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Rhie, Arang,Park, Weon Seo,Choi, Moon Kyung,Kim, Ji-Hyun,Ryu, Junsun,Ryu, Chang Hwan,Kim, Jong-Il,Jung, Yuh-Seog Williams & Wilkins Co 2015 Medicine Vol.94 No.50
ABSTRACT: Recently increasing high-risk HPV+ OSCC exhibits unique clinical and molecular characteristics compared to HPV-unrelated (HPV−) counterpart. Genomic copy number variations (CNVs), unique in HPV+ OSCCs, and their role for the prognosis prediction remains poorly studied. Here, we analyzed the distinct genomic copy number variations (CNVs) in human papillomavirus-related (HPV+) oropharyngeal squamous cell carcinoma (OSCC) and their role as a prognosticator after curative resection.For 58 consecutive, Korean OSCC patients that underwent surgery-based treatment with median 10 years of follow-up, HPV-related markers, and genome-wide CNV analysis were analyzed. Clinical associations between the CNV profile and survival analyses were followed.p16 expression predicted the overall survival (OS) (hazard ratio [HR] = 0.27, confidence interval [CI]: 0.39–0.80, P = 0.0006) better than HPV L1 PCR (HR = 0.83, CI: 0.66–1.29, P = 0.64), smoking, or other variables. Although the overall number of CNVs was not significantly different, 30 loci showed unique CNV patterns between the p16 and p16− groups. A region containing PRDM2 was amplified only in the p16 group, whereas EGFR and 11q13.3 showed increased amplification in p16− counterpart. Loss of a locus containing FGF18 led to a worse, but gain of region including CDK10 and RAD18 led to better overall survival (OS) in all OSCC patients. Meanwhile, subgroup analysis of p16 OSCC revealed that amplification of regions harboring HRAS and loss of locus bearing KDR led to better OS.p16 OSCC exhibit distinct CNV patterns compared with p16− counterpart. Specific patterns of CNVs predict better survival, especially in p16 OSCC. This might allow better insights of the outcome after curative resection for HPV+ and HPV− OSCC.
A Simple GUI-based Sequencing Format Conversion Tool for the Three NGS Platforms
Arang Rhie,이경은,Chin Ting Thong,박현석,양산덕 한국유전체학회 2010 Genomics & informatics Vol.8 No.2
To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In this respect, a format conversion tool, as well as quality conversion tool would be the minimum requirements to integrate reads from different platforms. We have developed the Pyrus NGS Sequencing Format Converter, a simple software toolkit which allows to convert three kinds of Next Generation Sequencing reads, into commonly used fasta or fastq formats. The converter modules are all implemented, uniformly, in Java GUI modules that can be integrated in software applications for displaying the data content in the same format.
Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats
이경은,장명하,Arang Rhie,Chin Ting Thong,양산덕,박현석 한국유전체학회 2010 Genomics & informatics Vol.8 No.2
Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
FX: an RNA-Seq analysis tool on the cloud.
Hong, Dongwan,Rhie, Arang,Park, Sung-Soo,Lee, Jongkeun,Ju, Young Seok,Kim, Sujung,Yu, Saet-Byeol,Bleazard, Thomas,Park, Hyun-Seok,Rhee, Hwanseok,Chong, Hyonyong,Yang, Kap-Seok,Lee, Yeon-Su,Kim, In-Hoo Oxford University Press 2012 Bioinformatics Vol.28 No.5
<P>FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-friendly web interface.</P>
De novo assembly and phasing of a Korean human genome
Seo, Jeong-Sun,Rhie, Arang,Kim, Junsoo,Lee, Sangjin,Sohn, Min-Hwan,Kim, Chang-Uk,Hastie, Alex,Cao, Han,Yun, Ji-Young,Kim, Jihye,Kuk, Junho,Park, Gun Hwa,Kim, Juhyeok,Ryu, Hanna,Kim, Jongbum,Roh, Mira Nature Publishing Group, a division of Macmillan P 2016 Nature Vol.538 No.7624
<P>Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing(2), next-generation mapping(3), microfluidics-based linked reads(4), and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.</P>
Yoo Jin Chun,함성일,San Duk Yang,Arang Rhie,박현석 한국유전체학회 2008 Genomics & informatics Vol.6 No.1
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model- View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
J2dpathway: A Global Metabolic Pathway Viewer with Node-Abstracting Features
Eun-Ha Song,,함성일,San-Duk Yang,Arang Rhie,Hyun-Seok Park,이상호 한국유전체학회 2008 Genomics & informatics Vol.6 No.2
The static approach of representing metabolic pathway diagrams offers no flexibility. Thus, many systems adopt automatic graph layout techniques to visualize the topological architecture of pathways. There are weaknesses, however, because automatically drawn figures are generally difficult to understand. The problem becomes even more serious when we attempt to visualize all of the information in a single, big picture, which usually results in a confusing diagram. To provide a partial solution to this thorny issue, we propose J2dpathway, a metabolic pathway atlas viewer that has node-abstracting features.
Chun, Yoo-Jin,Ham, Seong-Il,Yang, San-Duk,Rhie, Arang,Park, Hyun-Seok Korea Genome Organization 2008 Genomics & informatics Vol.6 No.1
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
Ham, Sung-Il,Song, Eun-Ha,Yang, San-Duk,Thong, Chin-Ting,Rhie, Arang,Galbadrakh, Bulgan,Lee, Kyung-Eun,Park, Hyun-Seok,Lee, San-Ho Korea Genome Organization 2009 Genomics & informatics Vol.7 No.3
The characteristics of metabolic pathways make them particularly amenable to layered graph drawing methods. This paper presents a visual Java-based tool for drawing and annotating biological pathways in two- and a-half dimensions (2.5D) as an alternative to three-dimensional (3D) visualizations. Such visualization allows user to display different groups of clustered nodes, in different parallel planes, and to see a detailed view of a group of objects in focus and its place in the context of the whole system. This tool is an extended version of J2dPathway.