• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Journal of Genetic Medicine
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• v.5 no.2
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• pp.145-149
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• 2008

46,XX male is a rare sex constitution characterized by the development of bilateral testis in persons who lack a Y chromosome. Manifestations of 46,XX males are usually hypogonadism, gynecomastia, azoospermia, and hyalinations of seminiferous tubules. The incidence of XX male reversal is approximately 1 in 20,000 male neonates. The SRYgene is located at the short arm of the Y chromosome(Yp11.31) and codes for testis determining factor in humans. Here, the patient, who presented with a normal male phenotype, was referred for azoospermia. Conventional cytogenetic analysis showed a 46,XX karyotype. Quantitative fluorescent polymerase chain reaction(QF-PCR) and Multiplex PCR studies identified SRY gene. And, Fluorescence In Situ Hybridization(FISH) confirmed the SRY gene on the distal short arm of chromosome X. We identified the SRY gene on the distal short arm of chromosome X by molecular cytogenetic and molecular analyses. Therefore, molecular-cytogenetics and molecular studies were proved to be clinically useful adjunctive tool to conventional prenatal cytogenetic analysis.

• Clinical and Experimental Reproductive Medicine
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• v.24 no.3
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• pp.393-398
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• 1997

Cytogenetic analysis was performed in 1321 couples and 141 women with history of abnormal reproductive outcome during 1988-1996. The use of high resolution banding technique and fluorescence in situ hybridization (FISH) in the chromosome analysis has made the precise evaluation of chromosome aberrations. The prevalence of balanced chromosomal translocation carriers were 3.74% (104/2783 patients). 70 cases (2.52%) were reciprocal translocation carriers and 34 (1.22%) had Robertsonian translocations. Chromosome aberrations were more frequent in women (73 cases) than in men (31 cases). No phenotypical abnormalities were found in all carriers, but they experienced abnormal reproductive outcomes such as recurrent spontaneous abortions, anomalous offsprings or infertility problem. Prenatal diagnosis was carried out on 36 subsequent pregnancies in balanced translocation carriers. The fetal karyotypes showed that 12 cases (33%) were normal, 22 (61%) were balanced translocations, and two (6%) were unbalanced translocations. It is concluded that the prevalence of balanced chromosomal translocations in patients with abnormal reproductive outcome is higher than that of the normal population. Most of the fetal samples showed normal karyotypes or balanced translocations. Although the incidence of chromosomal imbalance in the fetuses was relatively low in prenatal diagnosis, individuals with balanced translocations are predisposed to abnormal offspring with partial trisomy or monosomy. Therefore we recommend that genetic counselling and cytogenetic prenatal diagnosis for translocation carriers have to be offered to prevent recurrent chromosomal abnormal babies.

• Journal of Aquaculture
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• v.21 no.4
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• pp.259-264
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• 2008

Cytogenetic characteristics of three Hemibarbus species (H. labeo, H. longirostris and H. mylodon) were analyzed based on erythrocyte measurement, flow cytometric estimation of cellular DNA content, and karyological analysis. Average nuclear volumes for H. labeo, H. longirostris and H. mylodon were 22.5, 21.7 and $26.0\;{\mu}m^3$, respectively. The estimated genome sizes of those three species were not significantly different from one another, being recorded as 2.51, 2.33 and 2.35 pg/cell for H. labeo, H. longirostris and H. mylodon, respectively. Modal chromosome numbers of the three species were the same as 2n = 50. However, their karyotypes and fundamental numbers (FN) were different among species; 16M+16SM+18T/A (FN = 82) for H. labeo, 18M+16SM+16T/A (FN = 84) for H. longirostris and 18M+24SM+8T/A (FN = 92) for H. mylodon.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.34 no.1
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• pp.17-20
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• 2001

Cytogenetic characteristics of three species in Centropomidae (Coreoperca herzi, C. kawamebari and Siniperca schezeri) were evaluated, based on karyologcial analysis, erythrocytic measurement and genome size estimation using flow cytometry. Modal chromosome number of three species was same as 2n=48. Karyotypes were 4SM+44A$\cdot$T (NF=52) for Coreoperca herzi, 6SM+42 A$\cdot$T (NF=52) for C. kawamebari and 4SM+44A$\cdot$T (NF=52) for Siniperca schezeri. Heteromorphic sex chromosome was not found in both sexes of any species examined, Cellular and nuclear volumes of Siniperca schezeri were smaller than those of other two species, Average amounts of cellular DNA contents estimated by flow cytometry were well coincided with erythrocytic sizes. The estimated genome sizes were 1.83, 1.85 and 1.44 pg/cell for C. herzi, C. kawamebari and S. schezeri, respectively.

• Journal of Genetic Medicine
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• v.15 no.1
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• pp.8-12
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• 2018

Purpose: This study aimed to investigate fetal ultrasonographic findings in cases of prenatally diagnosed de novo balanced translocations and the role of fetal ultrasound in prenatal genetic counseling. Materials and Methods: We collected cases with de novo balanced translocations that were confirmed in chorionic villus sampling, amniocentesis, and cordocentesis between 1995 and 2016. A detailed, high-resolution ultrasonography was performed for prediction of prognosis. Chromosomes from the parents of affected fetuses were also analyzed to determine whether the balanced translocations were de novo or inherited. Results: Among 32,070 cases with prenatal cytogenetic analysis, 27 cases (1/1,188 incidence) with de novo balanced translocations were identified. Fourteen cases (51.9%) showed abnormal findings, and the frequency of major structural anomalies was 11.1%. Excluding the major structural anomalies, all mothers who continued pregnancies delivered healthy babies. Conclusion: Results of a detailed, high-resolution ultrasound examination are very important in genetic counseling for prenatally diagnosed de novo balanced translocations.

• The Korean Journal of Malacology
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• v.28 no.1
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• pp.37-43
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• 2012

In this study, we invesgated a cytogenetic analysis of the Pacific triploid abalone, Haliotis discus hannai induced by low temperature treatment. We got a lot of mitotic metaphase chromosome spreads from the triploid and diploid Pacific abalones' hatched larvae (trochophores). The chromosome number of diploid abalone was 2n = 36 and that of triploid abalone was 3n = 54, so the chromosome number of triploid abalone was 1.5 times higher than that of diploid abalone. We developed a modified flow cytometric method for Pacific abalone from the existing methods. We uesd 51 months aged triploid and diploid Pacific abalones' hemolymph to get the DNA contents by flow cytometry. The DNA content of diploid abalone was 1.743 pg/cell and the DNA content of triploid abalone was 1.49 times higher than that of diploid one. It proved that triploid abalone was consisted with two sets of maternal diploid and one set of paternal genome.

• Clinical and Experimental Reproductive Medicine
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• v.32 no.2
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• pp.113-119
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• 2005

Objective: The purposes of this study were to investigate the types and the incidences of chromosomal abnormalities, and to provide an explanation for the genetic causations of recurrent spontaneous abortions in Korean population. Methods: Cytogenetic studies were carried out in 535 couples with at least two spontaneous first trimester abortions from January 1981 to December 2003. For karyotype analysis, we used modified Moorhead method by Giemsa staining and Giemsa-Trypsin-Giemsa banding Results: The overall incidence of chromosome abnormality was 32 out of 535 cases (5.98%). There were 25 cases (4.67%) of translocation and 7 cases (1.31%) of inversion. In translocation, 5 cases (0.93%) of Robertsonian translocation and 20 cases (3.74%) of reciprocal translocation were observed. In inversion, 6 cases (1.12%) of inversion of chromosome 9 and one case (0.19%) of inversion of chromosome 18 were found. Conclusion: In this study, overall chromosomal abnormality rate in couples with recurrent spontaneous abortions is much higher than that in the general population. So, chromosomal analysis should be offered for the prognostic information in genetic counseling such as prenatal diagnosis in couples with repetitive reproductive failure.

• Korean Journal of Clinical Laboratory Science
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• v.52 no.4
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• pp.310-316
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• 2020

Microarray technology represents a critical new advance in molecular cytogenetics. The development of this approach has provided fundamental insights into the molecular pathogenesis in clinical cytogenetics and has provided a clue to many unidentified or unexplained diseases. The approach allows a comprehensive investigation of thousands and millions of genomic loci simultaneously and enables the efficient detection of copy number alterations. The application of this technology has shown tremendous fluidity and complexity of the human genome, and has provided accurate diagnosis and appropriate clinical management in a timely and efficient manner for identifying genomic alterations. The clinical impact of the genomic alterations identified by microarrays is evolving into a diagnostic tool to identify high-risk patients better and predict patient outcomes from their genomic profiles. The transformation of conventional cytogenetics into an automated discipline will improve diagnostic yield significantly, leading to accurate diagnosis and genetic counseling. This article reviews cytogenetic technologies used to identify human chromosome alterations and highlights the potential utility of present and future genome microarray technology in the diagnosis.

• Journal of Genetic Medicine
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• v.7 no.1
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• pp.59-66
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• 2010

Purpose: Quantitative fluorescent polymerase chain reaction (QF-PCR) allows for the rapid prenatal diagnosis of common aneuploidies. The main advantages of this assay are its low cost, speed, and automation, allowing for large-scale application. However, despite these advantages, it is not a routine method for prenatal aneuploidy screening in Korea. Our objective in the present study was to validate the performance of QF-PCR using short tandem repeat (STR) markers in a Korean population as a means for rapid prenatal diagnosis. Material and Methods: A QF-PCR assay using an Elucigene kit (Gen-Probe, Abingdon, UK), containing 20 STR markers located on chromosomes 13, 18, 21, X and Y, was performed on 847 amniotic fluid (AF) samples for prenatal aneuploidy screening referred for prenatal aneuploidy screening from 2007 to 2009. The results were then compared to those obtained using conventional cytogenetic analysis. To evaluate the informativity of STR markers, the heterozygosity index of each marker was determined in all the samples. Results: Three autosomes (13, 18, and 21) and X and Y chromosome aneuploidies were detected in 19 cases (2.2%, 19/847) after QF-PCR analysis of the 847 AF samples. Their results are identical to those of conventional cytogenetic analysis, with 100% positive predictive value. However, after cytogenetic analysis, 7 cases (0.8%, 7/847) were found to have 5 balanced and 2 unbalanced chromosomal abnormalities that were not detected by QF-PCR. The STR markers had a slightly low heterozygosity index (average: 0.76) compared to those reported in Caucasians (average: 0.80). Submicroscopic duplication of D13S634 marker, which might be a unique finding in Koreans, was detected in 1.4% (12/847) of the samples in the present study. Conclusion: A QF-PCR assay for prenatal aneuploidy screening was validated in our institution and proved to be efficient and reliable. However, we suggest that each laboratory must perform an independent validation test for each STR marker in order to develop interpretation guidelines of the results and must integrate QF-PCR into the routine cytogenetic laboratory workflow.