• Title/Summary/Keyword: DNA-index

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Increased Free Circulating DNA Integrity Index as a Serum Biomarker in Patients with Colorectal Carcinoma

  • El-Gayar, Dina;El-Abd, Nevine;Hassan, Noha;Ali, Reem
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.3
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    • pp.939-944
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    • 2016
  • Background: Cell-free DNA circulating in blood is a candidate biomarker for malignant tumors. Unlike uniformly truncated DNA released from apoptotic non diseased cells, DNA released from necrotic cancer cells varies in size. Objectives: To measure the DNA integrity index in serum and the absolute DNA concentration to assess their clinical utility as potential serum biomarkers for colorectal carcinoma (CRC) compared to CEA and CA19-9. Materials and Methods: Fifty patients with CRC, 10 with benign colonic polyps and 20 healthy sex and age matched volunteers, were investigated by real time PCR of ALU repeats (ALU q-PCR) using two sets of primers (115 and 247 bp) amplifying different lengths of DNA fragments. The DNA integrity index was calculated as the ratio of q-PCR results of ALU 247/ALU 115bp. Results: Serum DNA integrity was statistically significantly higher in CRC patients compared to the benign and control groups (p<0.001). ROC curves for differentiating CRC patients from normal controls and benign groups had areas under curves of 0.90 and 0.85 respectively. Conclusions: The DNA integrity index is superior to the absolute DNA concentration as a potential serum biomarker for screening and diagnosis of CRC. It may also serve as an indicator for monitoring the progression of CRC patients. Combining CEA and CA19-9 with either of the genetic markers studied is better than either of them alone.

Fast Construction of Suffix Arrays for DNA Strings (DNA 스트링에 대하여 써픽스 배열을 구축하는 빠른 알고리즘)

  • Jo, Jun-Ha;Kim, Nam-Hee;Kwon, Ki-Ryong;Kim, Dong-Kyue
    • Journal of KIISE:Computer Systems and Theory
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    • v.34 no.8
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    • pp.319-326
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    • 2007
  • To perform fast searching in massive data such as DNA strings, the most efficient method is to construct full-text index data structures of given strings. The widely used full-text index structures are suffix trees and suffix arrays. Since the suffix may uses less space than the suffix tree, the suffix array is proper for DNA strings. Previously developed construction algorithms of suffix arrays are not suitable for DNA strings since those are designed for integer alphabets. We propose a fast algorithm to construct suffix arrays on DNA strings whose alphabet sizes are fixed by 4. We reduce the construction time by improving encoding and merging steps on Kim et al.[1]'s algorithm. Experimental results show that our algorithm constructs suffix arrays on DNA strings 1.3-1.6 times faster than Kim et al.'s algorithm, and also for other algorithms in most cases.

Efficient Indexing for Large DNA Sequence Databases (대용량 DNA 시퀀스 데이타베이스를 위한 효율적인 인덱싱)

  • Won Jung-Im;Yoon Jee-Hee;Park Sang-Hyun;Kim Sang-Wook
    • Journal of KIISE:Databases
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    • v.31 no.6
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    • pp.650-663
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    • 2004
  • In molecular biology, DNA sequence searching is one of the most crucial operations. Since DNA databases contain a huge volume of sequences, a fast indexing mechanism is essential for efficient processing of DNA sequence searches. In this paper, we first identify the problems of the suffix tree in aspects of the storage overhead, search performance, and integration with DBMSs. Then, we propose a new index structure that solves those problems. The proposed index consists of two parts: the primary part represents the trie as bit strings without any pointers, and the secondary part helps fast accesses of the leaf nodes of the trio that need to be accessed for post processing. We also suggest an efficient algorithm based on that index for DNA sequence searching. To verify the superiority of the proposed approach, we conducted a performance evaluation via a series of experiments. The results revealed that the proposed approach, which requires smaller storage space, achieves 13 to 29 times performance improvement over the suffix tree.

Genetic status of Acanthamoeba spp. Korean isolates on the basis of RAPD markers (RAPD 표지자 분석 에 의한 가시아메바속 한국분리주의 유전적 지위)

  • 홍용표;오승환
    • Parasites, Hosts and Diseases
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    • v.33 no.4
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    • pp.341-348
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    • 1995
  • Genetic status of Acnnthamoebc sap. were tested on the basis of random amplified polymorphic DNA (RAPD) marker analysis. Four previously established Accnthcmoebn species, 4 Korean isolates of Acnnthamoeba sp., and one American isolate of Acanthcmoebc sp. were analyzed by RAPD-PCR using an arbitrary decamer primers. Amplification products were fractionated by agarose gel electrophoresis and slainrd by ethidium bromide . Eighteen primers produced DNA amplification profiles revealing clear differences among 4 species. Nine of them also produced DNA amplification profiles which included some isolate-specific amplification products. On the basis of amplified fragments by 18 primers, the pairwise similarity indices between A. culbensoni and other species (i.e. A. hntchetti, A. trinngularis, A. polyphaga) were 0.300, 0.308, and 0.313, respectively. Similarity index between A. hctchetti and A. triansulcris was 0.833. The mean similarity index among the 3 Korean isolates (YM-2, -3, -4) was 0.959 and 0.832 among them and 2 other species (A. hatchetti and A. triongulnris). The mean similarity index among YM-5 and other Korean isolates (YM-2, -3, -4) was 0.237. However, the similarity index between YM-5 and A. culbeksoni was 0.857, which suggests that YM-5 is genetically more similar to A. culbertsoni than other Korean isolates. Phonogram reconstructed by UPGMA method revealed that there are two groups: one group consists of A. hctchetti, A. tlonsulcns, and 3 Korean isolates (YM-2, -3, -4) , and the other group consists of A. cuLbensoni. A. polwphosc, HOV, and YM-5.

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Primers for typing Listeria spp. using Random Amplified Polymorphic DNA (RAPD) ANalysis (Listeria spp.의 RAPD typing을 위한 Primer의 분리력 비교)

  • 임형근;홍종해;박경진;최원상
    • Journal of Food Hygiene and Safety
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    • v.18 no.2
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    • pp.67-72
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    • 2003
  • Random amplified Polymorphic DNA (RAPD) analysis Is based on the amplification of random DNA segment using a single arbitrary primer. Polymorphic DNA patterns identified by this method can be used for typing Listeria monocytogenes. To select the primers for RAPD typing Listeria spp., the performance of 31 primers were compared by analyzing 13 Listeria spp. reference strains. Reproducible electrophoresis patterns were obtained. Among 31 primers, 6 primers (primer 6, HLWL74, UBC155, UBC127, Lis5, Lis11) showed better differentiation, when discrimination index, band clarity, band number, difficulty of band scoring were considered than the others. These primers will be useful far typing Listeria spp. in the future. Currently, we are under investigation for the RAPD typing of contaminated L. monocytogenes for the risk analysis of pork processing plant using these primers.

Cytogenic Effects of Transplacentally Administered 2-Bromopropane -Pattern of Replicative DNA Synthesis(RDS) by BrdU Labeling Method- (2-Bromopropane의 경태반 영향에 관한 연구 -마우스 태자로의 이행과 태자세포의 복제 DNA합성세포에 관하여-)

  • 김영환;배은상
    • Journal of environmental and Sanitary engineering
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    • v.13 no.3
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    • pp.37-42
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    • 1998
  • 2-Bromopropane has been implicated to be the reason for the mass intoxication of workers at an electronic company in Korea. 2-Bromopropane deposition and pattern of DNA replication in mouse fetuses were analyzed after intravenous injection of 2-bromopropane. Injections were administered to pregnant ICR mice in order to cytogenetically evaluate transplacental 2-bromopropane. The results are summarized as follows; 1. A dose-dependent effect on DNA replication was observed equally in the lung, liver and kideneys of fetuses has been exposed to 2-bromopropane transplacentally as reductions of the labeling index. 2. Deposition of transplacentally administred 2-bromopropane in the fetus was lower than placenta.

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Genetic Variation of Korean Lepista nuda (한국산 민자주방망이 버섯의 유전적 변이)

  • 김승희;김종봉
    • Journal of Life Science
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    • v.14 no.1
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    • pp.115-120
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    • 2004
  • Lepista nuda is a world-wide species which has and international reputation as a excellent edible species. In this study, we investigated the genetic variation and taxonomic relationship of L. nuda and other five Tricholomataceae species were analyzed by random amplied polymorphic DNA (RAPD). 15 kinds of random primers were used. The distance matrix was calculated using UPGMA and phyolgenetic relationship were inferred by neighnor-joining (NJ) method. Various bands of 100bp∼1600bp were observed in electrophoretic patterns of RAPD. Nei's genetic distance was calculated using a total of 228 DNA bands identified, and phylogenetic tree was made. The Nei's genetic variations of L. nuda, Lepista surdida, Collybia peronata, Collybia confluens, Lyophyllum cinerascens, Laccara laccata were 0∼21.3%, 21.2∼28.0%, 15.4∼23.0%, 14∼21.8%, 16.5∼34.6%, and 12.4∼27.4%, respectively The consistency index, the retention index and homoplasy index were 0.5217, 0.5769 and 0.5156, respectively. Also, two groups could be made by NJ tree. The genetic distance between L. nuda and C. confluens was closer than that between L. nuda and L. sordida.

A DNA Index Structure using Frequency and Position Information of Genetic Alphabet (염기문자의 빈도와 위치정보를 이용한 DNA 인덱스구조)

  • Kim Woo-Cheol;Park Sang-Hyun;Won Jung-Im;Kim Sang-Wook;Yoon Jee-Hee
    • Journal of KIISE:Databases
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    • v.32 no.3
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    • pp.263-275
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    • 2005
  • In a large DNA database, indexing techniques are widely used for rapid approximate sequence searching. However, most indexing techniques require a space larger than original databases, and also suffer from difficulties in seamless integration with DBMS. In this paper, we suggest a space-efficient and disk-based indexing and query processing algorithm for approximate DNA sequence searching, specially exact match queries, wildcard match queries, and k-mismatch queries. Our indexing method places a sliding window at every possible location of a DNA sequence and extracts its signature by considering the occurrence frequency of each nucleotide. It then stores a set of signatures using a multi-dimensional index, such as R*-tree. Especially, by assigning a weight to each position of a window, it prevents signatures from being concentrated around a few spots in index space. Our query processing algorithm converts a query sequence into a multi-dimensional rectangle and searches the index for the signatures overlapped with the rectangle. The experiments with real biological data sets revealed that the proposed method is at least three times, twice, and several orders of magnitude faster than the suffix-tree-based method in exact match, wildcard match, and k- mismatch, respectively.

Prognosis of Colorectal Cancer and Apoptosis Activation (대장암의 예후와 Apoptosis 활성)

  • 전소영;배옥석;김종봉
    • Biomedical Science Letters
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    • v.4 no.2
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    • pp.121-128
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    • 1998
  • We studied on the expression of apoptosis in colorectal cancer, lymph node, their corresponding normal mucosa and colorectal cancer patient's blood by genomic DNA electrophoresis and TUNEL labeling method. From 7 cases among 37, 20 cases among 47 and 5 cases among 15, DNA ladders were expressed in normal tissues, colorectal tissues and Iymph node tissues, respectively. A DNA ladder was not observed in 7 cases of colorectal cancer patients blood. In case of TUNEL labeling, we could observe TUNEL color espression in colorectal cancer and lymph node tissues. As these result suggest that apoptotic index may be associated with the colorectal cancer development, and mat be used as a prognostic indicator but further evaluations will be needed.

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The Genetic Analysis Study of Ancient Human Bones Excavated at Janggi-dong site, Gimpo (김포 장기동 유적 출토 인골의 유전자 분석 연구)

  • Seo, Min Seok;Cho, Eun Min;Kim, Yun Ji;Kim, Sue Hoon;Kang, So Yeong
    • Journal of Conservation Science
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    • v.30 no.4
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    • pp.409-416
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    • 2014
  • Most human bones of Joseon Dynasty period are so good condition that we can do research in physical anthropology, genetics and chemistry with them. In this study, we analyzed DNA typing using 6 human bones of Joseon dynasty period excavated at Janggi-dong, Gimpo. The DNA typing was mitochondrial DNA haplotype, Y-chromosome haplotype and sex determination. Prior to DNA analysis, we distinguished histological index of 6 human bones. As the result of mitochondrial DNA analysis, most of bones were confirmed as haplogroup G, R11, M7, A5, etc. As the result of sex determination, 4 human bones were female and 2 human bones were male. The male haplogroup was confirmed as haplogroup O by the single nucleotide polymorphism analysis of Y chromosome. For extensive ancient human bone analysis, researchers need to apply a histological index to select ancient human bones and explain a relationship among ancient human bones with various analyses of mitochondrial and nuclear DNA.