Services

NGS

Whole Genome Reseqeuncing

Whole Genome Resequencing

Whole genome resequencing (WGRS) priovides the most comprehensive information about the genetic variation or mutation through mapping of sequencing reads from the whole genome to the reference genome. Theragen Bio was one of the first companies in the world that completed and published a map of a human genome which in fact was the first map of the genome of a Korean person[1], and participated in study regarding[2] the evolution of ancient ethiopian genomes.

Application

  • Population genetics
  • Genetic rare diseases
  • Cancer research

Sample/Laboratory Information

샘플&실험정보
Sample Requirement gDNA > 500ng (minimum 100 ng), 5 ng/µl, DIN > 6
Library Kit Illumina, Pacbio
Sequencing Platform Illumina NovaSeq6000, Sequel Ⅱ
Recommended Sequencing Depth For rare disease >30X

BioinformaticsDetail View

WGRS Workflow
Insertsite Workflow

Standard Analysis

Read mapping

Variants calling

Variant annotation

No content

Standard Analysis

Advanced Analysis

Somatic variants calling

Copy number variants(CNV)

Structure variants(SV)

Multisample variants calling

Integration site analysis

Advanced Analysis

Reference

    [1] Ahn, S. M. et al., (2009). The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome research, 19(9)

    [2] Gallego Llorente, M. et al., (2015). Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science (New York, N.Y.), 350(6262), 820–822.

    [3] Kim, M. Y. et al., (2010). Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proceedings of the National Academy of Sciences, 107(51), 22032–22037. https://doi.org/10.1073/pnas.1009526107

    [4] Yoon, K. et al., (2013). Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers. Genome Research, 23(7), 1109–1117. https://doi.org/10.1101/gr.145706.112

    [5] Xu, X. et al., (2013). The Genetic Basis of White Tigers. Current Biology, 23(11), 1031–1035. https://doi.org/10.1016/j.cub.2013.04.054

    [6] Li, E. et al., (2020). Neural stem cells derived from the developing forebrain of YAC128 mice exhibit pathological features of Huntington’s disease. Cell Proliferation, 53(10). https://doi.org/10.1111/cpr.12893

FAQ
Whole Genome de novo Sequencing

Whole Genome de novo Sequencing

Whole genome de novo sequencing is a technology of predicting the genome size or finding out the entire genomic information of new species without reference genome. Long read sequencing enables more accurate geneome assembly of genomes with areas of high GC contents, long-repeated homopolymers, or palindromic sequences. Differences from other species and unique features can be identified. Theragen Bio succeeded in decoding of the genome of various animals and plants such as minke whale[1], tiger[2], and yeast[3], bellflower[4] and turnip[5].

Application

  • Phylogenetic classification
  • Species diversity studies

Sample/Laboratory Information

샘플&실험정보
Sample Requirement gDNA > 2µg (minimum 500 ng), 20 ng/µl, DIN > 6
Library Kit Illumina, Pacbio
Sequencing Platform Illumina NovaSeq6000, Pacbio Sequel Ⅱ
Recommended Sequencing Depth ≥ 10 milion read pair per sample

BioinformaticsDetail View

Workflow
Whole Genome de novo Sequencing

Standard Analysis

Genome denovo assembly

Genome annotation

Error correction

k-mer analysis

Standard Analysis image

Advanced Analysis

Construction of mitochondrial genome

Construction of chloroplast genome

Phylogenetic analysis

No content

Advanced Analysis image

Reference

    [1] Yim, H. S. et al., (2014). Minke whale genome and aquatic adaptation in cetaceans. Nature genetics, 46(1), 88–92.

    [2] Cho, Y. S. et al., (2013). The tiger genome and comparative analysis with lion and snow leopard genomes. Nature communications, 4, 2433.

    [3] Choo, J. H. et al., (2016). Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid. Biotechnology for biofuels, 9, 246.

    [4] Kim, J. et al., (2020). Whole-genome, transcriptome, and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus, a medicinal plant. Horticulture research, 7, 112.

    [5] Park, S. G. et al., (2021). Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance. Frontiers in genetics, 12, 651298.

FAQ
Whole Exome Sequencing

Whole Exome Sequencing

The exome area accounts for only 1% (30 Mb) of the whole genome, but it is very crucial for biological functions as it contains coding sites that determine protein sequences. Whole exome sequencing is a technology that selectively identifies the exome area and is mainly used in clinical research[1] since it has more cost-effectiveness than whole genome sequencing and can be effectively applied to disease-related genes.

Application

  • Genetic disease-related studies
  • Cancer research and drug development
  • Pathogenic mechanism and molecular characterization

Sample/Laboratory Information

샘플&실험정보
Sample Requirement gDNA 500ng (minimum 50ng) 10 ng/µl, DIN > 6
Library Kit SureSelect(Agilent), Twist, etc
Sequencing Platform Illumina NovaSeq6000
Recommended Sequencing Depth ≥100X (For tumor, ≥200X)

BioinformaticsDetail View

Workflow

Standard Analysis

Germline/Somatic

Read mapping + BQSR, VQSR

Variant calling (SNV, Indels)

Variant annotation

Standard Analysis

Advanced Analysis

Oncoplot

No content

No content

No content

No content

Advanced Analysis

Reference

    [1] Phi, J. H. et al., (2018). Genomic analysis reveals secondary glioblastoma after radiotherapy in a subset of recurrent medulloblastomas. Acta neuropathologica, 135(6), 939–953.

    [2] Chang, Y. H. et al., (2016). Use of whole-exome sequencing to determine the genetic basis of signs of skin youthfulness in Korean women. Journal of the European Academy of Dermatology and Venereology, 31(3), e138–e141. https://doi.org/10.1111/jdv.13904

FAQ
Targeted Sequencing

Targeted Sequencing

Targeted sequencing is a technique that sequences only the targeted areas of the genome using a customizable capture gene panel. As it obtains high sequencing depth (200-1000x) for the targeted area, mutations or variations can be effectively identified. Theragen Bio has developed tumor mutation burden(TMB) and microsatellite instability(MSI) panels for immunoonology clinical application[1].

Application

  • Tumor mutation burden (TMB)
  • Disease or phenotype-related studies
  • Detection of low-frequency alleles and rare variants
  • Identification of causative novel or inherited mutations
  • Drug response and discovery of therapeutic targets

Sample/Laboratory Information

샘플&실험정보
Sample Requirement gDNA > 700ng (minimum 500 ng), 10 ng/µl, DIN > 6
Library Kit Agilent, Twist
Sequencing Platform Illumina NovaSeq6000
Recommended Sequencing Depth 200X, 500X, 1000X

BioinformaticsDetail View

Workflow
Targeted Sequencing

Standard Analysis

Read mapping

Variant calling

Variant annotation

Standard Analysis

Advanced Analysis

Genomic rearrangement

Tumor mutation burden (TMB), Microsatellite instability (MSI)

Advanced Analysis

Reference

    [1] Kim, H. S. et al., (2018). Association of PD-L1 Expression with Tumor-Infiltrating Immune Cells and Mutation Burden in High-Grade Neuroendocrine Carcinoma of the Lung. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer, 13(5), 636–648.

FAQ
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