교통수요 예측을 위한 기준 및 절차 지침 연구(A study on the guideline to forecast travel demand)

노트 : 이 연구보고서의 내용은 국토연구원의 자체 연구물로서 정부의 정책이나 견해와는 상관없습니다

ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer

BACKGROUND: Alternative splicing events that result in the production of multiple gene isoforms reveals important molecular mechanisms. Gene isoforms are often differentially expressed across organs and tissues, developmental stages, and disease conditions. Specifically, recent studies show that aberrant regulation of alternative splicing frequently occurs in cancer to affect tumor cell transformation and growth. While analysis of isoform expression is important for discovering tumor-specific isoform signatures and interpreting relevant genomic mutations, there is currently no web-based, easy-to-use, and publicly available platform for this purpose. DESCRIPTION: We developed ISOexpresso to provide information regarding isoform existence and expression, which can be grouped by cancer vs. normal conditions, cancer types, and tissue types. ISOexpresso implements two main functions: First, the Isoform Expression View function creates visualizations for condition-specific RNA/isoform expression patterns upon query of a gene of interest. With this function, users can easily determine the major isoform (the most expressed isoform in a sample) of a gene with respect to the condition and check whether it matches the known canonical isoform. ISOexpresso outputs expression levels of all known transcripts to check alterations of expression landscape and to find potential tumor-specific isoforms. Second, the User Data Annotation function supports annotation of genomic variants to determine the most plausible consequence of a variation (e.g., an amino acid change) among many possible interpretations. As most coding sequence mutations are effective through the subsequent transcription and translation, ISOexpresso automatically prioritizes transcripts that act as backbones for mutation effect prediction by their relative expression. By employing ISOexpresso, we could investigate the consistency between the most expressed and known canonical/principal isoforms, as well as infer candidate tumor-specific isoforms based on their expression levels. In addition, we confirmed that ISOexpresso could easily reproduce previously known isoform expression patterns: recurrent observation of a major isoform across tissues, differential isoform expression patterns in a given tissue, and switching of major isoform during tumorigenesis. CONCLUSIONS: ISOexpresso serves as a web-based, easy-to-use platform for isoform expression and alteration analysis based on large-scale cancer database. We anticipate that ISOexpresso will expedite formulation and confirmation of novel hypotheses by providing isoform-level perspectives on cancer research. The ISOexpresso database is available online at http://wiki.tgilab.org/ISOexpresso/ .ope

Isoform specific gene expression analysis of KRAS in the prognosis of lung adenocarcinoma patients

BACKGROUND: Aberrant mutations in KRAS play a critical role in tumor initiation and progression, and are a negative prognosis factor in lung adenocarcinoma (LUAD). RESULTS: Using genomic analysis for K-Ras isoforms (K-Ras4A and K-Ras4B) and large-scale multi-omics data, we inspected the overall survival (OS) and disease-free survival (DFS) of LUAD patients based on the abundance of transcript variants by analyzing RNA expression and somatic mutation data from The Cancer Genome Atlas (n = 516). The expression of the minor transcript K-Ras4A and its proportion were positively correlated with the presence of KRAS mutations in LUAD. We found that both K-Ras4A abundance measures (expression and proportion) have a strong association with poor OS (p = 0.0149 and p = 3.18E-3, respectively) and DFS (p = 3.03E-4 and p = 0.0237, respectively), but only in patients harboring KRAS mutations. A Cox regression analysis showed significant results in groups with low expression (hazard ratio (HR) = 2.533, 95% confidence interval (CI) = 1.380-4.651, p = 2.72E-3) and low proportion (HR = 2.549, 95% CI = 1.387-4.684, p = 2.58E-3) of K-Ras4A. CONCLUSIONS: Based on the above results, we report the possible use of abundance measures for K-Ras4A for predicting the survival of LUAD patients with KRAS mutations.ope

Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification.ope

Cross-species oncogenic signatures of breast cancer in canine mammary tumors

Genomic and precision medicine research has afforded notable advances in human cancer treatment, yet applicability to other species remains uncertain. Through whole-exome and transcriptome analyses of 191 spontaneous canine mammary tumors (CMTs) that exhibit the archetypal features of human breast cancers, we found a striking resemblance of genomic characteristics including frequent PIK3CA mutations (43.1%), aberrations of the PI3K-Akt pathway (61.7%), and key genes involved in cancer initiation and progression. We also identified three gene expression-based CMT subtypes, one of which segregated with basal-like human breast cancer subtypes with activated epithelial-to-mesenchymal transition, low claudin expression, and unfavorable disease prognosis. A relative lack of ERBB2 amplification and Her2-enrichment subtype in CMT denoted species-specific molecular mechanisms. Taken together, our results elucidate cross-species oncogenic signatures for a better understanding of universal and context-dependent mechanisms in breast cancer development and provide a basis for precision diagnostics and therapeutics for domestic dogs.ope

Analysis of Kinship Index Distributions in Koreans Using Simulated Autosomal STR Profiles

Kinship testing in forensic casework is largely based on a likelihood ratio (LR) approach with short tandem repeat (STR) markers; however, in order to efficiently identify potential relatives in a specific population, the threshold values for kinship prediction should be determined by analyzing the kinship index distributions of the population in question. In this study, 250,000 DNA profiles were simulated using allele frequencies at 20 autosomal STR loci in Koreans, then the LRs were calculated for true close relatives and unrelated pairs. The LR distributions in related and unrelated pairs under a given relationship were compared in 2 sets of 13 Combined DNA Index System (CODIS) and 20 STR profiles. Using 13 CODIS STRs, true relatives in parent/child and full-sibling relationships were sufficiently discriminated from unrelated pairs with LR thresholds of 1,000 and 100, respectively. However, the CODIS STRs lacked the discriminatory power to differentiate between related and unrelated pairs in uncle/nephew and first cousin relationships due to high false-positive and false-negative rates with a LR threshold of 10. Increasing the number of STR loci to 20 increased discrimination of close relatives, but high false results remained in uncle/nephew and first cousin relationships. The kinship index data from this study will help make decisions on various kinship testing and familial searching in Koreans.ope

Sequence Generation and Genotyping of 15 Autosomal STR Markers Using Next Generation Sequencing

Recently, next generation sequencing (NGS) has received attention as the ultimate genotyping method to overcome the limitations of capillary electrophoresis (CE) based short tandem repeat (STR) analysis, such as the limited number of STR loci that can be measured simultaneously using fluorescent-labeled primers and the maximum size of STR amplicons. In this study, we analyzed 15 autosomal STR markers via the NGS method and evaluated their effectiveness in STR analysis. Using male and female standard DNA as single-sources and their 1:1 mixture, we sequentially generated sample amplicons by the multiplex polymerase chain reaction (PCR) method, constructed DNA libraries by ligation of adapters with a multiplex identifier (MID), and sequenced DNA using the Roche GS Junior Platform. Sequencing data for each sample were analyzed via alignment with pre-built reference sequences. Most STR alleles could be determined by applying a coverage threshold of 20% for the two single-sources and 10% for the 1:1 mixture. The structure of the STR in each allele was accurately determined by examining the sequences of the target STR region. The mixture ratio of the mixed sample was estimated by analyzing the coverage ratios between assigned alleles at each locus and the reference/variant ratios from the observed sequence variations. In conclusion, the experimental method used in this study allowed the successful generation of NGS data. In addition, the NGS data analysis protocol enables accurate STR allele call and repeat structure determination at each locus. Therefore, this approach using the NGS system will be helpful to interpret and analysis the STR profiles from singe-source and even mixed samples in forensic investigation.ope

Web-based Y-STR Database for Haplotype Frequency Estimation and Kinship Index Calculation

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討論

사회 : 李廷攻선생께서 그 동안 complementation에 대해 시도된 기술 방법에 대해 잘 요약해서 말씀해 주셨읍니다. 맨 먼저 본격적으로 complementation에 대해 시도하신 분이 李廷攻선생님이신데 먼저 李선생님께서 좀 말씀해 주시지요. 그 당시 취했던 기술방법과 지금 어떤 차이가 있다던지..

Next-generation sequencing reveals somatic mutations that confer exceptional response to everolimus

BACKGROUND: Given the modest responses to everolimus, a mTOR inhibitor, in multiple tumor types, there is a pressing need to identify predictive biomarkers for this drug. Using targeted ultra-deep sequencing, we aimed to explore genomic alterations that confer extreme sensitivity to everolimus. RESULTS: We collected formalin-fixed paraffin-embedded tumor/normal pairs from 39 patients (22 with exceptional clinical benefit, 17 with no clinical benefit) who were treated with everolimus across various tumor types (13 gastric cancers, 15 renal cell carcinomas, 2 thyroid cancers, 2 head and neck cancer, and 7 sarcomas). Ion AmpliSeqTM Comprehensive Cancer Panel was used to identify alterations across all exons of 409 target genes. Tumors were sequenced to a median coverage of 552x. Cancer genomes are characterized by 219 somatic single-nucleotide variants (181 missense, 9 nonsense, 7 splice-site) and 22 frameshift insertions/deletions, with a median of 2.1 mutations per Mb (0 to 12.4 mutations per Mb). Overall, genomic alterations with activating effect on mTOR signaling were identified in 10 of 22 (45%) patients with clinical benefit and these include MTOR, TSC1, TSC2, NF1, PIK3CA and PIK3CG mutations. Recurrently mutated genes in chromatin remodeling genes (BAP1; n = 2, 12%) and receptor tyrosine kinase signaling (FGFR4; n = 2, 12%) were noted only in patients without clinical benefit. CONCLUSIONS: Regardless of different cancer types, mTOR-pathway-activating mutations confer sensitivity to everolimus. Targeted sequencing of mTOR pathway genes facilitates identification of potential candidates for mTOR inhibitors.ope