Chang Geun Kim

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venters, 46.94% against Watsons, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.

Measurement Uncertainty Evaluation for High Speed Tensile Properties of Auto-body Steel Sheets

Evaluation of the crashworthiness is one of the important issues in the automotive industry. In order to evaluate the crashworthiness of auto-body structure, finite element method has been conducted for crash analysis. Generally, strain rates distribution of auto-body structure in the car crash ranges from 0.001/s to 500/s. Since material properties of steel sheets depend on the strain rates, the dynamic behavior of sheet metals must be examined and applied to the finite element model appropriately. This paper is concerned with the evaluation of measurement uncertainty of high speed tensile properties of auto-body steel sheets. Obtaining procedure of the true stress−true strain data at intermediate strain rates is properly designed for the experiment and data acquisition. The measurement uncertainty of the true stress is evaluated considering sources of uncertainties of input quantities and their associated sensitivity coefficients. A combined standard uncertainty is evaluated from not only the uncertainties of the input quantities but also influence factors of high speed tensile tests. The results show that the measurement uncertainty evaluation procedure has been successfully applied to high speed tensile properties.

KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses

High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.

Corrigendum: An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

This corrects the article DOI: 10.1038/ncomms13637.

Measurement Uncertainty in Spine Bone Mineral Density by Dual Energy X-ray Absorptiometry

Background The purpose of this study was to calculate the measurement uncertainty of the process of bone mineral density (BMD) analysis using dual energy X-ray absorptiometry with traceability. Methods Between March 2015 and October 2016, among healthy participants in their 20s and 30s, the study included those who had not taken calcium, vitamin D supplements and steroids and were without a history of osteoporosis, osteopenia and diseases related to osteoporosis. Relational expression of the model was established based on Guide to the Expression of Uncertainty in Measurements and Eurachem and the uncertainty from each factor was evaluated. Results The combined standard uncertainty was 0.015, while the expanded uncertainty was 0.0298. The factor-specific standard uncertainties that occurred in the process of measuring BMD were 0.72% for the calibration curve, 0.9% for the internal quality control (IQC) using Aluminum Spine Phantom, 0.58% for European Spine Phantom (ESP), and 0.9% for the inspector precision (IP). Conclusions The combined standard uncertainty of the spine BMD corrected with ESP was 0.015 when measured at one time and targeting one participant. The uncertainties of the accuracy of the IQC and the IP were higher than that of the other factors. Therefore, there will be a need for establishment of protocols to lower these uncertainties.

Ethnically relevant consensus Korean reference genome towards personal reference genomes

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific or personal genomic variations, which may be detected more efficiently using an ethnically-relevant and/or a personal reference. Here we report a hybrid assembly of Korean reference (KOREF) as a pilot case for constructing personal and ethnic references by combining sequencing and mapping methods. KOREF is also the first consensus variome reference, providing information on millions of variants from additional ethnically homogeneous personal genomes. We found that this ethnically-relevant consensus reference was beneficial for efficiently detecting variants. Systematic comparison of KOREF with previously established human assemblies showed the importance of assembly quality, suggesting the necessity of using new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

The Data Evaluation for Obtaining Accuracy and Reliability

Nemours scientific measurement results are flooded from the paper, data book, etc. as fast growing of internet. We meet many different measurement results on the same measurand. In this moment, we are face to choose most reliable one out of them. But it is not easy to choose and use the accurate and reliable data as we do at an ice cream parlor. Even expert users feel difficult to distinguish the accurate and reliable scientific data from huge amount of measurement results. For this reason, the data evaluation is getting more important as the fast growing of internet and globalization. Furthermore the expressions of measurement results are not in standardi-zation. As these need, the international movement has been enhanced. At the first step, the global harmonization of terminology used in metrology and the expression of uncertainty in measurement were published in ISO. These methods are wide spread to many area of science on their measurement to obtain the accuracy and reliability. In this paper, it is introduced that the GUM, SRD and data evaluation on atomic collisions.