• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2231-2235
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• 2015

Genome-wide association studies (GWASs) of the entire genome provide a systematic approach for revealing novel genetic susceptibility loci for breast cancer. However, genetic association studies have hitherto been primarily conducted in women of European ancestry. Therefofre we here performed a pilot GWAS with a single nucleotide polymorphism (SNP) array 5.0 platform from $Affymetrix^{(R)}$ that contains 443,813 SNPs to search for new genetic risk factors in 89 breast cancer cases and 46 healthy women of Indonesian ancestry. The case-control association of the GWAS finding set was evaluated using PLINK. The strengths of allelic and genotypic associations were assessed using logistic regression analysis and reported as odds ratios (ORs) and P values; P values less than $1.00{\times}10^{-8}$ and $5.00{\times}10^{-5}$ were required for significant association and suggestive association, respectively. After analyzing 292,887 SNPs, we recognized 11 chromosome loci that possessed suggestive associations with breast cancer risk. Of these, however, there were only four chromosome loci with identified genes: chromosome 2p.12 with the CTNNA2 gene [Odds ratio (OR)=1.20, 95% confidence interval (CI)=1.13-1.33, $P=1.08{\times}10^{-7}$]; chromosome 18p11.2 with the SOGA2 gene (OR=1.32, 95%CI=1.17-1.44, $P=6.88{\times}10^{-6}$); chromosome 5q14.1 with the SSBP2 gene (OR=1.22, 95%CI=1.11-1.34, $P=4.00{\times}10^{-5}$); and chromosome 9q31.1 with the TEX10 gene (OR=1.24, 95%CI=1.12-1.35, $P=4.68{\times}10^{-5}$). This study identified 11 chromosome loci which exhibited suggestive associations with the risk of breast cancer among Indonesian women.

• Journal of Dental Rehabilitation and Applied Science
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• v.30 no.1
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• pp.28-35
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• 2014

Osteochondroma is the most common benign bone tumor. The majority of osteochondromas (85%) present as solitary, nonhereditary lesions. In general, osteochondroma has no symptoms,however, facial asymmetry, malocclusion, crossbite and mouth opening can be occurred in case of temporomandibular joint involved. Radiologic analyses are indispensable element to diagnose osteochondroma and pathogenetic analysis showed that hereditary multiple osteochondromas are caused by mutations in either of two genes: exostosis(multiple)-1 (EXT1), which is located on chromosome 8q24.11 - q24.13 or exostosis(multiple)-2 (EXT2), which is located on chromosome 11p11 - 12. Recently, reduced mRNA of EXT1 was described in nonhereditary osteochondromas. The treatment of choice for osteochondroma is surgical unless the skeleton is still immature. Surgery associated with orthodontic treatment can be a valid approach to minimize facial asymmetry and malocclusion in case of temporomandibular with osteochondroma.

• Journal of Interdisciplinary Genomics
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• v.5 no.2
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• pp.13-17
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• 2023

KBG syndrome (KBGS) is a multisystem disorder characterized by short stature, distinctive facial features including macrodontia of upper central permanent incisors, and developmental/cognitive delay. It is caused by variants or deletion of Ankyrin Repeat Domain 11 (ANKRD11) located in chromosome 16q24.3. Since its initial report in 1975, KBG syndrome has been recognized as an exceedingly rare disorder. However, recent advancements in genetic diagnostic techniques have led to an increase in both the diagnosis rate and the number of reported cases, contributing to a rapid increase in its global prevalence. We review the clinical aspects of KBGS, including previously reported and newly reported cases, as well as the related genetic patterns discovered so far.

• Journal of Genetic Medicine
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• v.7 no.1
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• pp.78-81
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• 2010

Pericentric inversion is not rare in humans and is usually benign. However, pericentric inversion can lead to production of an unbalanced recombinant and might be a cause of repetitive pregnancy loss. Pericentric inversion of chromosome 22 is rare and only a few cases have been reported. We report a case of inv(22)(p13q12) carrier who had history of repetitive pregnancy loss including three spontaneous abortions and one fetal hydrops in which the chromosomal complement was rec(22)dup(22q) inv(22)(p13q12)mat. The maternal inv(22) and fetal rec(22) were confirmed by fluorescence in situ hybridization using region-specific probes (TUPLE1 on 22q11.2 and ARSA on 22q13). Because the identification of inv(22) or rec(22) in conventional karyotyping might be easily overlooked, great attention and additional molecular tests are required for accurate diagnosis of inv(22) and rec(22).

• Genomics & Informatics
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• v.7 no.3
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• pp.152-158
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• 2009

Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.

• Journal of Interdisciplinary Genomics
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• v.3 no.2
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• pp.35-40
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• 2021

Prader-Willi syndrome (PWS) is a rare genetic disorder which lead to severe neurodevelopmental, endocrine, and metabolic impairment. PWS is genetic disorder related to genomic errors which lead to inactivation of paternally-inherited genes on chromosome 15q11-q13. Epigenetic mechanisms are also involved in PWS, and epigenetic therapies are under investigation. Here we provide review about genetics of PWS, focused on genes involved in pathophysiology of PWS. We will also summarize epigenetics and genetic counseling of PWS.

• Clinical and Experimental Pediatrics
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• v.55 no.12
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• pp.487-490
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• 2012

We report a case of isodicentric chromosome 15 (idic(15) chromosome), the presence of which resulted in uncontrolled seizures, including epileptic spasms, tonic seizures, and global developmental delay. A 10-month-old female infant was referred to our pediatric neurology clinic because of uncontrolled seizures and global developmental delay. She had generalized tonic-clonic seizures since 7 months of age. At referral, she could not control her head and presented with generalized hypotonia. Her brain magnetic resonance imaging scans and metabolic evaluation results were normal. Routine karyotyping indicated the presence of a supernumerary marker chromosome of unknown origin (47, XX +mar). An array-comparative genomic hybridization (CGH) analysis revealed amplification from 15q11.1 to 15q13.1. Subsequent fluorescence in situ hybridization analysis confirmed a idic(15) chromosome. Array-CGH analysis has the advantage in determining the unknown origin of a supernumerary marker chromosome, and could be a useful method for the genetic diagnosis of epilepsy syndromes associated with various chromosomal aberrations.

• Biomedical Science Letters
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• v.26 no.4
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• pp.368-375
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• 2020

Metabolic syndrome (MetS) is a disease that is accompanied by various metabolic related problems and refers to a disease in which various adult diseases occur along with obesity. These metabolic syndromes appear according to the individual's genetic background. APOA5-ZPR1-BUD13, a gene cluster belonging to chromosome 11q23.3, is well known for its risk of plasma triglycerides and coronary artery disease. Recently, the GWAS results for metabolic syndrome were published in Koreans. The results included the APOA5-ZPR1-BUD13, and the SNPs that first appeared in Koreans in the ZPR1 and BUD13 were also discovered. In this study, the reproducibility was investigated for the newly discovered ZPR1 (rs964184) and BUD13 (rs2075295, rs1558861) using The Health Examinees (HEXA) cohort and showed significance. In addition, BUD13 (rs117548857, rs10488698, rs149527022, rs10790162), ZPR1 (rs2075290, rs145796806, rs201247587), APOA5 (rs12791103, rs1263173, rs7396835, rs17520254) were additionally discovered and significant results were obtained. For the SNPs that showed significant results, the effect on protein expression and the effect of expression quantitative trait loci (eQTL) were also confirmed. This study is expected to contribute to the prevention and treatment of diseases with differences in onset based on individual genetic patterns as well as presenting the effect of genetic mutations in the APOA5-ZPR1-BUD13 on metabolic syndrome and blood lipid levels.

• Clinical and Experimental Pediatrics
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• v.54 no.2
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• pp.55-63
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• 2011

Prader-Willi syndrome (PWS) is a complex multisystem genetic disorder that is caused by the lack of expression of paternally inherited imprinted genes on chromosome 15q11-q13. This syndrome has a characteristic phenotype including severe neonatal hypotonia, early-onset hyperphagia, development of morbid obesity, short stature, hypogonadism, learning disabilities, behavioral problems, and psychiatric problems. PWS is an example of a genetic condition caused by genomic imprinting. It can occur via 3 main mechanisms that lead to the absence of expression of paternally inherited genes in the 15q11.2-q13 region: paternal microdeletion, maternal uniparental disomy, and an imprinting defect. Over 99% of PWS cases can be diagnosed using DNA methylation analysis. Early diagnosis of PWS is important for effective long-term management. Growth hormone (GH) treatment improves the growth, physical phenotype, and body composition of patients with PWS. In recent years, GH treatment in infants has been shown to have beneficial effects on the growth and neurological development of patients diagnosed during infancy. There is a clear need for an integrated multidisciplinary approach to facilitate early diagnosis and optimize management to improve quality of life, prevent complications, and prolong life expectancy in patients with PWS.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7343-7350
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• 2015

Genetic changes associated with acute lymphoblastic leukemia (ALL) provide very important diagnostic and prognostic information with a direct impact on patient management. Detection of chromosome abnormalities by conventional cytogenetics combined with fluorescence in situ hybridization (FISH) play a very significant role in assessing risk stratification. Identification of specific chromosome abnormalities has led to the recognition of genetic subgroups based on reciprocal translocations, deletions and modal number in B or T-cell ALL. In the last twelve years 102 newly diagnosed childhood/adult ALL bone marrow samples were analysed for chromosomal abnormalities with conventional G-banding, and FISH (selected cases) using specific probes in our hospital. G-banded karyotype analysis found clonal numerical and/or structural chromosomal aberrations in 74.2% of cases. Patients with pseudodiploidy represented the most frequent group (38.7%) followed by high hyperdiploidy group (12.9%), low hyperdiploidy group (9.7%), hypodiploidy (<46) group (9.7%) and high hypertriploidy group (3.2%). The highest observed numerical chromosomal alteration was high hyperdiploidy (12.9%) with abnormal karyotypes while abnormal 12p (7.5%) was the highest observed structural abnormality followed by t(12;21)(p13.3;q22) resulting in ETV6/RUNX1 fusion (5.4%) and t(9;22)(q34.1;q11.2) resulting in BCR/ABL1 fusion (4.3%). Interestingly, we identified 16 cases with rare and complex structural aberrations. Application of the FISH technique produced major improvements in the sensitivity and accuracy of cytogenetic analysis with ALL patients. In conclusion it confirmed heterogeneity of ALL by identifying various recurrent chromosomal aberrations along with non-specific rearrangements and their association with specific immunophenotypes. This study pool is representative of paediatric/adult ALL patients in Oman.