• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.1999-2006
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• 2016

Background: Acute promyelocytic leukemia (APML) is characterized by the reciprocal translocation t(15;17) (p22;p12) resulting in the PML-$RAR{\alpha}$ fusion gene. A dual diagnostic and follow up approach was applied including cytogenetic demonstration of the t(15;17) translocation and detection dg PML-$RAR{\alpha}$ chimeric transcripts by molecular means. Purpose: Conventional cytogenetics involving bone marrow is beset with high probability of poor metaphase index and was substituted with phytohemagglutinin (PHA)-induced peripheral blood culture based cytogenetic analysis as a diagnostic & follow up modality in APML patients of Kashmir (North India). Both qualitative (RT-PCR) and quantitative (Q-PCR) tests were simultaneously carried out to authenticte the modified cytogenetics. Materials and Method: Patient samples were subjected to the said techniques to establish their baseline as well as follow-up status. Results: Initial cytogenetics revealed 30 patients (81%) Positive for t(15;17) whereas 7 (19%) had either cryptic translocation or were negative for t(15;17). Two cases had chromosome 16q deletion and no hallmark translocation t(15;17). Q-PCR status for PML-$RAR{\alpha}$ was found to be positive for all patients. All the APML patients were reassessed at the end of consolidation phase and during maintenance phase of chemotherapy where 6 patients had molecular relapse, wherein 4 also demonstrated cytogenetic relapse. Conclusions: It was found that PHA-induced peripheral blood cytogenetics along with molecular analysis could prove a reliable modality in the diagnosis and assessment of follow up response of APML patients.

• Horticultural Science & Technology
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• v.32 no.3
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• pp.366-374
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• 2014

The study was conducted to investigate the possibility that epigenetic DNA methylation causes tree phenotypic variation in autotetraploids through evaluating the phenotypic variation and DNA methylation in autotetraploids occurred spontaneously from diploid trifoliate orange. Chromosome analysis confirmed that fourteen trifoliate orange trees of selected by flow cytometry were tetraploids (2n = 4X = 36) without any aneuploids. Chromomycin A3 staining determined that these trees were all autotetraploid with doubled chromosome set. Tree phenotypes, such as tree height and width, branching number, length, and angle, internode length, and leaf characteristics, varied in the autotetraploids. Chlorophyll indices were diverse in the autotetraploids, but photosynthetic rates were not significantly different. In addition, a wide range of variation was observed in stomatal density and guard cell length. Analysis of global cytosine DNA methylation showed that there was a variation of the methylation level in autotetraploids. More than half of 14 autotetraploids had at least 2 times higher methylation level than diploid trifoliate orange. The results indicate that tree phenotypic variation in autotetraploids might be related to global DNA methylation for reducing gene redundancy.

• Molecules and Cells
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• v.19 no.3
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• pp.436-444
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• 2005

We describe the morphology and molecular organization of heterochromatin domains in the interphase nuclei, and mitotic and meiotic chromosomes, of Brassica rapa, using DAPI staining and fluorescence in situ hybridization (FISH) of rDNA and pericentromere tandem repeats. We have developed a simple method to distinguish the centromeric regions of mitotic metaphase chromosomes by prolonged irradiation with UV light at the DAPI excitation wavelength. Application of this bleached DAPI band (BDB) karyotyping method to the 45S and 5S rDNAs and 176 bp centromere satellite repeats distinguished the 10 B. rapa chromosomes. We further characterized the centromeric repeat sequences in BAC end sequences. These fell into two classes, CentBr1 and CentBr2, occupying the centromeres of eight and two chromosomes, respectively. The centromere satellites encompassed about 30% of the total chromosomes, particularly in the core centromere blocks of all the chromosomes. Interestingly, centromere length was inversely correlated with chromosome length. The morphology and molecular organization of heterochromatin domains in interphase nuclei, and in mitotic and meiotic chromosomes, were further characterized by DAPI staining and FISH of rDNA and CentBr. The DAPI fluorescence of interphase nuclei revealed ten to twenty conspicuous chromocenters, each composed of the heterochromatin of up to four chromosomes and/or nucleolar organizing regions.

• Journal of Genetic Medicine
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• v.8 no.1
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• pp.35-43
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• 2011

Purpose: We evaluated indications for chorionic villus sampling (CVS), the positive predictive value of CVS for fetal chromosomal abnormalities, and the fetal loss rate after CVS at CHA Medical Center. Materials and Methods: We reviewed the medical records of 511 cases of CVS performed between 67 and 120 days of gestation for prenatal cytogenetic diagnosis from April 2000 to April 2010. Fetal karyotypes were obtained by direct and indirect culture methods. Results: The most common indications for CVS were abnormal ultrasonic findings including increased nuchal translucency (294/635, 46.3%). The positive predictive value of abnormal karyotyping according to indication for CVS was highest in cases with abnormal parental karyotypes (14/21, 66.7%). Mosaicism revealed by CVS comprised 3.1% of the sample (16/509). Amniocentesis revealed two cases of true mosaicism and 11 cases of confined placental mosaicism. The fetal loss rate within 4 weeks of the procedure was 1.2% (6/511). Conclusion: If CVS is performed by an expert clinician, it is a feasible and reliable procedure for prenatal genetic diagnosis. When CVS indicates mosaicism, the finding should be confirmed by amniocentesis to distinguish true mosaicism from confined placental mosaicism.

• Journal of Ginseng Research
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• v.41 no.4
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• pp.469-476
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• 2017

Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

• Clinical and Experimental Reproductive Medicine
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• v.30 no.4
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• pp.293-298
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• 2003

목 적: 인간의 배아줄기세포는 전분화능과 영속성을 가지고 있어 발생 및 분화에 관련된 기초 연구 뿐 만 아니라 재생의학, 약물검색 등에서도 매우 유용한 재료로 이용될 수 있다.본 연구에서는 유전체의 변형이 배아줄기세포주의 확립 효율에 미치는 영향을 살펴보고자 비정상적인 포배기 배아에서 내세포괴를 분리하여 배양하였다. 연구 방법: 인간의 체외수정 및 배아이식술에서 공여 받은1개 또는3개의 전핵이 관찰되는 비정상 수정란 (n=20)과 착상전 유전진단에서 이수성이 확인된 배아 (n=27)를 대상으로 하였다. 일반적인 immunosurgery 방법으로 영양배엽세포들을 제거하고 내세포괴를 분리한 후 PMEF 혹은 STO feeder 세포위에서 배양하였다. 배아줄기세포의 배양시스템을 검증하기 위해서 이미 확립된 Miz-hES1 cell line을 동시에 같은 조건 하에서 계대배양하였다. 결 과: 비정상 수정란에서 발생된 포배기 배아에서 분리한 1개의 내세포괴가 배아줄기세포와 유사한 colony를 형성하였으나, 계대배양에는 실패하였다. 이수성 배아에서 발생된 포배기 배아의 내세포괴 배양에서는 두개의 colony가 계대배양 중에 영양배엽세포의 형태로 분화되어 미분화 상태를 유지하지 못하였다. 동일한 시기와 조건 하에서 계대배양된 Miz-hES1 cell line이 미분화상태로 유지됨을 karyotyping (46, XY)과 immunophenotyping (positive in SSEA-3 and -4)으로 확인하였다. 결 론: 본 연구의 결과에서 비정상 수정란과 이수성 배아에서 발생된 포배기 배아에서 유래한 내세포괴는 배아줄기세포주 확립 및 미분화 상태 유지 능력이 매우 저조한 것으로 여겨진다. 따라서, 인간의 배아줄기세포주를 확립하는데 있어 배아의 정상여부가 중요한 요소로 작용할 것으로 생각된다.

• Journal of Genetic Medicine
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• v.7 no.1
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• pp.37-44
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• 2010

Purpose : Kabuki syndrome is a multiple congenital malformation syndrome with mental retardation. It was named after its characteristic appearance, a face resembling that of an actor in a Kabuki play. To date, six Korean cases of Kabuki syndrome have ever been reported. Here, we present the phenotypic and genetic characteristics of six patients with Kabuki syndrome. Materials and Methods : Between 2003 and 2009, six Korean girls have been diagnosed and followed up as Kabuki syndrome at Center for Genetic Diseases of Ajou University Hospital. Their clinical and laboratory data were collected and analyzed by the retrospective review of medical records. Results : All six patients showed the characteristic facial dysmorphism and developmental delay. Persistent fingertip pads were also found in all patients. Most patients showed postnatal growth retardation (83.3%) and hypotonia (83.3%). Opthalmologic problems were common, particularly for strabismus (83.3%). Congenital heart defects were present in three patients (50%). Skeletal abnormalities including 5th finger shortening (83.3%), clinodactyly (50%), joint hypermobility (50%) and hip dislocation (16.7%) were also observed. There was no patient who had positive family history for Kabuki syndrome. Cytogenetic and molecular cytogenetic analyses including karyotyping and array CGH could not reveal any underlying genetic cause of Kabuki syndrome. Conclusion : Korean patients with Kabuki syndrome showed a broad spectrum of clinical features affecting multiple organ systems. Although clinical manifestations of Kabuki syndrome have been well established, our results failed to detect recurrent chromosome aberrations which could cause Kabuki syndrome. Its natural history and genetic background remains to be further studied for providing appropriate management and genetic counseling.

• Journal of Genetic Medicine
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• v.7 no.2
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• pp.133-137
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• 2010

Purpose: Beckwith-Wiedemann syndrome (BWS) is an overgrowth malformation syndrome caused by a methylation abnormality at chromosome 11p15, consisting of two imprinting centers, BWSIC1 (IGF2, H19) and BWSIC2 (LIT1, KvDMR). This study evaluated the applicability of a methylation-specific (MS) PCR RFLP method for the genetic diagnosis of BWS. Materials and Methods: A total of 12 patients were recruited based on clinical findings. Karyotyping was performed using peripheral blood leukocytes, and genomic DNA was treated with bisulfate and amplified using methylation-specific primers. RFLP was conducted with restriction enzymes in differentially methylated regions of LIT1, H19, and IGF2. Results: The 12 BWS patients had normal karyotypes. Abnormal methylation patterns in the BWSIC2 (LIT1) region were identified in seven patients (58.3%) using the MS-PCR RFLP method. Conclusions: The MS-PCR RFLP method is a simple, economical genetic test. It detected genetic abnormalities in 50-60% of BWS patients, suggesting that it can be used as a screening test. A more precise method is required, however, to enhance the detection rate of genetic abnormalities, especially in BWSIC1 region.

• Journal of Genetic Medicine
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• v.11 no.2
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• pp.56-62
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• 2014

Purpose: To assess the outcomes of increased fetal nuchal translucency (NT), to aid in prenatal counseling and management in our practice. Materials and Methods: We retrospectively reviewed the medical records of patients who underwent first trimester fetal karyotyping using chorionic villi sampling (CVS) and second trimester level II sonography for a fetal NT thickness ${\geq}3.0mm$ between 11 weeks and 13 weeks 6 days' gestation, at Gyeongsang National University Hospital. Pediatric medical records and a telephone interview were used to follow-up live-born children. Exclusion criteria included incomplete data and CVS for other indications. Results: Seventy cases met the inclusion criteria (median NT thickness, 4.7 mm; range, 3.0-16.1 mm). Twenty-nine cases (41.4%) were aneuploid. The prevalence of chromosomal defects increased with NT thickness: NT 3.0-3.4 mm, 16.7%; NT 3.5-4.4 mm, 27.3%; NT 4.5-5.4 mm, 66.7%; NT 5.5-6.4 mm, 37.5%; NT ${\geq}6.5mm$, 62.5%. The most common karyotype abnormality was trisomy 18 (n=12), followed by trisomy 21 (n=9). In chromosomally normal fetuses (n=41), fetal death occurred in 2 cases (4.9%), and structural malformations were found in 11 cases (26.8%). In chromosomally and anatomically normal fetuses (n=28), one child had neurodevelopmental delay (3.6%). Twenty-eight infants who had a prenatal increased NT were alive and well at follow-up (40%). Conclusion: Outcomes of increased fetal NT might help inform prenatal counseling and management. The high prevalence of chromosomal defects associated with increased fetal NT implies that CVS should be performed in the first trimester, particularly considering the stress associated with an uncertain diagnosis.

• Journal of Genetic Medicine
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• v.17 no.1
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• pp.11-15
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• 2020

Purpose: The objective of this study was to analyze the results of several noninvasive prenatal tests (NIPTs) from a single center and confirm their efficacy and reliability. In addition, we aimed to confirm the changes in the number of invasive tests performed after introducing NIPT. Materials and Methods: NIPT data from a large single center from March 2014 to November 2018 were analyzed. Karyotyping was confirmed based on chorionic villus sampling, amniocentesis, or postnatal cord/peripheral blood sampling. Data on maternal age, gestational age, fetal fraction, and ultrasonographic results were analyzed. As the secondary outcome, the number of amniocentesis cases before and after the introduction of NIPT was compared. Results: Overall, 1,591 single pregnancy cases that underwent NIPT were enrolled. The mean maternal age was 36.05 (22-45) years. The average gestational age and fetal fraction were 12⁺¹ (9⁺³ to 27⁺¹) weeks and 10.95% (3.6% to 31.3%), respectively. A total of 1,544 cases (97.0%) were reported to have negative NIPT results and 40 (2.5%) had positive NIPT results. The sensitivity and specificity of the overall abnormalities in NIPT were 96.29% and 99.36%, respectively. The positive predictive value (PPV) and negative predictive value were 72.22% and 99.93% respectively. The mean number of amniocentesis cases were 21.7 per month (21.7±3.9), which significantly decreased from 31.5 per month (31.5±4.8) before conducting NIPT as a screening test. Conclusion: NIPT is currently a useful, powerful, and safe screening test. In particular, trisomy 21 is highly specific due to its high PPV. NIPT can reduce the potential risks of procedure-related miscarriages during invasive testing.