VnD: a structure-centric database of disease-related SNPs and drugs.

Numerous genetic variations have been found to be related to human diseases. Significant portion of those affect the drug response as well by changing the protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases and drugs. We present the variations and drugs (VnD), a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. VnD was built in three steps. First, we integrated various resources systematically to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations and relevant drugs. VnD contains 137,195 disease-related gene records (13,940 distinct genes) and 16,586 genetic variation records (1790 distinct variations). Next, we carried out structure modeling and docking simulation for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs in the drug-related genes. Conformational changes in 590 wild-type and 4437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties. The VnD database, available at http://vnd.kobic.re.kr:8080/VnD/ or vandd.org, would be a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.

The genome of soybean (Glycine max), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja, the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja. This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max, is ∼0.31% different from that of G. max. In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja/G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.

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 Venter's, 46.94% against Watson's, 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.

Gevab: a prototype genome variation analysis browsing server.

BACKGROUND: The first Korean individual diploid genome sequence data (KOREF) was publicized in December 2008. RESULTS: A Korean genome variation analysis and browsing server (Gevab) was constructed as a database and web server for the exploration and downloading of Korean personal genome(s). Information in the Gevab includes SNPs, short indels, and structural variation (SV) and comparison analysis between the NCBI human reference and the Korean genome(s). The user can find information on assembled consensus sequences, sequenced short reads, genetic variations, and relationships between genotype and phenotypes. CONCLUSION: This server is openly and publicly available online at http://koreagenome.org/en/ or directly http://gevab.org.

ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database.

Deep sequencing has shown that over 90% of human genes undergo alternative splicing. The splicing process requires exon-intron boundary recognition. SNPs located in the boundaries (splice sites) influence exon configuration. Also, splice site SNPs (ssSNPs) alter translation efficiency of the mRNA and lead to important changes in disease susceptibility. We developed the ssSNPTarget database to provide ssSNPs on human and mouse genes. It includes: 1) ssSNP distribution information in human and mouse genes; 2) effects of SNPs in splice sites: junction strength change, protein domain change, and alternative splicing events (exon skipping, 5'- or 3'-exon extension); 3) splice site conservation in eukaryotes; and 4) associated disease information derived from OMIM, GAD, and HGMD. ssSNPTarget contains 1,576 human ssSNPs associated with 1,193 genes and 538 mouse ssSNPs associated with 281 genes. Users can query ssSNPTarget with several types of search terms (gene symbol, SNP rs number, transcript ID, or genomic position), and the information can be accessed at http://variome.kobic.re.kr/ssSNPTarget/ or http://ssSNPTarget.org.

MitoVariome: a variome database of human mitochondrial DNA.

BACKGROUND: Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forensics, degenerative diseases, cancers, and aging process. Typically, human mitochondrial DNA has various features such as HVSI, HVSII, single-nucleotide polymorphism (SNP), restriction enzyme sites, and short tandem repeat (STR). RESULTS: We present a variome database (MitoVariome) of human mitochondrial DNA sequences. Queries against MitoVariome can be made using accession numbers or haplogroup/continent. Query results are presented not only in text but also in HTML tables to report extensive mitochondrial sequence variation information. The variation information includes repeat pattern, restriction enzyme site polymorphism, short tandem repeat, disease information as well as single nucleotide polymorphism. It also provides a graphical interface as Gbrowse displaying all variations at a glance. The web interface also provides the tool for assigning haplogroup based on the haplogroup-diagnostic system with complete human mitochondrial SNP position list and for retrieving sequences that users query against by using accession numbers. CONCLUSION: MitoVariome is a freely accessible web application and database that enables human mitochondrial genome researchers to study genetic variation in mitochondrial genome with textual and graphical views accompanied by assignment function of haplogrouping if users submit their own data. Hence, the MitoVariome containing many kinds of variation features in the human mitochondrial genome will be useful for understanding mitochondrial variations of each individual, haplogroup, or geographical location to elucidate the history of human evolution.

PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs.

BACKGROUND: Parkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have created PD-related research resources. However, resources for brain and PD studies are still lacking. Therefore, we have constructed a database of PD-related gene and genetic variations using the substantia nigra (SN) in PD and normal tissues. In addition, we integrated PD-related information from several resources. RESULTS: We collected the 6,130 SN expressed sequenced tags (ESTs) from brain SN normal tissues and PD patients SN tissues using full-cDNA library and normalized cDNA library construction methods from our previous study. The SN ESTs were clustered in 2,951 unigene clusters and assigned in 2,678 genes. We then found up-regulated 57 genes and down-regulated 48 genes by comparing normal and PD SN ESTs frequencies with over 0.9 cut-off probability of differential expression based on the Audic and Claverie method. In addition, we integrated disease-related information from public resources. To examine the characteristics of these PD-related genes, we analyzed alternative splicing events, single nucleotide polymorphism (SNP) markers located in the gene regions, repeat elements, gene regulation elements, and pathways and protein-protein interaction networks. CONCLUSION: We constructed the PDbase database to capture the PD-related gene, genetic variation, and functional elements. This database contains 2,698 PD-related genes through ESTs discovered from human normal and PD patients SN tissues, and through integrating several public resources. PDbase provides the mitochondrion proteins, microRNA gene regulation elements, single nucleotide polymorphisms (SNPs) markers within PD-related gene structures, repeat elements, and pathways and networks with protein-protein interaction information. The PDbase information can aid in understanding the causation of PD. It is available at http://bioportal.kobic.re.kr/PDbase/. Supplementary data is available at http://bioportal.kobic.re.kr/PDbase/suppl.jsp.

Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries.

UNLABELLED: Bioinformatics involves the collection, organization and analysis of large amounts of biological data, using networks of computers and databases. Developing countries in the Asia-Pacific region are just moving into this new field of information-based biotechnology. However, the computational infrastructure and network bandwidths available in these countries are still at a basic level compared to that in developed countries. In this study, we assessed the utility of a BitTorrent-based Peer-to-Peer (btP2P) file distribution model for automatic synchronization and distribution of large amounts of biological data among developing countries. The initial country-level nodes in the Asia-Pacific region comprised Thailand, Korea and Singapore. The results showed a significant improvement in download performance using btP2P--three times faster overall download performance than conventional File Transfer Protocol (FTP). This study demonstrated the reliability of btP2P in the dissemination of continuously growing multi-gigabyte biological databases across the three Asia-Pacific countries. The download performance for btP2P can be further improved by including more nodes from other countries into the network. This suggests that the btP2P technology is appropriate for automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries in the Asia-Pacific region. AVAILABILITY: http://everest.bic.nus.edu.sg/p2p/

SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

BACKGROUND: Analysis of single nucleotide polymorphism (SNP) is becoming a key research in genomics fields. Many functional analyses of SNPs have been carried out for coding regions and splicing sites that can alter proteins and mRNA splicing. However, SNPs in non-coding regulatory regions can also influence important biological regulation. Presently, there are few databases for SNPs in non-coding regulatory regions. DESCRIPTION: We identified 488,452 human SNPs in the putative promoter regions that extended from the +5000 bp to -500 bp region of the transcription start sites. Some SNPs occurring in transcription factor (TF) binding sites were also predicted (47,832 SNP; 9.8%). The result is stored in a database: SNP@promoter. Users can search the SNP@Promoter database using three entries: 1) by SNP identifier (rs number from dbSNP), 2) by gene (gene name, gene symbol, refSeq ID), and 3) by disease term. The SNP@Promoter database provides extensive genetic information and graphical views of queried terms. CONCLUSION: We present the SNP@Promoter database. It was created in order to predict functional SNPs in putative promoter regions and predicted transcription factor binding sites. SNP@Promoter will help researchers to identify functional SNPs in non-coding regions.

SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.

BACKGROUND: Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date. DESCRIPTION: We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category. CONCLUSION: SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.

SNP2NMD: a database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay.

UNLABELLED: Elucidating the effects of genetic polymorphisms on genes and gene networks is an important step in disease association studies. We developed the SNP2NMD database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD). The SNP2NMD Web interfaces provide extensive genetic information on and graphical views of the queried SNP, gene, and disease terms. AVAILABILITY: SNP2NMD is available from http://variome.net, or directly from http://bioportal.kobic.re.kr/SNP2NMD. SUPPLEMENTARY INFORMATION: http://bioportal.kobic.re.kr/SNP2NMD/Wiki.jsp?page=Statistics.

Sulfamethazine detection with direct-binding optical waveguide lightmode spectroscopy-based immunosensor.

A direct-binding optical waveguide lightmode spectroscopy-based immunosensor detecting sulfamethazine (SMZ) was prepared, followed by the measurement of its specificity and sensitivity. System construction was undertaken with a peristaltic pump, an injector and the main unit comprising a sensor holder, two signal-harvesting photodiodes, a beam mirror, shutter and He-Ne laser source emitting a monochrome light (λ=632.8nm), plus a PC. Antibody immobilization was performed in situ by covalent binding of an anti-SMZ antibody over the surface of a glutaraldehyde-activated 3-aminopropyltriethoxysilane-treated sensor chip. The reaction buffer for the system was 4mM Tris-HCl (pH 7.2) that showed a medium surface coverage and stable baseline. Sensor response was quite specific to antibody-antigen complexation, as judged from no sensor response caused by bovine serum albumin immobilization. The sensor responses according to SMZ concentrations from 10(-8) to 10(-2)M increased linearly in a semi-logarithmic scale, with the limit of detection of 10(-8)M. The immunosensor was favorably reusable for SMZ screening.

Flatfish vitellogenin detection using optical waveguide lightmode spectroscopy-based immunosensor.

A sensitive optical waveguide lightmode spectroscopy-based immunosensor was developed to detect vitellogenin in seawater flatfish (Paralichthys olivaceus). For this purpose, anion-exchange column chromatography with DE-52 resin was used to purify flatfish vitellogenin from flatfish serum containing vitellogenin that had been induced using an intraperitoneal 17beta-estradiol injection. The anti-flatfish vitellogenin antibody used as the biological component of the above immunosensor was prepared using the purified flatfish vitellogenin. The change in the incoupling angle according to the complexation between the flatfish vitellogenin and its antibody, immobilized over an optical grating coupler sensor chip, was measured to calculate the sensor response. The immunosensor was quite specific to flatfish vitellogenin binding, based on no sensor response in the case of bovine serum albumin immobilization. When plotted using double-logarithmic scales, the sensor responses increased linearly in flatfish vitellogenin concentrations of 0.00675-67.5 nM, with a detection limit of 0.0675 nM. The reusability during seven repetitive measurements was reasonably fair for the preliminary screening of flatfish vitellogenin.

Endogenous retrovirus-related sequences provide an alternative transcript of MCJ genes in human tissues and cancer cells.

The MCJ gene is a member of the DNAJ family, and its transcriptional event is controlled by methylation of the CpG island. In our study, we found LTR33 and LTR7 elements provided an alternative transcript within the MCJ gene. To detect different expression patterns between the originally reported MCJ transcript and the LTR-related transcript, we performed a RT-PCR approach using various human tissues and cancer cells. The original MCJ transcript was detected in human tissues and cancer cells, whereas the LTR-related transcript was only revealed in some cancer cells (HCT106, MCF-3, TE-1, Hela, and CCHM). We also performed a PCR analysis to compare the insertion lineage of the LTR elements with the genomic DNAs of primates, indicating that those LTR33 and LTR7 elements of HERV-H have been integrated into the primate genome at different times. Taken together, we suggest that HERV-related elements trigger transcriptome diversification during primate evolution.

Measurement of polyphenol oxidase activity using optical waveguide lightmode spectroscopy-based immunosensor.

Polyphenol oxidase (PPO) is an important quality index during food processing involving heat-treatment and sensitive determination of PPO activity has been a critical concern in the food industry. In this study, a new measurement of PPO activity exploiting an optical waveguide lightmode spectroscopy-based immunosensor is presented using a polyclonal anti-PPO antibody that was immobilized in situ to the surface of a 3-aminopropyltriethoxysilane-treated optical grating coupler activated with glutaraldehyde. When analysed with a purified PPO fraction from potato tubers, a linear relationship was found between PPO activities of 0.0005607-560.7U/mL and the sensor responses obtained. The sensor was applicable to measurement of PPO activity in real samples that were prepared from potato tubers, grapes and Kimchi cabbage, and the analytical results were compared with those obtained by a conventional colorimetric assay measuring PPO activity. When tested for long-term stability, the sensor was reusable up to 10th day after preparation.

Identification of ethnically specific genetic variations in pan-asian ethnos.

Asian populations contain a variety of ethnic groups that have ethnically specific genetic differences. Ethnic variants may be highly relevant in disease and human differentiation studies. Here, we identified ethnically specific variants and then investigated their distribution across Asian ethnic groups. We obtained 58,960 Pan-Asian single nucleotide polymorphisms of 1,953 individuals from 72 ethnic groups of 11 Asian countries. We selected 9,306 ethnic variant single nucleotide polymorphisms (ESNPs) and 5,167 ethnic variant copy number polymorphisms (ECNPs) using the nearest shrunken centroid method. We analyzed ESNPs and ECNPs in 3 hierarchical levels: superpopulation, subpopulation, and ethnic population. We also identified ESNP- and ECNP-related genes and their features. This study represents the first attempt to identify Asian ESNP and ECNP markers, which can be used to identify genetic differences and predict disease susceptibility and drug effectiveness in Asian ethnic populations.

Purification and characterization of polyphenol oxidase from fresh ginseng.

Polyphenol oxidase (PPO) was purified from fresh ginseng roots using acetone precipitation, carboxymethyl (CM)-Sepharose chromatography, and phenyl-Sepharose chromatography. Two isoenzymes (PPO 1 and PPO 2) were separated using an ion-exchange column with CM-Sepharose. PPO 1 was purified up to 13.2-fold with a 22.6% yield. PPO 2 bound to CM-Sepharose, eluted with NaCl, and was purified up to 22.5-fold with a 17.4% yield. PPO 2 was further chromatographed on phenyl-Sepharose. The molecular weight of the purified PPO 2 from fresh ginseng was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and was about 40 kDa. The optimum temperature and pH were 20℃ and 7.0, respectively, using catechol as a substrate. Pyrogallol showed the highest substrate specificity. The effect of a PPO inhibitor showed that its activity increased slightly in the presence of a low concentration of citric acid. High concentrations of acidic compounds and sulfite agents significantly inhibited purified ginseng PPO 2.

Revising a personal genome by comparing and combining data from two different sequencing platforms.

For the robust practice of genomic medicine, sequencing results must be compatible, regardless of the sequencing technologies and algorithms used. Presently, genome sequencing is still an imprecise science and is complicated by differences in the chemistry, coverage, alignment, and variant-calling algorithms. We identified ~3.33 million single nucleotide variants (SNVs) and ~3.62 million SNVs in the SJK genome using SOLiD and Illumina data, respectively. Approximately 3 million SNVs were concordant between the two platforms while 68,532 SNVs were discordant; 219,616 SNVs were SOLiD-specific and 516,080 SNVs were Illumina-specific (i.e., platform-specific). Concordant, discordant, and platform-specific SNVs were further analyzed and characterized. Overall, a large portion of heterozygous SNVs that were discordant with genotyping calls of single nucleotide polymorphism chips were highly confident. Approximately 70% of the platform-specific SNVs were located in regions containing repetitive sequences. Such platform-specificity may arise from differences between platforms, with regard to read length (36 bp and 72 bp vs. 50 bp), insert size (~100-300 bp vs. ~1-2 kb), sequencing chemistry (sequencing-by-synthesis using single nucleotides vs. ligation-based sequencing using oligomers), and sequencing quality. When data from the two platforms were merged for variant calling, the proportion of callable regions of the reference genome increased to 99.66%, which was 1.43% higher than the average callability of the two platforms, representing ~40 million bases. In this study, we compared the differences in sequencing results between two sequencing platforms. Approximately 90% of the SNVs were concordant between the two platforms, yet ~10% of the SNVs were either discordant or platform-specific, indicating that each platform had its own strengths and weaknesses. When data from the two platforms were merged, both the overall callability of the reference genome and the overall accuracy of the SNVs improved, demonstrating the likelihood that a re-sequenced genome can be revised using complementary data.

Mapping human genetic diversity in Asia.

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Carp vitellogenin detection by an optical waveguide lightmode spectroscopy biosensor.

A label-free carp vitellogenin sensor has a strong potential for on-site monitoring on the possible contamination of edible fish with endocrine disruptors as a sum parameter in an inland carp farm. In this study, we performed a sensitive detection for carp vitellogenin with a direct-binding optical waveguide lightmode spectroscopy-based immunosensor. Carp vitellogenin bound over the sensor surface quite specifically, judging from the sensor responses according to stepwise antibody immobilization. This was also supported by a negligible sensor response found at bovine serum albumin immobilization. When plotted in double-logarithmic scale for carp vitellogenin concentrations of 0.00675-67.5 nM, a linear relationship was found between analyte concentration and sensor response, together with the limit of detection of 0.00675 nM. The reusability of the immunosensor after the regeneration with 10mM HCl was reasonably good, as presumed from the coefficient of variability of 6.02% for nine repetitive measurements. The model sample prepared by spiking a purified carp vitellogenin into a 10-fold diluted vitellogenin-free carp serum in 9.45 nM showed the response ratio of 96.70% against 9.45 nM of the purified carp vitellogenin. When a female and male carp sera induced with 17beta-estradiol injection were analyzed, biomarker induction was even identifiable at 2000-fold serum dilution.