• Genomics & Informatics
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• 제19권4호
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• pp.40.1-40.11
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• 2021

Mutation signatures represent unique sequence footprints of somatic mutations resulting from specific DNA mutagenic and repair processes. However, their causal associations and the potential utility for genome research remain largely unknown. In this study, we performed PanCancer-scale correlative analyses to identify the genomic features associated with tumor mutation burdens (TMB) and individual mutation signatures. We observed that TMB was correlated with tumor purity, ploidy, and the level of aneuploidy, as well as with the expression of cell proliferation-related genes representing genomic covariates in evaluating TMB. Correlative analyses of mutation signature levels with genes belonging to specific DNA damage-repair processes revealed that deficiencies of NHEJ1 and ALKBH3 may contribute to mutations in the settings of APOBEC cytidine deaminase activation and DNA mismatch repair deficiency, respectively. We further employed a strategy to identify feature-driven, de novo mutation signatures and demonstrated that mutation signatures can be reconstructed using known causal features. Using the strategy, we further identified tumor hypoxia-related mutation signatures similar to the APOBEC-related mutation signatures, suggesting that APOBEC activity mediates hypoxia-related mutational consequences in cancer genomes. Our study advances the mechanistic insights into the TMB and signature-based DNA mutagenic and repair processes in cancer genomes. We also propose that feature-driven mutation signature analysis can further extend the categories of cancer-relevant mutation signatures and their causal relationships.

• 한국콘텐츠학회논문지
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• 제7권11호
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• pp.94-101
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• 2007

본 논문에서는 알려지지 않은 변형 웜을 탐지하기 위한 방법을 제안한다. 그 방법으로, 페이로드 영역에서 시그니쳐 생성 방안들을 패턴인식 알고리즘으로 연구되었던 Suffix Tree중에서 Longest Common Subsequence(LCSeq) 기법을 이용하여 새로운 시그니쳐를 자동적으로 생성할 수 있는 프로그램을 설계하여 구현하였다. 테스트를 통해 코드레드 웜과 님다 웜의 변종을 검출하는 과정을 보여주고 기존 snort의 시그니쳐와 LCSeq를 이용해 생성된 시그니쳐를 비교 평가하였다.

• Experimental and Molecular Medicine
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• 제50권11호
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• pp.7.1-7.12
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• 2018

Recent findings from The Cancer Genome Atlas project have provided a comprehensive map of genomic alterations that occur in hepatocellular carcinoma (HCC), including unexpected mutations in apolipoprotein B (APOB). We aimed to determine the clinical significance of this non-oncogenetic mutation in HCC. An Apob gene signature was derived from genes that differed between control mice and mice treated with siRNA specific for Apob (1.5-fold difference; P < 0.005). Human gene expression data were collected from four independent HCC cohorts (n = 941). A prediction model was constructed using Bayesian compound covariate prediction, and the robustness of the APOB gene signature was validated in HCC cohorts. The correlation of the APOB signature with previously validated gene signatures was performed, and network analysis was conducted using ingenuity pathway analysis. APOB inactivation was associated with poor prognosis when the APOB gene signature was applied in all human HCC cohorts. Poor prognosis with APOB inactivation was consistently observed through cross-validation with previously reported gene signatures (NCIP A, HS, high-recurrence SNUR, and high RS subtypes). Knowledge-based gene network analysis using genes that differed between low-APOB and high-APOB groups in all four cohorts revealed that low-APOB activity was associated with upregulation of oncogenic and metastatic regulators, such as HGF, MTIF, ERBB2, FOXM1, and CD44, and inhibition of tumor suppressors, such as TP53 and PTEN. In conclusion, APOB inactivation is associated with poor outcome in patients with HCC, and APOB may play a role in regulating multiple genes involved in HCC development.

• 정보처리학회논문지C
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• 제10C권6호
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• pp.747-754
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• 2003

본 논문에서는 DNA 생체정보와 소유자 기반의 hardware RFID(Radio Frequency Identification) 스마트카드, 그리고 Software 인증 분야인 PKI 전자서명을 도입한 다중 사용자 인증시스템을 제시한다. 이는 현 시스템의 인가딘 자의 접근 방법인 ID or password 가 안전한 방법이 아니므로 논문[1] 에서 제안한 사항을 다음과 같이 개선하였다. 즉, 사용자 인증 카드인 two card(the biometric registered seal card and the DNA persional ID card) 대신 하나의 RFID 스마트카드로 사용자 인증을 할 수 있고, 카드 분실시 사용자 정보 노출의 위험을 저가의 RFID로 해결한다. 또한 DNA personal ID 민으로 일난성 쌍둥이, 수혈한 환다, 암세포에서 돌연변이가 발생한 경우의 사용자 인증이 어려운 경우까지 사용자 ID 에 대응하는 일회용 의사난수와 DNA 정보로 사용자 인증을 해결하였다. 그러므로 현 생체 정보 사용자 인증시스템의 단점인 패턴 매칭과 패턴 비교의 에러르 정확한 digital DNA 생체정보로 안전하게 스마트카드에 저장하여 터미널에 로그온하는 local applications에 적용할 수 있다. 스미트카드내 RFID는 사용자를 판독, 추적, 관리할 수 있으므로 카드 분실시 카드 위치를 추적하고 개인 정보를 관리할 수 있으며, 어떠한 개인 DNA 정보도 노출되지 않는다. 현 PKI 전자서명의 비밀키 안전성을 해결한다. 뿐만 아니라 이러한 시스템은 생체정보의 RFID 스마트카드 사용 확대 계기로, 신용카드, 신분증, 그리고 여권 등에서도 이용할 수 있다. 제시한 시스템의 안전성을 통계학적 분석으로 보여진다.

• Journal of Microbiology and Biotechnology
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• 제19권3호
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• pp.217-228
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• 2009

Mobile genetic segments, or transposons, are also referred to as jumping genes as they can shift from one position in the genome to another, thus inducing a chromosomal mutation. According to the target site-specificity of the transposon during a transposition event, the result is either the insertion of a gene of interest at a specific chromosomal site, or the creation of knockout mutants. The former situation includes the integration of conjugative transposons via site-specific recombination, several transposons preferring a target site of a conserved AT-rich sequence, and Tn7 being site-specifically inserted at attTn7, the downstream of the essential glmS gene. The latter situation is exploited for random mutagenesis in many prokaryotes, including IS (insertion sequence) elements, mariner, Mu, Tn3 derivatives (Tn4430 and Tn917), Tn5, modified Tn7, Tn10, Tn552, and Ty1, enabling a variety of genetic manipulations. Randomly inserted transposons have been previously employed for a variety of applications such as genetic footprinting, gene transcriptional and translational fusion, signature-tagged mutagenesis (STM), DNA or cDNA sequencing, transposon site hybridization (TraSH), and scanning linker mutagenesis (SLM). Therefore, transposon-mediated genetic engineering is a valuable discipline for the study of bacterial physiology and pathogenesis in living hosts.