KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing.

Database : the Journal of Biological Databases and Curation
Kwang Su JungMyungguen Chung

Abstract

Since 2012, the Center for Genome Science of the Korea National Institute of Health (KNIH) has been sequencing complete genomes of 1722 Korean individuals. As a result, more than 32 million variant sites have been identified, and a large proportion of the variant sites have been detected for the first time. In this article, we describe the Korean Reference Genome Database (KRGDB) and its genome browser. The current version of our database contains both single nucleotide and short insertion/deletion variants. The DNA samples were obtained from four different origins and sequenced in different sequencing depths (10× coverage of 63 individuals, 20× coverage of 194 individuals, combined 10× and 20× coverage of 135 individuals, 30× coverage of 230 individuals and 30× coverage of 1100 individuals). The major features of the KRGDB are that it contains information on the Korean genomic variant frequency, frequency difference between the Korean and other populations and the variant functional annotation (such as regulatory elements in ENCODE regions and coding variant functions) of the variant sites. Additionally, we performed the genome-wide association study (GWAS) between Korean genome variant sites for the 30×230 individuals and thr...Continue Reading

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
Jun 21, 2005·Genome Research·Gregory M CooperArend Sidow
Apr 19, 2008·Nature·David A WheelerJonathan M Rothberg
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Oct 18, 2008·Nucleic Acids Research·Kim D PruittDonna R Maglott
Nov 7, 2008·Nature·David R BentleyAnthony J Smith
Nov 7, 2008·Nature·Jun WangJian Wang
May 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucia A HindorffTeri A Manolio
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 10, 2009·Nature·Jong-Il KimJeong-Sun Seo
Aug 12, 2009·Nature Biotechnology·Dmitry PushkarevStephen R Quake
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Apr 1, 2010·Nature Methods·Ivan A AdzhubeiShamil R Sunyaev
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Sep 3, 2010·Nature·UNKNOWN International HapMap 3 ConsortiumJean E McEwen
Sep 9, 2010·Genome Biology·Pin TongBrendan Loftus
Dec 15, 2010·PLoS Computational Biology·Eugene V DavydovSerafim Batzoglou
Dec 21, 2010·Nature Biotechnology·Jacob O KitzmanJay Shendure
Jul 6, 2011·Nucleic Acids Research·Boris RevaChris Sander
Dec 6, 2011·Nucleic Acids Research·Eric W SayersJian Ye
Jan 28, 2012·BMB Reports·Chang Bum HongJong-Young Lee
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Apr 30, 2013·Bioinformatics·Sanghoon MoonBong-Jo Kim
Aug 28, 2013·BMB Reports·Young Uk KimKiejung Park
Nov 16, 2013·Nucleic Acids Research·Melissa J LandrumDonna R Maglott
Dec 10, 2013·Nucleic Acids Research·Paul FlicekStephen M J Searle
Oct 27, 2017·International Journal of Molecular Sciences·Ah Reum KimByung Yoon Choi
May 31, 2018·Proceedings of the National Academy of Sciences of the United States of America·Yoshikatsu HosodaKenji Yamashiro

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR

Software Mentioned

UCSC Genome browser
Ensembl
SNP DB
KGVDB
Siphy
HiSeq
ANNOVAR
GERP
PolyPhen
PICARD

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2021 Meta ULC. All rights reserved