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.

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

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of 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.