• Journal of Life Science
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• v.29 no.1
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• pp.1-8
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• 2019

In Hanwoo cattle (Korean native cattle), there is a scarcity of comparative analysis papers using highdepth sequencing and haplotype phasing, particularly a comparative analysis of the Truseq Synthetic Long-Read Haplotyping sequencing platform serviced by Illumina (TSLRH) versus the Chromium Genome Sequencing platform serviced by 10X Genomics (10XG). DNA was extracted from the sperm of a Hanwoo breeding bull (ID: TN1505D2184/27214) provided by Hanwoo research canter and used for the generation of sequence data from both the sequencing platforms. We then identified SNVs using an appropriate analysis pipeline tailored for each platform. The TSLRH and 10XG platforms generated a total of 355,208,304 and 1,632,772,004 reads, respectively, corresponding to a Q30 (%) of 89.04% and 88.60%, respectively, of which 351,992,768(99.09%) and 1,526,641,824(93.50%) were successfully mapped. For the TSLRH and 10XG platforms, the mean depth of the sequencing was 13.04X and 74.3X, the longest phase block was 1,982,706 bp and 1,480,081 bp, the N50 phase block was 57,637 bp and 114,394 bp, the total number of SNVs identified was 4,534,989 and 8,496,813, and the total phased rate was 72.29% and 87.67%, respectively. Moreover, for each chromosome, we identified unique and common SNVs using both sequencing platforms. The number of SNVs was directly proportional to the length of the chromosome. Based on our results, we recommend the use of the 10XG platform for haplotype phasing and SNV identification, as it generated a longer N50 phase block, in addition to a higher mean depth, total number of reads, total number of SNVs, and phase rate, than the TSLRH platform.

• 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.

• Genomics & Informatics
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• v.12 no.4
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• pp.165-170
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• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

• Journal of Korean Society of Transportation
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• v.22 no.5
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• pp.19-33
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• 2004

신호교차로 운영 최적화를 위한 4가지 변수인 주기, 현시순서, 현시녹색시간, 옵셋 중에서 지금 지 정형화된 지침이 없이 전문가의 경험이나 휴리스틱한 규칙(Heuristic rule)에 의해 결정되었던 현시순서에 대해 다양한 교통조건을 고려하여 최적현시와 지체변화를 분석하였다. 교통조건은 독립/연동교차로, 교차로 기하구조, 비혼잡/혼잡상태, 통과교통량에 대한 좌회전 교통량비(LT/Thru)에 따라 Dual ring에서 구현가능한 모든 현시순서를 대상으로 최적현시를 도출하였다. 분석과정에서 비혼잡상태의 경우 LT/Thru가 작을수록 직진 중첩 동시신호가 가장 우수하게 나왔으며, LT/Thru가 크게 증가할수록 선행양방향좌회전이 양호하게 나타났다. 혼잡상태의 경우는 LT/Thru 15%에서 공통적으로 최적현시가 변하였는데 이는 포화도와 이동류별 녹색시간비율이 크게 변하면서 급작스런 주기 증가에 기인한 것으로 판단되었다. 또한 독립교차로 및 연동교차로 현시순서 분석 결과를 보면 전반적으로 선행양방좌회전 현시와 직진 중첩 동시신호 현시가 가장 양호한 것으로 나타났으며, 양방 동시신호 현시는 대체로 지체가 높게 나타나 신호운영에 비효율적인 것을 다시 한번 입증하게 되었다. 특히 연동교차로에서는 연동에 중요한 요소인 옵셋과 진행대폭(bandwidth)의 상호관계를 탄력적으로 대응할 수 있는 직진 중첩 동시신호가 최적현시로 나타났다. 본 연구는 검지기가 설치되지 않은 고정식 신호기로 운영되는 지방부 및 도시 가로망의 교통류 효율성을 높이는 중요한 자료로 사용될 것으로 판단된다. 최근에는 실시간 교통신호 제어시스템이 활발히 연구. 운영되고 있는데 이 시스템 내에 포함되어 있는 TOD방식의 고정시간 제어(pretimed control)나 패턴선택제어(pattern selection control)에도 충분히 활용할 수 있을 것으로 사료된다.