Characteristics of <i>PPM1D</i> truncating mutation carriers.

Characteristics of PPM1D truncating mutation carriers.</p

Cancer types of people who have undergone NGS gene panel testing for hereditary cancer.

Cancer types of people who have undergone NGS gene panel testing for hereditary cancer.</p

Additional file 1 of A comparative study of next-generation sequencing and fragment analysis for the detection and allelic ratio determination of FLT3 internal tandem duplication

Additional file 1 Supplementary Table 1. List of genes included in the hematologic malignancy–target gene panel. Supplementary Table 2. Clinical information and FLT3 ITD results of samples obtained from patients. Supplementary Table 3. Clinical and biological characteristics of the studied patients with follow up samples. Supplementary Fig. 1. The bioinformatics pipelines used in this study. Supplementary Fig. 2. FLT3 ITD detection result by fragment analysis and by NGS in acute myeloid leukemia patient with discrepant case (Patient 7)

Table1_The Role of Ion Channel-Related Genes in Autism Spectrum Disorder: A Study Using Next-Generation Sequencing.DOCX

The clinical heterogeneity of autism spectrum disorder (ASD) is closely associated with the diversity of genes related to ASD pathogenesis. With their low effect size, it has been hard to define the role of common variants of genes in ASD phenotype. In this study, we reviewed genetic results and clinical scores widely used for ASD diagnosis to investigate the role of genes in ASD phenotype considering their functions in molecular pathways. Genetic data from next-generation sequencing (NGS) were collected from 94 participants with ASD. We analyzed enrichment of cellular processes and gene ontology using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). We compared clinical characteristics according to genetic functional characteristics. We found 266 genes containing nonsense, frame shift, missense, and splice site mutations. Results from DAVID revealed significant enrichment for “ion channel” with an enrichment score of 8.84. Moreover, ASD participants carrying mutations in ion channel-related genes showed higher total IQ (p = 0.013) and lower repetitive, restricted behavior (RRB)-related scores (p = 0.003) and mannerism subscale of social responsiveness scale scores, compared to other participants. Individuals with variants in ion channel genes showed lower RRB scores, suggesting that ion channel genes might be relatively less associated with RRB pathogenesis. These results contribute to understanding of the role of common variants in ASD and could be important in the development of precision medicine of ASD.</p

Additional file 1: of Next-generation sequencing with comprehensive bioinformatics analysis facilitates somatic mosaic APC gene mutation detection in patients with familial adenomatous polyposis

Table S1. Genes included in the hereditary cancer panel. Table S2. Primers used in the MEMO-PCR to confirm low-level variants in APC. Table S3. Pathogenic or likely pathogenic germline APC variants in patients suspicious for familial adenomatous polyposis. Table S4. All variants identified from NGS hereditary cancer panel. (DOCX 58 kb

DataSheet_1_Subsurface dispersion path and travel time of radiocesium from Fukushima by Mode Water.docx

The Fukushima Daiichi Nuclear Power Plant (FDNPP) accident on March 11, 2011 resulted in the release of immense amounts of radioactive materials into the ocean. However, the dispersion of radioactive materials in the subsurface has not yet been clarified due to the spatiotemporal limitation of observations. Thus, herein, a tracer experiment was implemented using a three-dimensional numerical model to estimate the dispersion path of 137Cs released directly from the FDNPP and its travel time in the subsurface of the North Pacific Ocean from 2011 to 2020. The results show that the subsurface 137Cs spreads by two mode waters, namely, Sub-Tropical Mode Water (STMW) and Central Mode Water (CMW). Subsurface 137Cs primarily spreads clockwise in the sub-tropical region, while a portion driven by STMW is dispersed southward. The clockwise dispersion path of 137Cs released into the ocean by STMW is relatively shallower and inward than that by CMW. The 137Cs that was spread clockwise reached the east of Taiwan and the Philippines via STMW and CMW nine years after the accident, respectively. The model described in this study is applicable for estimating the water path and travel time of tritium water planned to be discharged from Fukushima. </p

Additional file 1 of Application of CRISPR/Cas9-based mutant enrichment technique to improve the clinical sensitivity of plasma EGFR testing in patients with non-small cell lung cancer

Additional file 1. Additional Methods: The methods of qPCR and NGS assay. Additional Discussion: Evaluation of PCR step in CRISPR-CPPC using cfDNA from patients with NSCLC. Table S1: LOB and LOD of CRISPR-CPPC assay for T790M mutation. Table S2: Application of CRISPR-CPPC assay on patient samples. Table S3: Analytical performance of assays for detecting T790M mutation in cfDNA from patients with NSCLC presenting disease progression on 1st or 2nd generation EGFR-TKI. Table S4: Comparison of test results of qPCR to those of CRISPR-CPPC assay and ddPCR for EGFR T790M in cell-free plasma DNA. Table S5: Comparison of the test results of ddPCR to those of CRISPR-CPPC assay for EGFR T790M in cell-free plasma DNA. Table S6: Cases with different ddPCR and CRISPR-CPPC assay results. Table S7: Application of CRISPR-CPPC assay on follow-up patient samples. Table S8: Evaluation of PCR step in CRISPR-CPPC using cfDNA from patients with NSCLC. Fig S1: Study flow chart. Fig S2: Schematic illustration of the CRISPR target site around the human EGFR T790 locus. Fig S3: Distribution of T790M copies from sixty samples in this study

Datasheet1_Analysis of trio test in neurodevelopmental disorders.pdf

BackgroundTrio test has been widely used for diagnosis of various hereditary disorders. We aimed to investigate the contribution of trio test in genetically diagnosing neurodevelopmental disorders (NDD).MethodsWe retrospectively reviewed 2,059 NDD cases with genetic test results. The trio test was conducted in 563 cases. Clinical usefulness, optimal timing, and methods for the trio test were reviewed.ResultsPathogenic or likely pathogenic variants were detected in 112 of 563 (19.9%) patients who underwent the trio test. With trio test results, the overall diagnostic yield increased by 5.4% (112/2,059). Of 165 de novo variants detected, 149 were pathogenic and we detected 85 novel pathogenic variants. Pathogenic, de novo variants were frequently detected in CDKL5, ATP1A3, and STXBP1.ConclusionThe trio test is an efficient method for genetically diagnosing NDD. We identified specific situations where a certain trio test is more appropriate, thereby providing a guide for clinicians when confronted with variants of unknown significance of specific genes.</p

Characterization of mutations.

(A) Mutations classified according to the categories of gene functions. (B) Circos diagram showing co-occurrence and mutual exclusivity of mutations.</p

NGS data analysis flow and bioinformatics tools.

NGS data analysis flow and bioinformatics tools.</p