Services
서비스
NGS
적용 가능 연구
- Population genetics
- Genetic rare diseases
- Cancer research
샘플&실험정보
| Sample Requirement | gDNA > 500ng (minimum 100 ng), 5 ng/µl, DIN > 6 |
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| Library Kit | Illumina, Pacbio |
| Sequencing Platform | Illumina NovaSeq6000, Pacbio Sequel Ⅱ |
| Recommended Sequencing Depth | For rare disease >30X |
생명정보학 분석자세히 알아보기
- WGRS Workflow
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- Insertsite Workflow
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Standard Analysis
Read mapping
Variants calling
Variant annotation
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Advanced Analysis
Somatic variants calling
Copy number variants(CNV)
Structure variants(SV)
Multisample variants calling
Integration site 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
Whole Genome de novo Sequencing
Whole genome de novo sequencing은 유전체 크기를 예측하거나 참조 유전체 정보가 없는 새로운 생물종의 전체 유전체 정보를 알아내는 방법입니다. 반복 서열이 많거나, GC 비율이 높은 영역 또는 길게 반복되는 Homopolymer, Palindromic Sequence도 Long-read sequencing을 통해 보다 정확한 유전체 조립(Genome assembly)이 가능합니다. 다른 종과 비교했을 때 어떤 점이 다르고 어떤 특징과 관련된 유전자를 가지고 있는지 확인할 수 있습니다. 테라젠바이오는 고래[1], 호랑이[2], 누룩[3], 도라지[4], 순무[5] 등 다양한 동식물의 유전자 해독에도 성공한 바 있습니다.
적용 가능 연구
- Phylogenetic classification
- Species diversity studies
샘플&실험정보
| Sample Requirement | gDNA > 2µg (minimum 500 ng), 20 ng/µl, DIN > 6 |
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| Library Kit | Illumina, Pacbio |
| Sequencing Platform | Illumina NovaSeq6000, Pacbio Sequel Ⅱ |
| Recommended Sequencing Depth | ≥ 10 milion read pair per sample |
생명정보학 분석자세히 알아보기
- Workflow
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Standard Analysis
Genome denovo assembly
Genome annotation
Error correction
k-mer analysis
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Advanced Analysis
Construction of mitochondrial genome
Construction of chloroplast genome
Phylogenetic analysis
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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.
적용 가능 연구
- Genetic disease-related studies
- Cancer research and drug development
- Pathogenic mechanism and molecular characterization
샘플&실험정보
| Sample Requirement | gDNA 500ng (minimum 50ng) 10 ng/µl, DIN > 6 |
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| Library Kit | SureSelect(Agilent), Twist, etc |
| Sequencing Platform | Illumina NovaSeq6000 |
| Recommended Sequencing Depth | ≥100X (For tumor, ≥200X) |
생명정보학 분석자세히 알아보기
- Workflow
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Standard Analysis
Germlin & Somatic
Read mapping + BQSR, VQSR
Variant calling (SNV, Indels)
Variant annotation
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Advanced Analysis
Oncoplot
No content
No content
No content
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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
Targeted Sequencing
특정 질병 또는 유전자 패널 등 분석하고자 하는 선택 영역만을 확인하는 기법으로,별도 제작된 키트를 사용해 분석하는 방법입니다. 선택 영역에 대한 높은 Sequencing depth (200~1000x)을 얻을 수 있기 때문에 돌연변이를 효과적으로 확인할 수 있습니다. 또한, 비유전성 고형암 NGS 패널 검사인 Tumor mutation burden(TMB)와 Microsatellite instability(MSI)은 표적항암제 또는 면역항암제의 처방을 위해 임상적으로 적용할 수 있는 분석입니다[1].
적용 가능 연구
- 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
샘플&실험정보
| Sample Requirement | gDNA > 700ng (minimum 500 ng), 10 ng/µl, DIN > 6 |
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| Library Kit | Agilent, Twist |
| Sequencing Platform | Illumina NovaSeq6000 |
| Recommended Sequencing Depth | 200X, 500X, 1000X |
생명정보학 분석자세히 알아보기
- Workflow
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Standard Analysis
Read mapping
Variant calling
Variant annotation
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Advanced Analysis
Genomic rearrangement
Tumor mutation burden (TMB), Microsatellite instability (MSI)
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.
