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NGS

Unlike Sanger Sequencing, NGS (Next Generation Sequencing) by using high-throughput sequencing technology which can rapidly undergo massive parallel sequencing by fragmenting genes and reading them at once, then using advanced analysis systems to quickly decode genetic information. 

▷ NGS Order Form Download

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Cat. No.
S-3100
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Overview

Bioneer's NGS service provides wide range of NGS applications for various research purposes. We can provide gene decoding and analysis for whole genome, exome, transcriptome, and epigenome. Analysis based on De novo sequencing and reference genes can be done not only for humans, but also for various species such as marine animals/plants and bacteria with high GC contents.

Features and Benefits

  • Various service for NGS applications and customized research project consultations

  • Highly reliable data

  • Analysis for basic/customized bioinformatics

  • Associated service: Sanger Sequencing, RNA profiling

List of Services

Whole Genome Sequencing(WGS) is a method that can gain genetic information of the whole genomes of a model organism and human by reading them all at once.
By utilizing the data gained through WGS, analysis of various variants such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and copy number variants (CNVs), and structural variations can be done.
The report data studied through bioinformatics will be presented along with Variant Call Format (VCF), Annotation Result Excel Format (xls).

• Resequencing
Resequencing allows to find and compare genetic mutations by using a known reference genome.
▼Guide line

Individual Genome/ General Disease Population Genomics Cancer / Rare Disease
Objective Obtaining variants of each sample for downstream analysis Population and phylogenetic analysis disease and phenotype relationship analysis Detecting cancer specific and/or rare variants
Sufficient depth 30X 10X 100X/200X
Sample Requirements Minimum Quantity 1 µg, Minimum Concentration = 50 ng/µl, OD 260/280=1.6~2.0
Deliverables Raw data(FASTQ), statistics of raw data, Mapping to reference genome, SNPs and InDels calling,Variant annotation, Functional annotations
* May vary depending on the sample types, species, and data analysis.

• De novo sequencing
De novo sequencing is used for analysis of genetic information of a newly found species without any references, which allows to undergo comparative analysis for variant characteristics and gene variety in detail. Thus, De novo sequencing requires highly advanced technologies to generate a draft map and a fine map. For creating a successive, complete  de novo genome, various types of libraries (200 bp, 500 bp, 2 kb, 5 kb, 10 kb, 20 kb) are constructed to be used for the analysis.
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General sequencing depth Gene coverage Genome Coverage Accuracy Contig Sequence N50 Scaffold Sequence N50
Draft Map 60X 95% 90%
(except heterochromatin region)		 99.999% >50 kb >20 kb
Fine Map 80X 98% 95%
(except heterochromatin region)		 99.999% >20 kb >300 kb
Sample Requirements Minimum Quantity 3µg, Minimum Concentration = 50ng/µl, OD 260/280=1.6~2.0
Deliverables Raw data(FASTQ), statistics of raw data, de novo assembly, taxonomy profiling, k-mer analysis, Gene prediction, Gene annotation
* May vary depending on the sample types, species, and data analysis.

Whole exome sequencing(WES) undergoes selective gene analysis of exons only, which are protein coding regions comprising only 1% of the whole genome (~30 Mb).
Targeted sequencing can selectively analyze regions of a specific area of a gene.
As the specific kit is used for capturing the target region before undergoing the sequencing process, this not only increases the sequencing depth, but also can be more economic than the whole genome sequencing. This sequencing technology can be also used for clinical researches, diagnostics, and forensics to distinguish variants and genes.

▼Guide line

Whole Exome Sequencing Target Region Sequencing
Objective Accurate variants detection within exon region Detecting cancer specific and/ or rare variants
Sufficient depth
(human exome)		 100X 500X
Capture region Agilent SureSelect Exome Capture Kit/ Customized capture kit
Sample Requirements Minimum Quantity 1 µg, Minimum Concentration = 50 ng/µl, OD 260/280=1.6~2.0
Deliverables Raw data(FASTQ/VCF), Summary of data production, Mapping statistics, Statistics of sequencing reads, SNPs and InDels calling, Variant annotation, SNVs concordance, Tumor-Normal paired analysis, Trio(Family-based) analysis
* May vary depending on the sample types, species, and data analysis.

▼ Exome / Targeted DNA Sequencing Process

RNA sequencing(Transcriptome) can provide information for genes activated in a specific point which can be used for quantification and analysis for their structures and functions. Also, this technology can be applied in the fields of general RNA studies, medical researches, pharmacogenetics, and customized medical researches (gene expression profiles, post-translational modifications, SNPs or mutation over time)
This service can be also done for total RNA, small RNA (miRNA, tRNA), de novo sequencing.
* Linked services > RNA Profiling Service: A qPCR array service which can undergo a gene search and validation.

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Reference Based De novo
Objective RNA expression analysis gene structure prediction-Alternative sliced transcriptome Novel gene detection comparative expression analysis gene structure prediction
Sufficient data quantity Raw data 4Gb Raw data 6Gb
Sample Requirements Minimum Quantity 1 µg, Minimum Concentration = 65 ng/µl, OD 260/280=1.6~2.0, RIN≥7, 28S:18S>1.0
Deliverables Mapping statistics, SNPs and InDels calling, Gene expression profiles, Differentially Expressed Gene(DEGs), Variant annotation, Fusion gene, Identification of alternative spliced transcripts, Prediction of novel transcripts de novo Assembly statistics, Gene annotations, Gene expression profiles, Differentially Expressed Gene(DEGs), Gene ontology analysis, Comparative analysis
* May vary depending on the sample types, species, and data analysis.

All epigenetic gene regulation mechanisms for their activation are controlled by DNA methylation and histone modifications. Those can be inherited, but can also be affected by diets, habits, and environments. Epigenetic gene modifications are being widely studied as those have been known to be related to occurrence or progress of various diseases, including cancers. Data gained from those types of analysis can be useful for not  only diagnostics, but also surgeries to predict the response and conditions after the treatments or the progress of a disease.
Analysis can be done through CHIP-Seq, which have advantages of high resoutions, MeDIP-Seq, or bisulfite-Seq for the whole genome.

Metagenome Sequencing is not only for a single species or an organism, but for samples collected in a specific environment to analyze their genes to compare the differences in the patterns or interactions of genes for a microbial community.
This service is widely used for analysis in clinical researches, biotechnology, or a microbial biogeography of gut microbiota, which have raised interests of many researchers through 16S rRNA or 18S rRNA, which are widely used as markers for species identification.

 

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