• Title/Summary/Keyword: Y chromosome

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Development of a Window Program for Searching CpG Island (CpG Island 검색용 윈도우 프로그램 개발)

  • Kim, Ki-Bong
    • Journal of Life Science
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    • v.18 no.8
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    • pp.1132-1139
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    • 2008
  • A CpG island is a short stretch of DNA in which the frequency of the CG dinucleotide is higher than other regions. CpG islands are present in the promoters and exonic regions of approximately $30{\sim}60$% of mammalian genes so they are useful markers for genes in organisms containing 5-methylcytosine in their genomes. Recent evidence supports the notion that the hypermethylation of CpG island, by silencing tumor suppressor genes, plays a major causal role in cancer, which has been described in almost every tumor types. In this respect, CpG island search by computational methods is very helpful for cancer research and computational promoter and gene predictions. I therefore developed a window program (called CpGi) on the basis of CpG island criteria defined by D. Takai and P. A. Jones. The program 'CpGi' was implemented in Visual C++ 6.0 and can determine the locations of CpG islands using diverse parameters (%GC, Obs (CpG)/Exp (CpG), window size, step size, gap value, # of CpG, length) specified by user. The analysis result of CpGi provides a graphical map of CpG islands and G+C% plot, where more detailed information on CpG island can be obtained through pop-up window. Two human contigs, i.e. AP00524 (from chromosome 22) and NT_029490.3 (from chromosome 21), were used to compare the performance of CpGi and two other public programs for the accuracy of search results. The two other programs used in the performance comparison are Emboss-CpGPlot and CpG Island Searcher that are web-based public CpG island search programs. The comparison result showed that CpGi is on a level with or outperforms Emboss-CpGPlot and CpG Island Searcher. Having a simple and easy-to-use user interface, CpGi would be a very useful tool for genome analysis and CpG island research. To obtain a copy of CpGi for academic use only, contact corresponding author.

Improvement of Pregnancy Rate in Preimplantation Genetic Diagnosis with FISH Procedure by the Laboratory Optimization and Experiences (형광직접보합법을 이용한 착상전 유전진단 기법의 최적화와 경험 축적에 의한 임신율의 향상)

  • Lim, Chun-Kyu;Min, Dong-Mi;Lee, Hyoung-Song;Byun, Hye-Kyung;Park, So-Yeon;Ryu, Hyun-Mee;Kim, Jin-Young;Koong, Mi-Kyoung;Kang, Inn-Soo;Jun, Jin-Hyun
    • Clinical and Experimental Reproductive Medicine
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    • v.31 no.1
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    • pp.29-39
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    • 2004
  • Objectives: This study was performed to evaluate the laboratory system for successful PGD using fluorescence in situ hybridization (FISH) and the clinical outcome of PGD cycles in five years experiences. Methods: A total of 181 PGD-FISH cycles of 106 couples were performed, and diagnosed chromosome normality in the preimplantation embryos. The laboratory and clinical data were classified by the following optimization steps, and statistically analyzed. Phase I: Blastomere biopsy with two kinds of pipettes, removal of cytoplasmic proteins without treatment of pepsin and culture of biopsied embryos with single medium; Phase II: Blatomere biopsy with single pipette, removal of cytoplasmic proteins with pepsin and culture of biopsied embryos with single medium; Phase III: Blastomere biopsy with single pipette, removal of cytoplasmic proteins with pepsin and culture of biopsied embryos with sequential media. Results: A total of 3, 209 oocytes were collected, and 83.8% (2, 212/2, 640) of fertilization rate was obtained by ICSI procedure. The successful blastomere biopsies were accomplished in 98.6% (2, 043/2, 071) of embryos, and the successful diagnosis rate of FISH was 94.7% (1, 935/ 2, 043) of blastomeres from overall data. Embryo transfers with normal embryos were conducted in 93.9% (170/181) of started cycles. There was no difference in the successful rate of biopsy and diagnosis among Phase I, II and III. However, the pregnancy rate per embryo transfer of Phase III (38.8%, 26/67) was significantly (p<0.05) higher than those of Phase I (13.9%, 5/36) and Phase II (14.9%, 10/67). Conclusions: The laboratory optimization and experience for the PGD with FISH procedure can increase the pregnancy rate to 38.8% in the human IVF-ET program. Our facility of PGD with FISH provides the great possibility to get a normal pregnancy for the concerned couples by chromosomal aberrations.

Development of Disease-resistant Japonica Rice Varieties and Effects of Pyramiding Resistance Genes (내병성 자포니카 벼 계통 육성과 저항성 유전자 집적효과)

  • Kim, Woo-Jae;Baek, Man-Kee;Park, Hyeon-Su;Lee, Geon-Mi;Lee, Chang-Min;Kim, Seok-Man;Cho, Young-Chan;Seo, Jeong-Phil;Jeong, O-Young
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.65 no.4
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    • pp.314-326
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    • 2020
  • This study was carried out to develop a resistant variety against the K3a race of bacterial blight, Xanthomonas oryzae pv. oryzae, through expansion and pyramiding of resistance genes. To develop an elite bacterial blight-resistant cultivar, the breeding process and bacterial blight resistance reactions in advanced backcross lines (ABLs) were analyzed. ABLs21 which contain Xa3 and Xa21, were developed by double backcrossing japonica cultivar Hwanggeumnuri, which has bacterial blight resistant Xa3 gene, and indica variety IRBB21, which havs Xa21 gene, followed by disease resistance bioassay and marker-assisted selection. The resistance genes of ABLs21 were amplified by PCR with the molecular markers 9643.T4 (Xa3) and U1/I1 (Xa21). Hwanggeumnuri and IRBB3 showed resistance reactions against K1, K2, and K3 races, and a susceptible reaction against K3a, K4, and K5 races. IRBB21 showed resistance reactions against K2, K3, K3a, K4 and K5 races, and a susceptible reaction against K1 race. Hwanggeumnuri showed susceptible reactions at the seedling, tillering and adult stages (all stages), whereas ABL21-1 showed moderate resistance at the tillering stage. ABL21-1 showed stable resistance against 18 isolates of K3a race, and the lesion length was shorter than that of the donor parents. In cluster analysis, the HB4032 isolate showed the highest pathogenicity among the 18 isolates. The molecular marker polymorphisms and average substituted chromosome segment lengths of ABLs21 were 63.2 % and 86.1 cM, respectively. Insertion of the donor chromosomal segments occurred in the predicted region of the Xa21 gene of ABLs21.

The spectrum of 5p deletion in Korean 20 patients with Cri du chat syndrome (한국인 묘성증후군 20명 환자에서의 5p 결실 양상 분석)

  • Park, Sang-Jin;Kim, Sook-Ryung;Baek, Kum-Nyeo;Yoon, Joon-No;Jeong, Eun-Jeong;Kown, Ji-Eun;Kim, Hyon-J.
    • Journal of Genetic Medicine
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    • v.4 no.2
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    • pp.133-141
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    • 2007
  • Purpose : Cri-du-Chat syndrome (CdCs) is a rare but clinically recongnizable condition with an estimated incidence of 1:50,000 live births. The clinical characteristics of the syndrome include severe psychomotor and mental retardation, microcephaly, hypertelorism, hypotonia, and slow growth. Also the size of the chromosome 5p deletion ranges were known from the region 5p13 to the terminal region. In this study, we report the spectrum of 5p deletion in Korean 20 pts. with CdCs and genotype-phenotype associations in CdCs. Methods : In order to delineate genotype-phenotype correlation, molecular cytogenetic studies including GTG banding and clinical characterization were performed on Korean 20 pts with CdCs including parents. CGH array and Fluorescence in situ hybridization (FISH) analysis were used to confirm a terminal deletion karyotype and map more precisely the location of the deletion breakpoint. Results : Molecular analysis of the spectrum of 5p deletion revealed 9 pts (45%) with a del (5)(p14), 7 pts. (35%) a del (5)(p13), 3 pts. (15%) a del (5)(p15.1) and 1 pt. (5%) a del (5)(p15.2) in 20 pts with CdCs. 4(20%)pts were identified to have additional chromosome abnormalites of deficiency and duplication involving chromosomes of 6, 8, 18, & 22. Parental study identified 3 familial case (2 paternal and 1 maternal origin) showing parents being a balanced translocation carrier. And the comparison study of the deletion break points among these 20 pts. with their phenotype has showed the varying clinical pheno-types in the CdCs critical region. Conclusion : The characterization of 5p deletion including parental study may help to delineate the genotypephenotype correlation in CdCs. Also these molecular cytogenetic analyses will be able to offer better information for accurate genetic diagnosis in CdCs and further make possible useful genetic counseling in pts. and family.

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Development of Microsatellite Markers using BAC clone Sequencing on Porcine Chromosome 6q28 - 6q32 (돼지 6번 염색체(6q28 - 6q32)의 BAC clone 염기서열 분석에 의한 Microsatellite Markers 개발)

  • Chang, K.W.;Lee, K.T.;Park, E.W.;Choi, B.H.;Kim, T.H.;Cheong, I.C.;Oh, S.J.
    • Journal of Animal Science and Technology
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    • v.46 no.3
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    • pp.301-306
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    • 2004
  • This study was conducted to develop new markers at the region that was related to QTL affecting intramuscular fat and backfat thickness on chromosome 6q28 - 6q32 in pigs. Dozens of repeated sequences were founded using shotgun sequencing of several BAC clones corresponding to that region, of which five new microstellite markers that identified polymorphism were discovered. The mean number of alleles at each locus observed 2.13(KP0290F2), 4.63(KP0248Cll), 7.38(KP1231C91), 2.75(KPI23IC92) and 6.2S(KP1231C93) in 8 breeds(Landrace, Korean native pig, Duroc, Yorkshire, Berkshire, Wuzhishan pig, Xiang pig, Min pig). The average estimated heterozygosity values at each locus varied from 0.2100(KP0290F2) to 0.8304(KPI23IC91) in all populations. In other hand, the average allele of all loci WlL'I within range of 0.4517(Berkshire) and 0.6957 (Yorkshire). Of these markers, KP0248C11, KP1231C91 and KP1231C93 were identified to have optimal number of alleles, high heterozygosity values and low standard deviation values. Especially, KPI23IC91 and KPI231C93 might be considered as a useful marker for genetic mapping and diversity study.

Stability of Human Centromeric Alphoid DNA Repeat during Propagation in Recombination-Deficient Yeast Strains (효모의 재조합 변이주를 이용한 인간 Centromeric Alphoid DNA Repeat의 안정성에 관한 연구)

  • Kim, Kwang-Sup;Shin, Young-Sun;Lee, Sang-Yeop;Ahn, Eun-Kyung;Do, Eun-Ju;Park, In-Ho;Leem, Sun-Hee;SunWoo, Yang-Il
    • Korean Journal of Microbiology
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    • v.43 no.4
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    • pp.243-249
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    • 2007
  • The centromere is a highly differentiated structure of the chromosome that fulfills a multitude of essential mitotic and meiotic functions. Alphoid DNA (${\alpha}$-satellite) is the most abundant family of repeated DNA found at the centromere of all human chromosomes, and chromosomes of primates in general. The most important parts in the development of Human Artificial Chromosomes (HACs), are the isolation and maintenance of stability of centromeric region. For isolation of this region, we could use the targeting hook with alphoid DNA repeat and cloned by Transformation-Associated Recombination (TAR) cloning technique in yeast Saccharomyces cerevisiae. The method includes rolling-circle amplification (RCA) of repeats in vitro to 5 kb-length and elongation of the RCA products by homologous recombination in yeast. Four types of $35\;kb{\sim}50\;kb$ of centromeric DNA repeat arrays (2, 4, 5, 6 mer) are used to examine the stability of repeats in homologous recombination mutant strains (rad51, rad52, and rad54). Following the transformation into wild type, rad51 and rad54 mutant strains, there were frequent changes in inserted size. A rad52 mutant strain showed extremely low transformation frequency, but increased stability of centromeric DNA repeat arrays at least 3 times higher than other strains. Based on these results, the incidence of large mutations could be reduced using a rad52 mutant strain in maintenance of centromeric DNA repeat arrays. This genetic method may use more general application in the maintenance of tandem repeats in construction of HAC.

GENETIC ALTERATIONS OF HUMAN ORAL CANCERS USING COMPARATIVE GENOMIC HYBRIDIZATION (Comparative genomic hybridization 기법을 이용한 인체 구강암의 유전자 변화에 대한 연구)

  • Lee, Myeong-Reoyl;Shim, Kwang-Sup;Lee, Young-Soo;Woo, Soon-Seop;Kong, Gu
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • v.26 no.3
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    • pp.245-253
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    • 2000
  • The development and progression of oral cancer is associated with an accumulation of multiple genetic alterations through the multistep processes. Comparative genomic hybridization(CGH), newly developed cytogenetic and molecular biologic technique, has been widely accepted as a useful method to allow the detection of genetic imbalance in solid tumors and the screening for chromosome sites frequently affected by gains or losses in DNA copy number. The authors examined 19 primary oral squamous cell carcinomas using CGH to identify altered chromosome regions that might contain novel oncogenes and tumor suppressor genes. Interrelationship between these genetic aberrations detected and major oncogenes and tumor suppressor genes previously recognized in carcinogenesis of oral cancers was studied. 1. Changes in DNA copy number were detected in 14 of 19 oral cancers (78.9%, mean: 5.58, range: $3{\sim}13$). High level amplification was present in 4 cases at 9p23, $12p21.1{\sim}q13.1$, 3q and $8q24{\sim}24.3$. Fourteen cases(78.9%, mean: 3.00, range: $1{\sim}8$) showed gains of DNA copy number and 12 cases(70.5%, mean: 2.58, range: $1{\sim}9$) revealed losses of DNA copy number. 2. The most common gains were detected on 3q(52.6%), 5p(21.0%), 8q(21.0%), 9p(21.0%), and 11q(21.0%). The losses of DNA copy number were frequently occurred at 9p(36.8%), 17q(36.8%), 13q(26.3%), 4p(21.0%) and 9p(21.0%). 3. The minimal common regions of gains were repeatedly observed at $3q24{\sim}26.7$, $3q27{\sim}29$, $1q22{\sim}31$, $5p12{\sim}13.3$, $8q23{\sim}24$, and 11q13.1-13.3. The minimal common regions of losses were detected at $9q11{\sim}21.3$, 17p31, $13q22{\sim}34$, and 14p16. 4. In comparison of CGH results with tumor stages, the lower stage group showed more frequent gain at 3q, 5q, 9p, and 14q, whereas gains at 1q($1q22{\sim}31$) and 11q($11q13.1{\sim}13.3$) were mainly detected in higher stage group. The loss at $13q22{\sim}34$ was exclusively detected in higher stage. The results indicate that the most frequent genetic alterations in the development of oral cancers were gains at $3q24{\sim}26.3$, $1q22{\sim}31$, and $5p12{\sim}13.3$ and losses at $9q11{\sim}21.3$, 17p31, and 13q. It is suggested that genetic alterations manifested as gains at $3q24{\sim}26.3$, $3q27{\sim}29$, $5p12{\sim}13.3$ and 5p are associated with the early progression of oral cancer. Gains at $1q22{\sim}31$ and $11q13.1{\sim}13.3$ and loss at 13q22-34 could be involved in the late progression of oral cancers.

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Loss of Heterozygosity on the Long Arm of Chromosome 21 in Non-Small Cell Lung Cancer (비소세포폐암에서 21q 이형체 소실)

  • Chai, Po-Hee;Bae, Nack-Cheon;Lee, Eung-Bae;Park, Jae-Yong;Kang, Kyung-Hee;Kim, Kyung-Rok;Bae, Moon-Seob;Cha, Seung-Ik;Chae, Sang-Chul;Kim, Chang-Ho;Jung, Tae-Hoon
    • Tuberculosis and Respiratory Diseases
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    • v.50 no.6
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    • pp.668-675
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    • 2001
  • Background : Non-smalll lung cancer(NSCLC) develops as a result of the accumulation of multiple genetic abnormalities. Loss of heterozygosity(LOH) is one of the most frequent genetic alterations that is found in NSCLC, and the chromosomal regions that display a high rate of LOH are thought to harbor tumor suppressor genes(TSGs). This study was done to determine the frequency of LOH in 21q with the aim of identifying potential TSG loci. Method : Thirty-nine surgically resected NSCLCs were analysed. Patients peripheral lymphocytes were used as the source of the normal DNA. Five microsatellite Inarkers of 21q were used to study LOH : 21q21.1(D21S1432, and D21S1994); 21q21.2-21.3(D21S1442) ; 21q22.1(21S1445) ; and 21q22.2-22.3(D21S266). The fractional allelic loss(FAL) in a tumor was calculated as the ratio of the number of markers showing LOH to the number of informative markers. Result : LOH for at least one locus was detected in 21 of 39 tumors(53.8%). Among the 21 tumors with LOH, 5(21.8%) showed LOH at almost all informative loci. Although statistically not significant, LOH was found more frequently in squamous cell carcinomas(15 of 23, 65.2%) than in adenocarcinomas(6 of 16, 37.5%). In the squamous cell carcinomas the frequency of LOH was higher in stage II-III (80.0%) than in stage I (53.8%). The FAL value in squamous cell carcinomas($0.431{\pm}0.375$) was significantly higher than that found in adenocarcinomas($0.l92{\pm}0.276$). Conclusion : These results suggest that LOH on 21q may be involved in the development of NSCLC, and that TSG(s) that contribute to the pathogenesis of NSCLC may exist on 21q.

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Immunohistochemical Study of Phosphatase and Tensin Homolog Deleted on Chromosome Ten in Gefitinib Treated Nonsmall Cell Lung Cancer Patients (폐암 조직에서의 PTEN 발현 정도와 Gefitinib의 반응율과의 관계)

  • Lee, Sung Yong;Lee, Ju Han;Jung, Jin Yong;Lee, Kyoung Ju;Lee, Seung Hyeun;Kim, Se Joong;Lee, Eun Joo;Hur, Gyu Young;Jung, Ki Hwan;Jung, Hye Cheol;Lee, Sang Yeub;Kim, Je Hyeong;Shin, Chol;Shim, Jae Jeong;In, Kwang Ho;Kang, Kyung Ho;Yoo, Se Hwa
    • Tuberculosis and Respiratory Diseases
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    • v.58 no.5
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    • pp.473-479
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    • 2005
  • Background : Gefitinib targets the epidermal growth factor receptor r(EGFR), and Gefitinib has antitumor activity in patient with non-small cell lung cancer (NSCLC). However, only 10 to 20 percent of patients show a clinical response to this drug, and the molecular mechanisms underlying patient sensitivity to gefitinib are unknown. PTEN (Phosphatase and tensin homolog deleted on chromosome Ten) plays a role for the modulation of the phosphatidylinositol 3-kinase pathway (PI3K), which is involved in cell proliferation and survival, so that it can inhibit cell cycle progression and induce G1 arrest. Therefore, we analyzed the relationship between PTEN expression and gefitinib's responsiveness in patients having advanced non small cell lung cancer that had progressed after previous chemotherapy. Methods : The expression of PTEN was studied by immunohistochemistry in paraffin-embedded tumor blocks that were obtained from 22 patients who had been treated with gefitinib from JAN, 2001 to AUG. 2004. For the evaluation of the relationships between the PTEN expression, the clinical stage and the basal characteristics, those cases that showed the respective antigen expression in >50% of the tumor cells were considered positive. Results : The positive rate of PTEN staining was 55% of the total of 22 patients. There was a significant relationship between the increased expression of PTEN and the response group (p=0.039). However, there was no significant relationship between the expression of PTEN and other clinicopathologic characteristics. Conclusion: The expression of PTEN in patients with advanced non small cell lung cancer that has progressed after previous chemotherapy may play a role in gefitinib's responsiveness.

Clinical Characteristics and Genetic Analysis of Prader-Willi Syndrome (Prader-Willi 증후군의 임상 양상 및 유전학적 진단에 관한 고찰)

  • Lee, Ji Eun;Moon, Kwang Bin;Hwang, Jong Hee;Kwon, Eun Kyung;Kim, Sun Hee;Kim, Jong Won;Jin, Dong Kyu
    • Clinical and Experimental Pediatrics
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    • v.45 no.9
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    • pp.1126-1133
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    • 2002
  • Purpose : Prader-Willi syndrome(PWS) is a complex disorder affecting multisystems with characteristic clinical features. Its genetic basis is an expression defect in the paternally derived chromosome 15q11-q13. We analyzed the clinical features and genetic basis of PWS patients for early detection and treatment. Methods : We retrospectively studied 24 patients with PWS in Department of Pediatrics, Samsung Medical Center, from September 1997 to September 2001. We performed cytogenetic and molecular genetic techniques using high resolution GTG banding techniques, fluorescent in situ hybridization and methylation-specific PCR for CpG island of SNRPN gene region. Results : The average birth weight of PWS patients was $2.67{\pm}0.47kg$ and median age at diagnosis was 1.3 years. The average height and weight of PWS patients under one year at diagnostic time were located in a 3-10 percentile relatively, and a rapid weight gain was seen between two and six years. Feeding problems in infancy and neonatal hypotonia were the two most consistently positive major criteria in over 95% of the patients. In 18 of the 24 cases(75%), deletion of chromosome 15q11-q13 was demonstrated and one case among 18 had an unbalanced 14;15 translocation. In four cases without any cytogenetic abnormality, it may be considered as maternal uniparental disomy and the rest showed another findings. Conclusion : We suggest diagnostic testing for PWS in all infants/neonates with unexplained feeding problems and hypotonia. It is necessary for clinically suspicious patients to undergo an early genetic test. As the genetic basis of PWS was heterogenous and complex, further study is required.