Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population

Background

Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.

Results

Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.

Conclusions

Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-673) contains supplementary material, which is available to authorized users.     

Removal or maintenance of inositol-linked acyl chain in glycosylphosphatidylinositol is critical in trypanosome life cycle

The protozoan parasite Trypanosoma brucei is coated by glycosylphosphatidylinositol (GPI)-anchored proteins. During GPI biosynthesis, inositol in phosphatidylinositol becomes acylated. Inositol is deacylated prior to attachment to variant surface glycoproteins in the bloodstream form, whereas it remains acylated in procyclins in the procyclic form. We have cloned a T. brucei GPI inositol deacylase (GPIdeAc2). In accordance with the acylation/deacylation profile, the level of GPIdeAc2 mRNA was 6-fold higher in the bloodstream form than in the procyclic form. Knockdown of GPIdeAc2 in the bloodstream form caused accumulation of an inositol-acylated GPI, a decreased VSG expression on the cell surface and slower growth, indicating that inositol-deacylation is essential for the growth of the bloodstream form. Overexpression of GPIdeAc2 in the procyclic form caused an accumulation of GPI biosynthetic intermediates lacking inositol-linked acyl chain and decreased cell surface procyclins because of release into the culture medium, indicating that overexpression of GPIdeAc2 is deleterious to the surface coat of the procyclic form. Therefore, the GPI inositol deacylase activity must be tightly regulated in trypanosome life cycle.     

Enhancement of activity of lipase-displaying yeast cells and their application to optical resolution of (R,S)-1-benzyloxy-3-chloro-2-propyl monosuccinate

Rhizopus oryzae lipase (ROL) was displayed on the cell surface of Saccharomyces cerevisiae via the Flo1 N-terminal region (1100 amino acids), which corresponds to a flocculation functional domain. The activity of lipase-displaying yeast whole-cell biocatalysts was enhanced 7.3-fold by incubation of the yeast cells at 20 degrees C in distilled water for 8 days after 8 day cultivation. The amount of lipase molecules present in cell wall and intracellular fractions was found to be increased 4.5- and 1.8-fold, respectively, by incubation, which proves that ROL molecules are expressed during incubation. The ROL-displaying yeast whole-cell biocatalyst with enhanced activity was successfully catalyzed by optical resolution of the pharmaceutical precursor (R,S)-1-benzyloxy-3-chloro-2-propyl monosuccinate. Moreover, it showed stable activity through at least eight reaction cycles. These results demonstrate that ROL-displaying yeast cells with enhanced activity by incubation in distilled water are very effective in industrial bioconversion processes.     

Genome Sequence of Kitasatospora setae NBRC 14216T: An Evolutionary Snapshot of the Family Streptomycetaceae

Kitasatospora setae NBRC 14216^T (=KM-6054^T) is known to produce setamycin (bafilomycin B1) possessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the genus Streptomyces, although they are distinguishable from each other on the basis of cell wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of K. setae NBRC 14216^T as the first Streptomycetaceae genome other than Streptomyces. The genome is a single linear chromosome of 8 783 278 bp with terminal inverted repeats of 127 148 bp, predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes. Although these features resemble those of Streptomyces, genome-wide comparison of orthologous genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the Streptomyces genus. Although many of the genes related to morphological differentiation identified in Streptomyces were highly conserved in K. setae, there were some differences such as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the copy number and variation of paralogous components involved in cell wall synthesis.     

mRNA expression of lysyl oxidase and matrix metalloproteinase-12 in mouse skin

Elastic fibers in the dermis play an important role in skin elasticity. The desmosine crosslinking structure constructed of lysyl oxidase (LOX) in elastic fibers contributes to elasticity, while elastic fibers are primarily degraded by one of the matrix metalloproteinases (MMPs), MMP-12. We investigated the gender differences and diurnal variation of these enzymes. Gender-based differences in LOX mRNA expression were detected, and were significantly lower in females. In contrast, higher MMP-12 mRNA expression was observed in the light period, suggesting that elastic fibers might be degraded in the light rather than the dark period.     

Self‐quenching in the electrochemiluminescence of Ru(bpy)32+ using ascorbic acid as co‐reactant

In this study, electrochemiluminescence (ECL) of Ru(bpy)₃²⁺ (bpy = 2,2′‐bipyridyl) using ascorbic acid (H₂A) as co‐reactant was investigated in an aqueous solution. When H₂A was co‐existent in a Ru(bpy)₃²⁺‐containing buffer solution, ECL peaks were observed at a potential corresponding to the oxidation of Ru(bpy)₃²⁺, and the intensity was proportional to H₂A concentration at lower concentration levels. The formation of the excited state *Ru(bpy)₃²⁺ was confirmed to result from the co‐reaction between Ru(bpy)₃³⁺and the intermediate of ascorbate anion radical (A⁻•), which showed the maximum ECL at pH = 8.8. It is our first finding that the ECL intensity would be quenched significantly when the concentration of H₂A was relatively higher, or upon ultrasonic irradiation. In most instances, quenching is observed with four‐fold excess of H₂A over Ru(bpy)₃²⁺. The diffusional self‐quenching scheme as well as the possible reaction pathways involved in the Ru(bpy)₃²⁺–H₂A ECL system are discussed in this study. Copyright © 2008 John Wiley & Sons, Ltd.     

The relation between recalcitrancy of a mangrove plant, Kandelia obovata, and high endogenous level of abscisic acid

Kandelia obovata Sheue, Liu & Yong sp. nov. is one of the cold tolerant mangrove plants. Some callus formation was obtained from the leaves of K. obovata in liquid medium containing 10 μM of 2,4-dichlorophenoxyacetic acid. However, recalcitrancy was found when subculturing them. Endogenous levels of gibberellins (GAs) and abscisic acid (ABA) in leaf protoplasts of K. obovata were determined using micro-scale extraction and purification steps, including thin layer chromatography and quantification by micro-bioassay or enzyme linked immunosorbent assays. Very high amounts of ABA and low activities of GAs were found in leaf protoplasts of K. obovata. Low concentrations of gibberellic acid and uniconazole-P were effective of enhancing cell enlargement in protoplast cultures. Exogenous application of ABA was inhibitory to protoplast culture. All cytokinins tested were inhibitory to both leaf and protoplast cultures. The high endogenous level of ABA is most likely the underlying cause of recalcitrancy of mangrove cultures.