total Knee Arthroplasty for the Varus Osteoarthritic Knee.

The aim of the present study was to evaluate the radiologic factors related to ankle pain before and after total knee arthroplasty (TKA) among patients with a varus osteoarthritic knee. Fifty-five patients (65 ankles) with a varus osteoarthritic knee who had undergone TKA and were followed up for >24 months were enrolled. For clinical assessment, the visual analog scale for pain and the American Orthopaedic Foot and Ankle Society ankle-hindfoot scale were used. For radiologic assessment, the mechanical axis deviation angle, talar tilt, tibial anterior surface angle, distal medial clear space, medial tibiotalar joint space, frontal tibial ground angle, and hindfoot alignment view angle were measured. The patients with ankle pain before TKA (11 ankles) had a larger hindfoot alignment view angle (9.2° ± 2.6°) than that of patients without ankle pain before TKA (54 ankles; 5.5° ± 4.8°; p = .007). The patients with newly developed ankle pain or experienced an aggravation of existing pain after TKA (8 ankles) had a significantly larger degree of residual varus (5.1° ± 2.1°) than did the patients without ankle pain before and after TKA or those with ankle pain before surgery. However, the severity of the pain was not different during the follow-up period (52 ankles; 1.6° ± 2.5°; p = .001). The results of the present study showed that residual varus deformity was associated with ankle pain after TKA. Surgeons should perform evaluations of the ankles of patients who complain of pain before and after TKA and should give careful attention to the correction of alignment during TKA.

Placental growth factor-1 and -2 induce hyperplasia and invasiveness of primary rheumatoid synoviocytes.

Inflammation-mediated oncogenesis has been implicated in a variety of cancer types. Rheumatoid synovial tissues can be viewed as a tumor-like mass, consisting of hyperplastic fibroblast-like synoviocytes (FLSs). FLSs of rheumatoid arthritis (RA) patients have promigratory and invasive characteristics, which may be caused by chronic exposure to genotoxic stimuli, including hypoxia and growth factors. We tested whether a transformed phenotype of RA-FLSs is associated with placental growth factor (PlGF), a representative angiogenic growth factor induced by hypoxia. In this study, we identified PlGF-1 and PlGF-2 as the major PlGF isoforms in RA-FLSs. Global gene expression profiling revealed that cell proliferation, apoptosis, angiogenesis, and cell migration were mainly represented by differentially expressed genes in RA-FLSs transfected with small interfering RNA for PlGF. Indeed, PlGF-deficient RA-FLSs showed a decrease in cell proliferation, migration, and invasion, but an increase in apoptotic death in vitro. PlGF gene overexpression resulted in the opposite effects. Moreover, exogeneous PlGF-1 and PlGF-2 increased survival, migration, and invasiveness of RA-FLSs by binding their receptors, Flt-1 and neuropilin-1, and upregulating the expression of antiapoptotic molecules, pErk and Bcl2. Knockdown of PlGF transcripts reduced RA-FLS proliferation in a xenotransplantation model. Collectively, in addition to their role for neovascularization, PlGF-1 and -2 promote proliferation, survival, migration, and invasion of RA-FLSs in an autocrine and paracrine manner. These results demonstrated how primary cells of mesenchymal origin acquired an aggressive and transformed phenotype. PlGF and its receptors thus offer new targets for anti-FLS therapy.

Comparison of histologic healing and biomechanical characteristics between repair techniques for a delaminated rotator cuff tear in rabbits.

BACKGROUND: The purpose of this study was to compare histologic healing and biomechanical characteristics between 2 repair techniques (layer by layer, repair of each layer to bone separately; and whole layer, repair of each layer to the bone en masse) for delaminated rotator cuff tear. MATERIALS AND METHODS: Rabbits were used as subjects and classified into 2 groups: group A, right side, the layer-by-layer repair group; and group B, left side, the whole-layer repair group. Histologic evaluations were done at 3 weeks (n = 7) and 6 weeks (n = 4) after operation. Biomechanical tests to evaluate the tensile property were done at time 0 (n = 5) and 3 weeks (n = 5) after operation. RESULTS: Histologic healing improved in all groups. A smaller cleft was found between layers in group B compared with the cleft in group A at 3 weeks after operation. At time 0, group A showed a higher yield load and ultimate failure load (67 ± 10.5 N and 80 ± 7.8 N, respectively). However, at 3 weeks after operation, group B showed a higher yield load (48 ± 7.6 N). CONCLUSIONS: In the delaminated rotator cuff tear model in the rabbit, the whole-layer repair showed a narrow gap between layers and a higher yield load at 3 weeks after operation. Surgical techniques that unite the cleft in a delaminated tear could improve biomechanical strength after operation.

IdMotif: An Interactive Motif Identification in Protein Sequences.

This article presents a visual analytics framework, idMotif, to support domain experts in identifying motifs in protein sequences. A motif is a short sequence of amino acids usually associated with distinct functions of a protein, and identifying similar motifs in protein sequences helps us to predict certain types of disease or infection. idMotif can be used to explore, analyze, and visualize such motifs in protein sequences. We introduce a deep-learning-based method for grouping protein sequences and allow users to discover motif candidates of protein groups based on local explanations of the decision of a deep-learning model. idMotif provides several interactive linked views for between and within protein cluster/group and sequence analysis. Through a case study and experts' feedback, we demonstrate how the framework helps domain experts analyze protein sequences and motif identification.

Epigenetic age prediction using costal cartilage for the investigation of disaster victims and missing persons.

The DNA intelligence tool, DNA methylation-based age prediction, can help identify disaster victims and suspects in criminal investigations. In this study, we developed a costal cartilage-based age prediction tool that uses massive parallel sequencing (MPS) of age-associated DNA methylation markers. Costal cartilage samples were obtained from 85 deceased Koreans, aged between 26 and 89 years. An MPS library was prepared using two rounds of multiplex polymerase chain reaction of nine genes (TMEM51, MIR29B2CHG, EDARADD, FHL2, TRIM59, ELOVL2, KLF14, ASPA, and PDE4C). The DNA methylation status of 45 CpG sites was determined and used to train an age prediction model via stepwise regression analysis. Nine CpGs in MIR29B2CHG, FHL2, TRIM59, ELOVL2, KLF14, and ASPA were selected for regression model construction. A leave-one-out cross-validation analysis revealed the high performance of the age prediction model, with a mean absolute error (MAE) and root mean square error of 4.97 and 6.43 years, respectively. Additionally, our model showed good performance with a MAE of 6.06 years in the analysis of data of 181 costal cartilage samples collected from Europeans. Our model effectively estimates the age of deceased individuals using costal cartilage samples; therefore, it can be a valuable forensic tool for disaster victim and missing person investigation.

Mutational analysis of 23 autosomal short tandem repeats based on trio paternity testing in the Korean population.

This study aimed to estimate A-STR mutation rates in 2,317 Korean parent-child trios by examining 20 Combined DNA Index System (CODIS) core loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045) and three non-CODIS loci (Penta E, Penta D, and SE33). Locus-specific mutation rate estimates varied from 0.00 to 8.63 × 10-3 per generation, with an average mutation rate of 1.62 × 10-3 (95 % CI, 1.39-1.88 × 10-3). We also combined data from previous studies to obtain comprehensive genetic values for the Korean population, and the average mutation rate was 1.59 × 10-3 (95 % CI, 1.38-1.82 × 10-3). Single-step mutations (95.69 %) and double-step mutations (3.35 %) were observed in the mutation pattern analysis, and cases expected to have multi-step mutations (0.96 %) were also observed. Large-sized alleles exhibited more loss mutations than gain mutations, and paternal mutations (62.68 %) were more frequently observed than maternal mutations (19.62 %). The calculated values and features of the 23 A-STRs explored in this study are expected to play a crucial role in establishing criteria for forensic genetic interpretation.