• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.159-169
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• 2019

Objective: Models for genomic selection assume that the reference population is an unselected population. However, in practice, genotyped individuals, such as progeny-tested bulls, are highly selected, and the reference population is created after preselection. In dairy cattle, the intensity of selection is higher in males than in females, suggesting that cows can be added to the reference population with less bias and loss of accuracy. The objective is to develop formulas applied to any genomic prediction studies or practice with preselected animals as reference population. Methods: We developed formulas for calculating the reliability and bias of genomically enhanced breeding values (GEBV) in the reference population where individuals are preselected on estimated breeding values. Based on the formulas presented, deterministic simulation was conducted by varying heritability, preselection percentage, and the reference population size. Results: The number of bulls equal to a cow regarding the reliability of GEBV was expressed through a simple formula for the reference population consisting of preselected animals. The bull population was vastly superior to the cow population regarding the reliability of GEBV for low-heritability traits. However, the superiority of reliability from the bull reference population over the cow population decreased as heritability increased. Bias was greater for bulls than cows. Bias and reduction in reliability of GEBV due to preselection was alleviated by expanding reference population. Conclusion: Cows are easier in expanding reference population size compared with bulls and alleviate bias and reduction in reliability of GEBV of bulls which are highly preselected than cows by expanding the cow reference population.

• Journal of Animal Science and Technology
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• v.62 no.4
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• pp.438-448
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• 2020

This study was performed to increase the accuracy of genomic estimated breeding value (GEBV) predictions for domestic pigs using single-breed and admixed reference populations (single-breed of Berkshire pigs [BS] with cross breed of Korean native pigs and Landrace pigs [CB]). The principal component analysis (PCA), linkage disequilibrium (LD), and genome-wide association study (GWAS) were performed to analyze the population structure prior to genomic prediction. Reference and test population data sets were randomly sampled 10 times each and precision accuracy was analyzed according to the size of the reference population (100, 200, 300, or 400 animals). For the BS population, prediction accuracy was higher for all economically important traits with larger reference population size. Prediction accuracy was ranged from -0.05 to 0.003, for all traits except carcass weight (CWT), when CB was used as the reference population and BS as the test. The accuracy of CB for backfat thickness (BF) and shear force (SF) using admixed population as reference increased with reference population size, while the results for CWT and muscle pH at 24 hours after slaughter (pH) were equivocal with respect to the relationship between accuracy and reference population size, although overall accuracy was similar to that using the BS as the reference.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1232-1246
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• 2021

Recently, the cattle genome sequence has been completed, followed by developing a commercial single nucleotide polymorphism (SNP) chip panel in the animal genome industry. In order to increase statistical power for detecting quantitative trait locus (QTL), a number of animals should be genotyped. However, a high-density chip for many animals would be increasing the genotyping cost. Therefore, statistical inference of genotype imputation (low-density chip to high-density) will be useful in the animal industry. The purpose of this study is to investigate the effect of the reference population size and marker density on the imputation accuracy and to suggest the appropriate number of reference population sets for the imputation in Hanwoo cattle. A total of 3,821 Hanwoo cattle were divided into reference and validation populations. The reference sets consisted of 50k (38,916) marker data and different population sizes (500, 1,000, 1,500, 2,000, and 3,600). The validation sets consisted of four validation sets (Total 889) and the different marker density (5k [5,000], 10k [10,000], and 15k [15,000]). The accuracy of imputation was calculated by direct comparison of the true genotype and the imputed genotype. In conclusion, when the lowest marker density (5k) was used in the validation set, according to the reference population size, the imputation accuracy was 0.793 to 0.929. On the other hand, when the highest marker density (15k), according to the reference population size, the imputation accuracy was 0.904 to 0.967. Moreover, the reference population size should be more than 1,000 to obtain at least 88% imputation accuracy in Hanwoo cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.9
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• pp.1369-1377
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• 2020

Objective: The main objectives of the present study were to assess the genetic diversity, population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis. Methods: Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with the use of F_i or ΔF_i as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep. Results: Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37, and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio f_e/f_a obtained in the study was 1.21, which is an indicator of bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree. Conclusion: Study suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended for the herd.

• Journal of Bone Metabolism
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• v.25 no.4
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• pp.235-241
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• 2018

Background: Procollagen type I N-terminal propeptide (PINP) is one of the most clinically useful bone formation biomarkers. Therefore, the purpose of this study was to independently evaluate the performance of automated total PINP assay and established age- and gender- specific reference intervals for PINP in healthy Korean population. Methods: The imprecision, linearity, and detection capability of Elecsys total PINP assay was determined and reference interval was established using 599 serums from Korean population with normal bone mineral densities based on bone densitometry. Age groups were divided into 20s, 30s, 40s, 50s, 60s and over. Results: Elecsys total PINP had excellent performance in imprecision, linearity, and detection capability. When partitioning age groups in Korean male and female populations, there was significant difference in total PINP between different age groups. In male populations, PINP level was decreased with increasing age, then it remained steady after middle-age. In female populations, there was a decreasing tendency similar to that in the male population with a sharp increase in the 50 to 59 age group. Conclusions: Elecsys total PINP assay showed precise and reliable performance in our study. We established age-related PINP reference intervals for Korean male and female population with normal bone mineral densities.

• BMB Reports
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• v.49 no.12
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• pp.653-654
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• 2016

The human reference genome, maintained by the Genome Reference Consortium, is conceivably the most complete genome assembly ever, since its first construction. It has continually been improved by incorporating corrections made to the previous assemblies, thanks to various technological advances. Many currently-ongoing population sequencing projects have been based on this reference genome, heightening hopes of the development of useful medical applications of genomic information, thanks to the recent maturation of high-throughput sequencing technologies. However, just one reference genome does not fit all the populations across the globe, because of the large diversity in genomic structures and technical limitations inherent to short read sequencing methods. The recent success in de novo construction of the highly contiguous Asian diploid genome AK1, by combining single molecule technologies with routine sequencing data without resorting to traditional clone-by-clone sequencing and physical mapping, reveals the nature of genomic structure variation by detecting thousands of novel structural variations and by finally filling in some of the prior gaps which had persistently remained in the current human reference genome. Now it is expected that the AK1 genome, soon to be paired with more upcoming de novo assembled genomes, will provide a chance to explore what it is really like to use ancestry-specific reference genomes instead of hg19/hg38 for population genomics. This is a major step towards the furthering of genetically-based precision medicine.

• Korean Journal of Agricultural Science
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• v.42 no.4
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• pp.397-406
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• 2015

Quantitative traits are mostly controlled by a large number of genes. Some of these genes tend to have a large effect on quantitative traits in cattle and are known as major genes primarily located at quantitative trait loci (QTL). The genetic merit of animals can be estimated by genomic selection, which uses genome-wide SNP panels and statistical methods that capture the effects of large numbers of SNPs simultaneously. In practice, the accuracy of genomic predictions will depend on the size and structure of reference and training population, the effective population size, the density of marker and the genetic architecture of the traits such as number of loci affecting the traits and distribution of their effects. In this review, we focus on the structure of Hanwoo reference and training population in terms of accuracy of genomic prediction and we then discuss of genetic architecture of intramuscular fat(IMF) and marbling score(MS) to estimate genomic breeding value in real small size of reference population.

• Nutrition Research and Practice
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• v.17 no.1
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• pp.135-148
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• 2023

BACKGROUND/OBJECTIVES: In times of disaster, simplified and minimized nutritional standards are necessary for a quick response to provide nutritious relief food. This study aimed to develop nutrient-based nutritional standards for foodservice at shelters during disasters in the Republic of Korea (South Korea). SUBJECTS/METHODS: The standards were developed in 2 phases. First, nutrients to be included in the standards were selected. Initial candidates were selected considering 3 aspects: preceding standards, insufficient intake during disasters, and inadequate intake among South Koreans. Final selection was made by excluding nutrients for 3 reasons: nutrients for which there is no deficiency concern in South Korea, nutrients whose intake data were not available, or nutrients whose values presented by Dietary Reference Intakes for Koreans are difficult to achieve based on the current diet among South Koreans. Second, the reference values of energy and the selected nutrients were calculated. The reference values for the entire population who were 1-year-old and over were calculated by multiplying the estimated energy requirements or the recommended nutrient intake and the proportion of each age and sex group. Respective reference values were also calculated for 4 different age groups (1-5, 6-11, 12-64, and ≥ 65-year-old). RESULTS: The standards for the entire population were 2,000 kcal for energy, 55 g for protein, 650 ㎍ retinol activity equivalents for vitamin A, 95 mg for vitamin C, 1.1 mg for thiamin, 1.3 mg for riboflavin, 14 mg niacin equivalents for niacin, 350 ㎍ dietary folate equivalents for folic acid, 750 mg for calcium, and 11 mg for iron. Four additional standards corresponding to each age group were developed. CONCLUSIONS: The nutritional standards during disasters were developed for South Korea, including energy and 9 nutrients with reference values for the entire population and 4 different age groups. The standards will contribute to maintaining the health of disaster evacuees in South Korea.

• Nutrition Research and Practice
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• v.5 no.3
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• pp.266-274
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• 2011

Accurate assessment of nutrient adequacy of a population should be based on usual intake distribution of that population. This study was conducted to adjust usual nutrient intake distributions of a single 24-hour recall in 2001 Korean National Health and Nutrition Surveys (KNHNS) in order to determine the magnitude of limitations inherent to a single 24-hour recall in assessing nutrient intakes of a population. Of 9,960 individuals who provided one 24-hour recall in 2001 KNHNS, 3,976 subjects provided an additional one-day 24-hour recall in 2002 Korean National Nutrition Survey by Season (KNNSS). To adjust for usual intake distribution, we estimated within-individual variations derived from 2001 KNHNS and 2002 KNNSS using the Iowa State University method. Nutritionally at risk population was assessed in reference to the Dietary Reference Intakes for Koreans (KDRIs). The Korean Estimated Average Requirement (Korean EAR) cut-point was applied to estimate the prevalence of inadequate nutrient intakes except for iron intakes, which were assessed using the probability approach. The estimated proportions below Korean EAR for calcium, riboflavin, and iron were 73%, 41%, and 24% from usual intake distribution and 70%, 51%, and 39% from one-day intake distribution, respectively. The estimated proportion of sodium intakes over the Intake Goal of 2,000 mg/day was 100% of the population after adjustment. The energy proportion from protein was within Korean Acceptable Macronutrient Distribution Ranges (Korean AMDR), whereas that of carbohydrate was higher than the upper limit and that of fat was below the lower limit in the subjects aged 30 years or older. According to these results, the prevalence of nutritional inadequacy and excess intake is over-estimated in Korea unless usual intake distributions are adjusted for one-day intakes of most nutrients.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6391-6395
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• 2012

Background: Ovarian cancer is ranked as the fifth most common cause of cancer death in women. In Malaysia, it is the fourth most common cancer in females. CA125 has been the tumor marker of choice in ovarian cancer but its diagnostic specificity in early stages is only 50%. Hence, there is a critical need to identify an alternative tumor marker that is capable of detecting detect ovarian cancer at an early stage. HE4 is a new tumor marker proposed for the early diagnosis of ovarian cancer and disease recurrence. Currently, none of the normal ranges of HE4 quoted in the literature are based on data for a multiethnic Asian population. Therefore, the aim of this study was to determine reference intervals for HE4 in an Asian population presenting in University Malaya Medical Centre, a tertiary reference hospital. Materials and Methods: 300 healthy women were recruited comprising 150 premenopausal and 150 postmenopausal women, aged from 20-76 years. All women were subjected to a pelvic ultrasonograph and were confirmed to be free from ovarian pathology on recruitment. Serum HE4 levels were determined by chemiluminescent microparticle immunoassay (CMIA, Abbott Architect). The reference intervals were determined following CLSI guidelines (C28-A2) using a non-parametric method. Results: The upper limits of the $95^{th}$ percentile reference interval (90%CI) for all the women collectively were 64.6 pmol/L, and 58.4 pmol/L for premenopausal) and 69.0 pmol/L for postmenopausal. The concentration of HE4 was noted to increase with age especially in women who were more than 50 years old. We also noted that our proposed reference limit was lower compared to the level given by manufacturer Abbott Architect HE4 kit insert (58.4 vs 70 pmol/L for premenopausal group and 69.0 vs 140 pmol/L in the postmenopausal group). The study also showed a significant difference in HE4 concentrations between ethnic groups (Malays and Indians). The levels of HE4 in Indians appeared higher than in Malays (p<0.05), while no significant differences were noted between the Malays and Chinese ethnic groups. Conclusions: More data are needed to establish a reference interval that will better represent the multiethnic Malaysian population. Probably a larger sampling size of equal representation of the Malay, Chinese, Indians as well as the other native ethnic communities will give us a greater confidence on whether genetics plays a role in reference interval determination.