Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine.

Introduction: A population-specific genomic reference is important for research and clinical practice, yet it remains unavailable for Han Chinese (HC) in Taiwan. Objectives: We report the first whole genome sequencing (WGS) database of HC (1000 Taiwanese genome (1KTW-WGS)) and demonstrate several applications to cardiovascular medicine. Methods: Whole genomes of 997 HC were sequenced to at least 30X depth. A total of 20,117 relatively healthy HC individuals were genotyped using a customized Axiom GWAS array. We performed a genome-wide genotype imputation technique using IMPUTE2. Results: We identified 26.7 million single-nucleotide variants (SNVs) and 4.2 million insertions-deletions. Of the SNVs, 16.1% were novel relative to dbSNP (build 152), and 34.2% were novel relative to gnomAD. A total of 18,450 healthy HC individuals were genotyped using a customized Genome-Wide Association Study (GWAS) array. We identified hypertension-associated variants and developed a hypertension prediction model based on the correlation between the WGS data and GWAS data (combined clinical and genetic models, AUC 0.887), and also identified 3 novel hyperlipidemia-associated variants. Each individual carried an average of 16.42 (SD = 3.72) disease-causing variants. Additionally, we established an online SCN5A (an important cardiac gene) database that can be used to explore racial differences. Finally, pharmacogenetics studies identified HC population-specific SNVs in genes (CYP2C9 and VKORC1) involved in drug metabolism and blood clotting. Conclusion: This research demonstrates the benefits of constructing a population-specific genomic reference database for precision medicine.

VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases.

Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments.

The GFF3toolkit: QC and Merge Pipeline for Genome Annotation.

The GFF3toolkit ( https://github.com/NAL-i5K/GFF3toolkit ) supported by the i5k Workspace@NAL provides a suite of tools to handle gene annotations in GFF3 format from arthropod genome projects and their research communities. To improve GFF3 formatting of gene annotations, a quality control and merge procedure is proposed along with the GFF3toolkit. In particular, the toolkit provides functions to sort a GFF3 file, detect GFF3 format errors, merge two GFF3 files, and generate biological sequences from a GFF3 file. This chapter explains when and how to use the provided tools to obtain nonredundant arthropod gene sets in high quality.

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water.

BACKGROUND: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. RESULTS: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. CONCLUSIONS: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.

Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant.

Background: The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. Results: We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. Conclusions: This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.

Suppressors of cytokine signaling in tuberculosis.

Tuberculosis (TB), a global disease mainly infected by Mycobacterium tuberculosis, remains leading public health problem worldwide. Suppressors of cytokine signaling (SOCSs) play important roles in the protection against microbial infection. However, the relationship between members of the SOCS family and tuberculosis infection remains unclear. Using peripheral blood mononuclear cells, we investigated the mRNA expression profiles of SOCS subfamilies among active TB, latent tuberculosis infection (LTBI), and healthy individuals. Our results showed that active tuberculosis subjects had higher levels of SOCS-3 mRNA, lower expressions of SOCS-2, -4, -5, -6, -7, and cytokine-inducible SH2-containing protein-1 (CIS-1) mRNAs, but not SOCS-1 mRNA than healthy and LTBI subjects. In men, LTBI patients had lower SOCS-3 than healthy subjects, and active TB patients had lower levels of SOCS-4, -5, and CIS-1 mRNAs but higher levels of SOCS-3 mRNA than healthy subjects. In women, LTBI patients had lower SOCS-3 mRNA level than healthy subjects, and active TB patients had lower CIS-1 mRNA level than healthy subjects. In non-aged adults (< 65 years old), TB patients had higher SOCS-3 mRNA and lower levels of SOCS-2, -4, -5, -6, -7, and CIS-1 mRNAs; whereas, aged TB patients (≥ 65 years old) had lower levels of SOCS-5 and CIS-1 mRNAs. These data suggest that particular SOCS members and their correlative relationships allow discrimination of active TB from healthy and LTBI subjects.