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Background: The Hanwoo industry must develop technologies that can increase the production of preferred cuts to match changing consumer trends. In this study, we aimed to estimate the genetic parameters for carcass traits (carcass weight, eye muscle area, back fat thickness, and intramuscular fat) and primal cut traits (tenderloin, loin, strip loin, neck, clod, top round, bottom round, brisket, shank, and rib) in a Hanwoo population to obtain basic data for improving primal cut productivity. Methods: Data from 1,905 Hanwoo steers, including carcass traits and primal cut weights, were collected. Genetic parameters were estimated using REMLF90 in a multi-trait analysis. Results: High heritability was found for carcass weight (0.52) and strip loin yield (0.63). Genetic correlations between carcass weight and primal cut weights ranged from 0.52 to 0.93. Conclusions: This study demonstrates the significant potential for genetic improvement in Hanwoo cattle through selective breeding, particularly for traits with high heritability and genetic correlations. These findings provide crucial insights into optimizing breeding programs to improve Hanwoo cattle production efficiency.

Background: As the number of households raising companion dogs increases, the pet genetic analysis market also continues to grow. However, most studies have focused on specific purposes or native breeds. This study aimed to collect genomic data through single nucleotide polymorphism (SNP) chip analysis of companion dogs in South Korea and perform genetic diversity analysis and SNP annotation. Methods: We collected samples from 95 dogs belonging to 26 breeds, including mixed breeds, in South Korea. The SNP genotypes were obtained for each sample using an Axiom™ Canine HD Array. Quality control (QC) was performed to enhance the accuracy of the analysis. A genetic diversity analysis was performed for each SNP. Results: QC initially selected SNPs, and after excluding non-diverse ones, 621,672 SNPs were identified. Genetic diversity analysis revealed minor allele frequencies, polymorphism information content, expected heterozygosity, and observed heterozygosity values of 0.220, 0.244, 0.301, and 0.261, respectively. The SNP annotation indicated that most variations had an uncertain or minimal impact on gene function. However, approximately 16,000 non-synonymous SNPs (nsSNPs) have been found to significantly alter gene function or affect exons by changing translated amino acids. Conclusions: This study obtained data on SNP genetic diversity and functional SNPs in companion dogs raised in South Korea. The results suggest that establishing an SNP set for individual identification could enable a gene-based registration system. Furthermore, identifying and researching nsSNPs related to behavior and diseases could improve dog care and prevent abandonment.

Background: Copy number variation (CNV) can be identified using next-generation sequencing and microarray technologies, the research on the analysis of its association with meat traits in livestock breeding has significantly increased in recent years. Hanwoo is an inherent species raised in the Republic of Korea. It is now considered one of the most economically important species and a major food source mainly used for meat (Hanwoo beef). Methods: In this study, CNVs and the relationship between the obtained CNV regions (CNVRs) can be identified in the Hanwoo steer samples (n = 473) using Illumina Hanwoo SNP 50K bead chip and bioinformatic tools, which were used to locate the required data and meat traits were investigated. The PennCNV software was used for the identification of CNVs, followed by the use of the CNV Ruler software for locating the different CNVRs. Furthermore, bioinformatics analysis was performed. Results: We found a total of 2,575 autosomal CNVs (933 losses, 1,642 gains) and 416 CNVRs (289 gains, 111 losses, and 16 mixed), which were established with ranged in size from 2,183 bp to 983,333 bp and 10,004 bp to 381,836 bp, respectively. Upon analyzing the restriction of minor alleles frequency > 0.05 for meat traits association, 6 CNVRs in the carcass weight, 2 CNVRs in the marbling score, 3 CNVRs in the backfat thickness, and 2 CNVRs in the longissimus muscle area were related to the meat traits. In addition, we identified an overlap of 347 CNVRs. Moreover, 3 CNVRs were determined to have a gene that affects meat quality. Conclusions: Our results confirmed the relationship between Hanwoo CNVR and meat traits, and the possibility of overlapping candidate genes, annotations, and quantitative trait loci that results depended on to contribute to the greater understanding of CNVs in Hanwoo and its role in genetic variation among cattle livestock.

This study has evaluated the genomic estimated breeding value (GEBV) of the commercial Hanwoo population using the genomic best linear unbiased prediction (GBLUP) method and genomic information. Furthermore, it analyzed the accuracy and realized accuracy of the GEBV. 1,740 heads of the Hanwoo population which were analyzed using a single nucleotide polymorphism (SNP) Chip has selected as the test population. For carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS), the mean GEBVs estimated using the GBLUP method were 3.819, 0.740, -0.248, and 0.041, respectively and the accuracy of each trait was 0.743, 0.728, 0.737, and 0.765, respectively. The accuracy of the breeding value was affected by heritability. The accuracy was estimated to be low in EMA with low heritability and high in MS with high heritability. Realized accuracy values of 0.522, 0.404, 0.444, and 0.539 for CWT, EMA, BFT, and MS, respectively, showing the same pattern as the accuracy value. The results of this study suggest that the breeding value of each individual can be estimated with higher accuracy by estimating the GEBV using the genomic information of 18,499 reference populations. If this method is used and applied to individual selection in a commercial Hanwoo population, more precise and economical individual selection is possible. In addition, continuous verification of the GBLUP model and establishment of a reference population suitable for commercial Hanwoo populations in Korea will enable a more accurate evaluation of individuals.

A number of Korean Chicken breeds were registered in Domestic Animal Diversity Information System (DAD-IS, http://dad.fao.org/) of the Food and Agriculture Organization (FAO). Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. Therefore, this study aimed to analysis the genetic diversity and relationship of 22 Korean Chicken breeds using 12 microsatellite (MS) markers. The mean number of alleles for each variety was 5.52, ranging from a 3.75 (Leghorn F; NF) to a 7.0 (Ross). The most diverse breed was the Hanhyup3 (HCC), which had the highest expected heterozygosity (HExp) (0.754) and polymorphic information content (PIC) (0.711). The NF was the least diverse population, having the lowest HExp (0.467) and PIC (0.413). As a result of the principal coordinates analysis (PCoA) and factorial correspondence analysis (FCA) confirmed that Hy-line Brown (HL) and Lohmann Brown (LO) are very close to each other and that Leghorn and Rhode Island Red (RIR) are clearly distinguished from other groups. Thus, the reliability and power of identification using 12 types of MS markers were improved, and the genetic diversity and probability of individual discrimination were confirmed through statistical analysis. This study is expected to be used as basic data for the identification of Korean chicken breeds, and our results indicated that these multiplex PCR marker sets will have considerable applications in population genetic structure analysis.

Halla horse is crossbreed between Jeju and Thoroughbred horses and is used for riding, racing and meat production. Thus, molecular genetic studies are needed to establish and preserve the industrially valuable Halla horses. This study aimed to analyses the genetic diversity and population structure through 12 microsatellite (MS) markers for Halla and putatively related 3 breeds (Jeju, Mongolian and Thoroughbred horses). On average, the number of alleles, observed heterozygosity (Hobs), expected heterozygosity (Hexp), and polymorphic information content (PIC) among all horses were 10, 0.767, 0.799, and 0.771, respectively. Neighbor-joining tree and STRUCTURE analysis showed that Halla horses were between Thoroughbred and Jeju horses, tend to more influenced by Thoroughbred horses. Therefore, these results could be considered for use as the basic genetic breed relationships resource among the horse breeds (Jeju, Mongolian, and Thoroughbred horses) related to the origins of the Halla horse.

Meat and carcass quality attributes are important factors influencing consumer preference and profitability in the pork industry. Single nucleotide polymorphisms (SNPs) are essential for livestock breeding and improvement. In the present study, the pig Perilipin 2 (PLIN2) gene was characterized with the aim of detecting genetic variation at these loci in relation to economic traits in Berkshire pigs. Four SNPs (G6714C, G6813A, G10340A, and G10632A) were detected in this studied. Statistical analysis indicated that G6714C was significantly associated with the National Pork Producers Council (NPPC) color score, G6813A, and G10340A significantly affected NPPC color score and NPPC marbling score, and G10632A significantly affected backfat thickness (BF) (p < 0.05). Therefore, the molecular markers used in the present study might provide a useful basis for identification and improvement of traits in the Berkshire pigs.

Food and agricultural production sector, especially livestock production is vital for Mongolia’s economic and social development. Domestic sheep play key roles for Mongolians, providing food (meat, milk) and raw materials (wool, sheepskin), but genetic diversity, origin of sheep populations in Mongolia have not been well studied. Studies of population genetic diversity is important research field in conservation and restoration of animal breeds and genetic resources. Therefore, this study aimed to investigate genetic characteristics and estimate origin through the analysis of mitochondrial DNA control region D-loop and Cytochrome b of Mongolian indigenous sheep (Mongolian native, Orkhon and Altanbulag) and one Europe sheep (Suffolk). As a result of there were found, 220 SNPs (Single nucleotide polymorphism) in the D-loop region, 28 SNPs in the Cytochrome B region, furthermore, 77 Haplotypes. The nucleotide diversity was only found in D-loop region (n = 0.0184). Phylogenetic analysis showed that 3 (A, B, and C) of 5 haplogroups of sheep have been identified in our research. Haplogroup C was only found in Mongolian indigenous sheep. Haplogroup D and E were not observed. As a result of haplogroups, haplogroup A was dominant (n = 46 of 94 sheeps), followed by haplogroup B (n = 36) and haplogroup C (n = 12). Sequence analysis showed that T deletion, insertion and heteroplasmy in D-loop region occurred at a high rate in Mongolian indigenous sheep population (T insertion = 47, T deletion = 83). The heteroplasmy, which has never been found in Mongolian sheep, has been newly discovered in this study. As a result, the Mongolian sheep varieties, which mainly derived from Asia, were in hybridization with European sheep varieties.

The aim of this study was to assess the levels of genetic diversity and relationships of Korean native black goat (n = 58), compared with the exotic breed, Boer (n = 97). For the analysis of genetic characterization 11 microsatellite markers (MAF065, INRA063, CSRD247, OarFCB20, SRCRSP5, INRA006, ILSTS008, ILSTS011, INRA005, ILSTS087, SRCRSP8) were genotyped. The number of alleles was observed 3 (INRA005) to 10 (SRCRSP8) each markers. The mean expected and observed heterozygosity (Hexp and Hobs) and polymorphism information content (PIC) for the Korean native black goat breed varied from 0.551 to 0.860, 0.517 to 0.948 and 0.464 to 0.835, respectively. Principal Components Analysis (PCoA) and FCA results showed that Korean native black goat breed was confirmed to be clearly separated from bore breed. These results were scientific evidence that Korean native black goat represents a unique and valuable animal genetic resource.

Background Human leukocyte antigen class I (HLA-I) molecules play important roles in regulating immune responses. Loss or reduction of HLA-I expression has been shown to be associated with prognosis in several cancers. Regulatory T-cells (Tregs) also play critical functions in immune response regulation. Evaluation of HLA-I expression status by the EMR8-5 antibody and its clinical impact in breast cancer have not been well studied, and its relationship with Tregs remains unclear. Methods We evaluated HLA-I expression and Treg infiltration by immunohistochemistry in 465 surgically resected breast cancer samples. We examined the correlation between HLA-I expression and Treg infiltration and clinicopathologic characteristics and survival analyses were performed. Results Total loss of HLA-I expression was found in 84 breast cancer samples (18.1%). Univariate survival analysis revealed that loss of HLA-I expression was significantly associated with worse disease-specific survival (DSS) (p = .029). HLA-I was not an independent prognostic factor in the entire patient group, but it was an adverse independent prognostic factor for DSS in patients with advanced disease (stage II–IV) (p = .031). Treg numbers were significantly higher in the intratumoral stroma of HLA-I–positive tumors than in HLA-I–negative tumors (median 6.3 cells/high power field vs 2.1 cells/high power field, p < .001). However, Tregs were not an independent prognostic factor in our cohort. Conclusions Our findings suggest that the loss of HLA-I expression is associated with poor prognosis in breast cancer patients, highlighting the role of HLA-I alterations in immune evasion mechanisms of breast cancer. HLA-I could be a promising marker that enables the application of more effective and precise immunotherapies for patients with advanced breast cancer.

We present a case of 55-year-old man who complained of dyspnea and sputum for a month. He was an ex-smoker with a history of prostate cancer and pulmonary tuberculosis. Chest radiographs revealed bilateral pleural effusions of a small to moderate amount. Pigtail catheters were inserted for drainage. The pleural fluid consisted of large clusters and tightly cohesive groups of malignant cells, which however could not be ascribed to prostate cancer with certainty. We performed immunocytochemical panel studies to determine the origin of cancer metastasis. The immunostaining results were positive for prostate-specific antigen, alpha-methylacyl-coenzyme A racemase, and Nkx 3.1, consistent with prostate cancer. Pleural effusion associated with prostate cancer is rare. To our knowledge, this is the first case report in Korea to describe cytologic features of malignant pleural effusion associated with prostate cancer.

Bacterial leaf blight caused by Pseudomonas syringae pv. porri is one of the major bacterial diseases of garlic (Allium sativum). In South Korea, the disease has only been observed in garlic-growing regions of Jeju island. The spatial distribution pattern of the disease was analyzed by binary power law, in which the natural logarithm of the observed variance is regressed on the natural logarithm of the binomial variance. The estimated slope (b=1.361) of the regression was greater than 1 which meant that the diseased plants were aggregated. The sequential sampling plans were developed for estimating the mean incidence rate (pm) and classifying the mean incidence as being below or above the critical incidence rate (pt). These results could be used on more efficient and higher precisive sampling for bacterial blight of garlic compared to fixed sample sized sampling.

Background: One of the major concerns with biobanking is the absence of standard operating procedures to eliminate pre-analytical variation arising from sample collection, preparation, and storage. Currently, there is a lack of tools to carry out quality control procedures for stored blood samples. The aim of this study is to assess the quality of stored blood samples in our biobank and to suggest appropriate indicators for their quality control., Methods: The stored blood samples that we tested have been registered into our biobank since 2003. These were transferred to our biobank after carrying out routine requested tests, because the samples would have otherwise been discarded. For the purpose of quality control, we analyzed the concentrations and the integrity of DNA and RNA extracted from the stored samples and tested the levels of several serum proteins; the results were compared with the corresponding pre-storage levels., Results: A total of 19 samples were stored from 2006 to 2009. Of the 22 samples stored between 2003 and 2005, 50% showed complete DNA integrity. However, sufficient RNA integrity was noted in only 1 sample stored as recently as 2009. High blood urea nitrogen levels were also noted in the stored sera, but the increase did not correlate to the duration of storage., Conclusions: The amount and integrity of nucleic acids extracted from stored blood samples are potential indicators that can be used for quality control. A guideline for the quality assessment of stored blood samples in a biobank is urgently needed.

Background: Late-onset neutropenia (LON) following rituximab therapy has been reported in recent years. However, its incidence has not been reported in Korea. The aim of this study is to investigate the incidence of LON after rituximab therapy in Korean patients with diffuse large B-cell lymphoma (DLBCL)., Methods: Ninety-eight cases of DLBCL treated with rituximab between 2004 and 2008 were evaluated. We identified LON as defined by the neutrophil count of <1.5 × 10(9)/L without apparent cause after the recovery of neutrophil count following rituximab therapy. Bone marrow aspiration and biopsy specimens at the time of neutropenia were available for retrospective review in only 5 of the patients., Results: LON was observed in 15 (15.3%) of the 98 patients. In the bone marrow specimens of the 5 patients, promyelocytes were relatively increased and the maturation index of the granulopoiesis was 2:1-3:1, which reflects maturation arrest., Conclusions: The incidence of LON following rituximab therapy was 15.3% in Korean patients with DLBCL. Although there are several hypotheses about the causative mechanisms of LON, we suggest that maturation arrest at the promyelocyte stage of granulopoiesis may be one of the mechanisms involved in the development of LON.

Inversion of chromosome 16 [inv(16)(p13.1q22)] and t(16;16)(p13.1;q22) are associated with acute myelomonocytic leukemia (AMML) with eosinophilia and a favorable prognosis. On the other hand, patients with del(16)(q22) usually present with MDS or chronic myelomonocytic leukemia (CMML), which can evolve to AMML without eosinophilia, and this chromosomal aberration is associated with older age, a complex karyotype, and a poor prognosis. We report a case of AML with del(16)(q22) which showed a complex karyotype, absence of eosinophilia in bone marrow study and a poor response to chemotherapy.

A case of hemophagocytic syndrome associated with ulcerative colitis is very rare. A 32-year-old man visited the hospital complaining of fever and severe abdominal pain for 7 days. He was diagnosed to have ulcerative colitis 2 years ago and had been treated with sulfasalazine. Three months ago, he had abdominal pain, weight loss, and hematochezia, so prednisolone and mercaptopurine were added to the treatment. On admission, the physical examination showed splenomegaly. Peripheral blood counts revealed pancytopenia, and bone marrow aspirate smears showed many histiocytes with active hemophagocytosis. There was no evidence of viral and bacterial infections and other neoplasms, which were commonly associated with hemophagocytic syndrome. He was successfully treated with high dose steroid. We report this case along with a review of the related literatures.

Thiazolidinediones (TZD), which are widely used as insulin sensitizers, and fibrates, which are lipid-lowering drugs, are used in the treatment of dyslipidemia that commonly accompanies diabetes. Several reports suggest elevated levels of high-density lipoprotein (HDL) cholesterol, but the paradoxical reduction of HDL cholesterol level during single or combined TZD and fibrate therapies has been occasionally reported. Herein, we report a case of paradoxical decrease in HDL cholesterol and apolipoprotein A-1 levels during rosiglitazone and fenofibrate treatment for the first time in Korea. The patient was a 56-yr-old man presenting with type 2 diabetes mellitus and dyslipidemia. His HDL cholesterol and apolipoprotein A-1 levels returned to normal after the cessation of fenofibrate therapy. Since diabetes is an established risk factor of cardiovascular diseases, low HDL cholesterol can be a key cause of concern for patients with diabetes. Therefore, HDL cholesterol level should be determined before and after starting TZD and/or fibrate therapy in diabetic patients.

Tetraploidy or near-tetraploidy is a rare cytogenetic abnormality found in AML, and is divided into primary and secondary forms. The secondary tetraploidy or near-tetraploidy found in AML is known to be specifically associated with t(8;21). In this case report, FISH analysis detected RUNX1-RUNX1T1 gene rearrangement in the absence of cytogenetic abnormality of t(8;21), which suggests the presence of unvailed t(8;21). This is the first case report of tetraploidy or near-tetraploidy AML with cryptic RUNX1/RUNX1T1 in Korea. Although the prognosis of tetraploidy or near- tetraploidy with t(8;21) is known to be poor, this patient shows a relatively good clinical course compared to other reported cases.

Background: Immunoglobulin heavy chain (IGH) gene rearrangement, 13q14 deletion and trisomy 1q are frequently observed in Korean patients with multiple myeloma. The purpose of our study was to analyze the statistical correlation between chromosomal aberrations and routine laboratory test results as prognostic markers and to evaluate the potential of chromosomal aberrations for the indirect assessment of prognosis in multiple myeloma patients., Methods: We investigated the prevalence of cytogenetic aberrations in 41 patients with newly diagnosed multiple myeloma. Cytogenetic analysis was conducted by conventional karyotyping and FISH for the presence of IGH/CCND1 translocation, 13q14 deletion, and trisomy 1q using bone marrow aspirates. The records of routine laboratory tests were reviewed and their correlation with cytogenetic abnormalities was investigated., Results: Sixteen (39.0%) of 41 patients had at least one cytogenetic abnormalities in conventional karyotyping or FISH. In FISH analysis of 37 patients, 8 (21.6%) showed positive result for IGH/CCND1 translocation, 8 (21.6%) for trisomy 1q, and 5 (13.5%) for 13q14 deletion. Cytogenetic abnormalities, especially trisomy 1q, were associated with significantly lower hemoglobin level and significantly higher bone marrow plasma cell percentage and beta(2)-microglobulin level., Conclusions: Statistical correlation between the presence of trisomy 1q and prognostic markers suggests that the evaluation of trisomy 1q in multiple myeloma patients may be used for the indirect assessment of prognosis in these patients.

Ionizing radiation including I(131) might produce chromosomal translocation, causing hematologic malignancy. The incidence of leukemia following radioactive iodine treatment for thyroid cancer has been reported to be approximately 0.1 to 2.0% in Western countries, whereas fewer cases have been reported in Korea. We hereby report four cases of secondary hematologic malignancy, who received iodine therapy for thyroid cancer after thyroidectomy: two cases of acute lymphoblastic leukemia with t(9;22)(q34;q11.2), a case of MDS with 5q deletion, and a case of MDS with normal karyotype. Three cases of hematologic malignancy have developed after cumulative dosage of less than 800 mCi. The treatment intervals in two cases were less than 12 months, and the other two cases had I(131) therapy only once. Assessment of causality using the Naranjo probability scale for adverse drug reactions showed that a 'possible' relationship existed between the use of I(131) and secondary hematologic malignancy in all of the four cases in this report.

Background: FISH and immunohistochemistry (IHC) on formalin-fixed paraffin embedded (FFPE) tissue are currently used in the clinical laboratory to determine HER2 status in invasive breast cancer patients. Since tissue-based methods are relatively time-consuming and have a limitation for standardization of procedure, we evaluated the availability of fine needle aspirates (FNA) for the assessment of HER2 status in invasive breast cancer patients., Methods: FNA were obtained from 51 invasive breast cancer patients and were submitted for the evaluation of HER2 status. After invasive breast cancer components were ascertained by morphological evaluation, HER2 gene amplification was evaluated by FISH. The results of HER2 FISH on FNA cells were compared with those of both FISH and IHC on corresponding FFPE tissues. FISH results were interpreted by American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines issued in 2007., Results: Of 51 FNA specimens, one was excluded due to an insufficient number of cancer cells for tests. Excluding the cases that showed 'equivocal' results, 47 (98%) out of 48 cases were concordant between the results of FISH on FNA and FISH on corresponding FFPE tissue (kappa, 0.969), and 43 (93%) out of 46 cases were concordant between the results of FISH on FNA and IHC on corresponding FFPE tissue (kappa, 0.912)., Conclusions: An excellent correlation was found between FISH on FNA cells and corresponding FFPE sections. We recommend FNA specimens for more rapid determination of HER2 status by FISH, which will be helpful for patient selection for individualized therapy.

Background: Working Formulation and Revised European American Classification of Lymphoid Neoplasms (REAL) have mainly been used in the studies for bone marrow involvement of malignant lymphoma in Korea. We investigated the incidence and histologic patterns of malignant lymphoma according to the WHO classification., Methods: This study included 507 cases of malignant lymphoma that were requested for bone marrow study for the staging during the period January 1999-December 2005 in Korea Cancer Center Hospital. Medical records, peripheral blood smears, bone marrow aspiration smears, biopsy sections, and histopathologic findings were analyzed retrospectively., Results: Of the 507 cases of malignant lymphoma, 473 (93.3%) were non-Hodgkin lymphoma (NHL) and 34 (6.7%) were Hodgkin lymphoma (HL). The overall incidence of bone marrow involvement by NHL and HL was 12.5% (59/473) and 11.8% (4/34), respectively. Among NHL cases, the incidence of bone marrow involvement by B-cell and T-cell neoplasms was 11.4% (43/377) and 16.7% (16/96), respectively. Although the incidences of bone marrow involvement by several B-cell neoplasms were more than 30%, diffuse large B cell lymphoma showed a relatively low incidence of bone marrow involvement (4.6%). Of bone marrow involvement patterns, diffuse infiltration pattern was the most common (40.0%). Peripheral blood involvement by lymphoma was observed in 35.6% of cases with bone marrow involvement., Conclusions: We used WHO classification in the study for the bone marrow involvement of malignant lymphoma, and this single-institution study should give a useful, up-to-date histopathologic information.