Next Generation Sequencing and Bioinformatics

국문 초록 (Abstract)

매우 빠른 속도로 발전하고 있는 차세대 염기서열 분석 플랫폼과 최신 생물정보학적 분석도구들로 말미암아, 1,000달러 이하의 가격으로 인간 유전체 염기서열을 해독하고자 하는 궁극적인 목표가 조만간 곧 실현될 수 있을것 같다. 차세대 염기서열 분석 분야의 급속한 기술적 진전은 NGS 데이터의 분석과 관리를 위한 통계적 방법과 생물정보학적 분석도구들에 대한 수요를 꾸준히 증대시키고 있다. NGS 플랫폼이 상용화되어 쓰이기 시작한 초창기부터, NGS 데이터를 분석하고 해석하거나, 가시화 해주는 다수의 응용프로그램이나 도구들이 개발되어 활용되어 왔다. 그러나, NGS 데이터의 엄청난 범람으로 데이터 저장, 데이터 분석 및 관리 등에 있어서 해결해야 할 많은 문제들이 부각되고 있다. NGS 데이터 분석은 단편서열과 참조서열간의 서열정렬, 염기식별, 다형성 발견, 쌍단편 서열이나 비쌍단편 서열 등을 이용한 어셈블리 작업, 구조변이 발견, 유전체 브라우징 등을 본질적으로 포함한다. 본 논문은 주요 차세대 염기서열 결정기술과 NGS 데이터 분석을 위한 생물정보학적 분석도구들에 대해 개관적으로 소개하고자 한다.

다국어 초록 (Multilingual Abstract)

With the ongoing development of next-generation sequencing (NGS) platforms and advancements in the latest bioinformatics tools at an unprecedented pace, the ultimate goal of sequencing the human genome for less than $1,000 can be feasible in the near future. The rapid technological advances in NGS have brought about increasing demands for statistical methods and bioinformatics tools for the analysis and management of NGS data. Even in the early stages of the commercial availability of NGS platforms, a large number of applications or tools already existed for analyzing, interpreting, and visualizing NGS data. However, the availability of this plethora of NGS data presents a significant challenge for storage, analyses, and data management. Intrinsically, the analysis of NGS data includes the alignment of sequence reads to a reference, base-calling, and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection, and genome browsing. While the NGS technologies have allowed a massive increase in available raw sequence data, a number of new informatics challenges and difficulties must be addressed to improve the current state and fulfill the promise of genome research. This review aims to provide an overview of major NGS technologies and bioinformatics tools for NGS data analyses.

목차 (Table of Contents)

• Introduction
• Next Generation Sequencing Technologies
• Methods for Mapping/Alignment, Assembly and Polymorphism Detection
• Conclusions
• References
• 초록

참고문헌 (Reference)

1 Kosakovsky, P. S., "Windshield splatter analysis with the Galaxy metagenomic pipeline" 19 : 2144-2153, 2009

2 Langmead, B., "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome" 3 : R25-, 2009

3 Nagalakshmi, U., "The transcriptional landscape of the yeast genome defined by RNA sequencing" 320 : 1344-1349, 2008

4 Lorenzi, H. A., "The Viral Meta-Genome Annotation Pipeline(VMGAP) : an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data" 4 : 418-429, 2011

5 Li, H., "The Sequence Alignment/Map format and SAMtools" 16 : 2078-2079, 2009

6 McKenna, A., "The Genome Analysis Toolkit : a MapReduce framework for analyzing next-generation DNA sequencing data" 20 : 1297-1303, 2010

7 Nothnagel, M., "Technology-specific error signatures in the 1000 Genomes Project data" 130 : 505-516, 2011

8 Milne, I., "Tablet－next generation sequence assembly visualization" 3 : 401-402, 2010

9 Whiteford, N., "Swift : primary data analysis for the Illumina Solexa sequencing platform" 25 : 2194-2199, 2009

10 Feuk, L., "Structural variation in the human genome" 7 : 85-97, 2006

11 Adessi, C., "Solid phase DNA amplification : characterisation of primer attachment and amplification mechanisms" 28 : e87-, 2000

12 Pareek, C. S., "Sequencing technologies and genome sequencing" 52 : 413-435, 2011

13 Flicek, P., "Sense from sequence reads: methods for alignment and assembly" 6 : S6-S12, 2009

14 Ning, Z., "SSAHA : a fast search method for large DNA databases" 11 : 1725-1729, 2001

15 Li, R., "SOAP2 : an improved ultrafast tool for short read alignment" 15 : 1966-1967, 2009

16 Li, R., "SOAP : short oligonucleotide alignment program" 5 : 713-714, 2008

17 Lassmann, T., "SAMStat : Monitoring biases in next generation sequencing data" 27 : 130-131, 2011

18 Grada, A., "Next-generation sequencing: methodology and appliction" 133 : e11-, 2013

19 Scholz, M. B., "Next generation sequencing and bioinformatics bottlenecks : the current state of metagenomics data analysis" 23 : 9-15, 2012

20 Dalloul, R. A., "Multi-platform next generation sequencing of the domestic turkey(Meleagris gallopavo) : Genome assembly and analysis" 8 : e1000475-, 2010

21 Krawitz, P., "Microindel detection in short-read sequence data" 26 : 722-729, 2010

22 Li, H., "Mapping short DNA sequencing reads and calling variants using mapping quality scores" 11 : 1851-1858, 2008

23 Bao, H., "MapView : visualization of short reads alignment on a desktop computer" 12 : 1554-1555, 2009

24 Tawfik, D. S, "Man-made cell-like compartments for molecular evolution" 16 : 652-656, 1998

25 Mitra, R. D., "In situ localized amplification and contact replication of many individual DNA molecules" 27 : e34-, 1999

26 Campbell, P. J., "Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing" 40 : 722-729, 2008

27 Chiang, D. Y., "High-resolution mapping of copy-number alterations with massively parallel sequencing" 6 : 99-103, 2009

28 Malhis, N., "High quality SNP calling using Illumina data at shallow coverage" 26 : 1029-1035, 2010

29 Dalca, A. V., "Genome variation discovery with high-throughput sequencing data" 11 : 3-14, 2010

30 Alkan, C., "Genome structural variation discovery and genotyping" 12 : 363-376, 2011

31 Jimenez-Lopex, J. C., "Genome sequencing and next-generation sequence data analysis : a comprehensive compilation of bioinformatics tools and databases" 3 : 115-130, 2013

32 Giardine, B., "Galaxy : a platform for interactive large-scale genome analysis" 15 : 1451-1455, 2005

33 Dinsdale, E. A., "Functional metagenomic profiling of nine biomes" 452 : 629-632, 2008

34 Li, H., "Fast and accurate short read alignment with Burrows-Wheeler transform" 25 : 754-1760, 2009

35 Li, H., "Fast and accurate long-read alignment with Burrows-Wheeler transform" 5 : 589-595, 2010

36 Huang, W., "EagleView : a genome assembly viewer for next-generation sequencing technologies" 9 : 1538-1543, 2008

37 Magi, A., "Detecting common copy number variants in high-throughput sequencing data by using Joi"

38 Xie, W., "Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries" 5 : 414-426, 2011

39 Olshen, A. B., "Circular binary segmentation for the analysis of array-based DNA copy number data" 5 : 557-572, 2005

40 Park, P. J., "ChIP-seq : advantages and challenges of a maturing technology" 10 : 669-680, 2009

41 Magi, A., "Bioinformatics for next generation sequencing data" 1 : 294-307, 2010

42 Fedurco, M., "BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies" 34 : e22-, 2006

43 Kent, W. J., "BLAT-the BLAST-like alignment tool" 4 : 656-664, 2002

44 Gogol-Döring, A., "An overview of the analysis of next generation sequencing data" 802 : 249-257, 2012

45 Shendure, J., "Accurate multiplex polony sequencing of an evolved bacterial genome" 309 : 1728-1732, 2005

46 Schadt, E. E., "A window into third generation sequencin" 19 : R227-R240, 2010

47 Hoberman, R., "A probabilistic approach for SNP discovery in high-throughput human resequencing data" 19 : 1542-1552, 2009

48 Hyman, E. D., "A new method of sequencing DNA" 174 : 423-436, 1988

49 Turcatti, G., "A new class of cleavable fluorescent nucleotides : synthesis and optimization as reversible terminators for DNA sequencing by synthesis" 36 : e25-, 2008

50 Durbin, R. M., "A map of human genome variation from population-scale sequencing" 467 : 1061-1073, 2010

51 Marth, G. T., "A general approach to single-nucleotide polymorphism discovery" 23 : 452-456, 1999