오래된 유해의 mtDNA 염기서열 분석을 위한 Sanger 염기서열 분석과 차세대 염기서열 분석의 비교
Comparison of Sanger Sequencing and Next Generation Sequencing for mtDNA Sequencing of Old Human Skeletal Remains
3
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
본 연구에서 사용된 차세대 염기서열 분석 기반의 비교시험은 Applied Biosystems社의 3130 xl과Roche社의 GS junior (454 GS FLX) 염기서열 분석 장비를 이용하여 60년 이상 오래된 유해 100구의mtDNA 염기서열 분석을 수행하였다. 그 결과, GS junior가 95%에 해당하는 mtDNA 고변이 좌위에서더 높은 민감도와 식별력을 갖는 것으로 나타났다. 또한, 전반적인 염기서열 분석 결과의 base-calling 오류는 ‘random sampling’ 오류를 감안하더라도 높은 coverage 및 depth에 의해 상대적으로 낮은 수치를 나타냈다. GS junior는 상대적으로 많은 리드를 확보할 수 있기 때문에 단일 염기 변이 분석 결과에서3130 xl에 비해 6% 더 많은 염기 변이를 찾은 것으로 나타났다. 그러나 HV2의 309와 315에서 C insertion 으로 6 량체 이상 늘어나게 되면 poly C-stretch 현상이 발생하여 분석 성공률이 낮아진다. GS junior에서는 309와 315의 분석 성공률이 3130 xl에 비해 25%와 70%로 나타나 상대적으로 낮게 분석되었다.
Abstract
To comparison these systems for NGS platform, we analyzed mtDNA sequence generated by the Applied Biosystems 3130 xl and Roche GS junior (454 GS FLX) technologies for the over 60 years skeletal remains of 100 individuals. Consequently, a comparison of the base calls of overlapping ABI 3130 xl Sangersequence generated for the same samples showed that the NGS platforms all have high sensitivity, identifying 95% of mtDNA hypervariable region. At high coverage, depth base-calling error are systematic, resulting from local sequence contexts; as the coverage is lowered additional 'random sampling' errors in base-calling occur. GS junior because you can gain a lot of re from a single variant analysis showed that 6% more as compared to the 3130 xl variant is found. However, the C insertion occurs of HV2 in the 309 and 315, increases more than 6 mer poly C-stretch phenomenon occurs, it becomes very difficult to analyze. Analysis of GS junior analyze the success rate in the 309 and 315 is shown as 25% and 70% compared to the 3130 xl relatively low.
참고문헌 (29)
- F Sanger, "DNA sequencing with chain-terminating inhibitors", Proc. Nati. Acad. Sci. USA, 74(5), pp.463~5467 (1977)
- J Shendure, "Advanced sequencing technologies: methods and goals", Nat Rev Genet, 5, pp.335~344 (2004)
- ER Mardis, "The impact of next-generation sequencing technology on genetics", Trends in Genetics, 24(3), pp.133~141 (2008)
- International Human Genome Sequencing Consortium, "Initial sequencing and analysis of the human genome", NATURE, 49, pp.860~921 (2001)
- HJ Jin, "Forensic genetic analysis of mitochondrial DNA hypervariable region I", II sequences: an expanded Korean population database, 2006, pp.158, 125~130
- HJ Jin, "The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers", PLoS One, 4, pp.e4210~ (2009)
- W Kim, "Mitochondrial DNA haplogroup analysis reveals no association between the common genetic lineages and prostate cancer in the Korean population", PLoS One, 3, pp.e2211~ (2008)
- W Parson, "Extended guidelines for mtDNA typing of population data in forensic science", Forensic Sci Int Genet, 1, pp.13~19 (2007)
- 홍승범, "오래된 유해의 mtDNA 염기서열 분석률 향상에 관한 연구", 과학수사학, 5(1), pp.61~69 (2011), 한국과학수사학회
- "Manual for CLC Genomics Workbench 6.0 Windows", Mac OS X and Linux, ~ (2013)
- M Knapp, "Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives", Genes, 1, pp.227~243 (2010)
- MX Sosa, "Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency", PLoS Computational Biology, 8(10), pp.e1002737~ (2012)
- MB Scholz, "Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis", Current Opinion in Biotechnology, 23, pp.9~15 (2012)
- S Suzuki, "Comparison of Sequence reads Obtained from Three Next-Generation Sequencing Platforms", PLoS One, 6(5), pp.e19534~ (2011)
- S Anderson, "Sequence and organization of the human mitochondrial genome", Nature, 290(5806), pp.457~465 (1981)
- RM Andrews, "Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA", Nature Genetics, 23, pp.147~ (1999)
- JH Park, "High Efficiency DNA Extraction from Old Skeletal Remains by Organic Extraction Method", Korean J Forensic Sci, 11, pp.19~23 (2010)
- H Niederstatter, "A modular real-time PCR concept for determining the quantity and quality of human nuclear and mitochondrial DNA", Forensic Sci Int Genet, 1, pp.29~34 (2007)
- B Cordula, "Mini-midi-mito: Adapting the amplification and sequencing strategy of mtDNA to the degradation state of crime scene samples", Forensic Sci Int Genet, 31, pp.149~153 (2009)
- 홍승범, "PrepFiler™ Forensic DNA Extraction Kit를 이용한 DNA 추출 시험방법의 유효화", 과학수사학, 6(1), pp.45~51 (2012), 한국과학수사학회
- "Amplicon Library Preparation Method Manual: GS Junior Titanium Series", Roche 454 Sequence, ~ (2010)
- "emPCR Amplification Method Manual-Lib-A: GS Junior Titanium Series", Roche 454 Sequence, ~ (2011)
- "Sequencing Method Manual: GS Junior Titanium Series", Roche 454 Sequence, ~ (2010)
- B Ewing, "Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities", Genome Res, 8, pp.186~194 (1998)
- SM Huse, "Accuracy and quality of massively parallel DNA pyrosequencing", Genome Biology, 8(7), pp.R143~ (2007)
- ML Metzker, "Sequencing technologies-the next generation", Nature Genetics, 11, pp.31~46 (2010)
- EY Chan, "Next-Generation Sequencing Methods: Impact of Sequencing Accuracy on SNP Discovery", Single Nucleotide Polymorphisms, 578, pp.95~111 (2009)
- SC Schuster, "Next-generation sequencing transforms today's biology", Nature Methods, 5(1), pp.16~18 (2008)
- HY Lee, "Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control", Int J Leg Med, 120, pp.5~14 (2006)