Long-read sequencing to understand genome biology and cell function

被引：30

作者：

Kraft, Florian ^{[1
]}

Kurth, Ingo ^{[1
]}

机构：

[1] Rhein Westfal TH Aachen, Med Fac, Inst Human Genet, Aachen, Germany

来源：

INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY | 2020年 / 126卷

关键词：

Third-generation sequencing; Long-read sequencing; Nanopore sequencing; SMRT sequencing; Genomics; SINGLE-MOLECULE; DNA METHYLATION; 3; DECADES; NANOPORE;

D O I：

10.1016/j.biocel.2020.105799

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Determining the sequence of DNA and RNA molecules has a huge impact on the understanding of cell biology and function. Recent advancements in next-generation short-read sequencing (NGS) technologies, drops in cost and a resolution down to the single-cell level shaped our current view on genome structure and function. Third-generation sequencing (TGS) methods further complete the knowledge about these processes based on long reads and the ability to analyze DNA or RNA at single molecule level. Long-read sequencing provides additional possibilities to study genome architecture and the composition of highly complex regions and to determine epigenetic modifications of nucleotide bases at a genome-wide level. We discuss the principles and advancements of long-read sequencing and its applications in genome biology.

引用

页数：7

共 77 条

[1] Opportunities and challenges in long-read sequencing data analysis [J].

Amarasinghe, Shanika L. ;

Su, Shian ;

Dong, Xueyi ;

Zappia, Luke ;

Ritchie, Matthew E. ;

Gouil, Quentin .

GENOME BIOLOGY, 2020, 21 (01)

[2] Single-Molecule Sequencing: Towards Clinical Applications [J].

Ameur, Adam ;

Kloosterman, Wigard P. ;

Hestand, Matthew S. .

TRENDS IN BIOTECHNOLOGY, 2019, 37 (01) :72-85

[3]

[Anonymous], 2018, BIORXIV

[4] Detecting AGG Interruptions in Male and Female FMR1 Premutation Carriers by Single-Molecule Sequencing [J].

Ardui, Simon ;

Race, Valerie ;

Zablotskaya, Alena ;

Hestand, Matthew S. ;

Van Esch, Hilde ;

Devriendt, Koenraad ;

Matthijs, Gert ;

Vermeesch, Joris R. .

HUMAN MUTATION, 2017, 38 (03) :324-331

[5]

Beyter, 2019, LONG READ SEQUENCING, DOI 10.1101/848366

[6] Multi-platform discovery of haplotype-resolved structural variation in human genomes [J].

Chaisson, Mark J. P. ;

Sanders, Ashley D. ;

Zhao, Xuefang ;

Malhotra, Ankit ;

Porubsky, David ;

Rausch, Tobias ;

Gardner, Eugene J. ;

Rodriguez, Oscar L. ;

Guo, Li ;

Collins, Ryan L. ;

Fan, Xian ;

Wen, Jia ;

Handsaker, Robert E. ;

Fairley, Susan ;

Kronenberg, Zev N. ;

Kong, Xiangmeng ;

Hormozdiari, Fereydoun ;

Lee, Dillon ;

Wenger, Aaron M. ;

Hastie, Alex R. ;

Antaki, Danny ;

Anantharaman, Thomas ;

Audano, Peter A. ;

Brand, Harrison ;

Cantsilieris, Stuart ;

Cao, Han ;

Cerveira, Eliza ;

Chen, Chong ;

Chen, Xintong ;

Chin, Chen-Shan ;

Chong, Zechen ;

Chuang, Nelson T. ;

Lambert, Christine C. ;

Church, Deanna M. ;

Clarke, Laura ;

Farrell, Andrew ;

Flores, Joey ;

Galeev, Timur ;

Gorkin, David U. ;

Gujral, Madhusudan ;

Guryev, Victor ;

Heaton, William Haynes ;

Korlach, Jonas ;

Kumar, Sushant ;

Kwon, Jee Young ;

Lam, Ernest T. ;

Lee, Jong Eun ;

Lee, Joyce ;

Lee, Wan-Ping ;

Lee, Sau Peng .

NATURE COMMUNICATIONS, 2019, 10 (1)

[7] Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2 [J].

Corbett, Mark A. ;

Kroes, Thessa ;

Veneziano, Liana ;

Bennett, Mark F. ;

Florian, Rahel ;

Schneider, Amy L. ;

Coppola, Antonietta ;

Licchetta, Laura ;

Franceschetti, Silvana ;

Suppa, Antonio ;

Wenger, Aaron ;

Mei, Davide ;

Pendziwiat, Manuela ;

Kaya, Sabine ;

Delledonne, Massimo ;

Straussberg, Rachel ;

Xumerle, Luciano ;

Regan, Brigid ;

Crompton, Douglas ;

van Rootselaar, Anne-Fleur ;

Correll, Anthony ;

Catford, Rachael ;

Bisulli, Francesca ;

Chakraborty, Shreyasee ;

Baldassari, Sara ;

Tinuper, Paolo ;

Barton, Kirston ;

Carswell, Shaun ;

Smith, Martin ;

Berardelli, Alfredo ;

Carroll, Renee ;

Gardner, Alison ;

Friend, Kathryn L. ;

Blatt, Ilan ;

Iacomino, Michele ;

Di Bonaventura, Carlo ;

Striano, Salvatore ;

Buratti, Julien ;

Keren, Boris ;

Nava, Caroline ;

Forlani, Sylvie ;

Rudolf, Gabrielle ;

Hirsch, Edouard ;

Leguern, Eric ;

Labauge, Pierre ;

Balestrini, Simona ;

Sander, Josemir W. ;

Afawi, Zaid ;

Helbig, Ingo ;

Ishiura, Hiroyuki .

NATURE COMMUNICATIONS, 2019, 10 (1)

[8] Mapping and phasing of structural variation in patient genomes using nanopore sequencing [J].

Stancu, Mircea Cretu ;

van Roosmalen, Markus J. ;

Renkens, Ivo ;

Nieboer, Marleen M. ;

Middelkamp, Sjors ;

de Ligt, Joep ;

Pregno, Giulia ;

Giachino, Daniela ;

Mandrile, Giorgia ;

Valle-Inclan, Jose Espejo ;

Korzelius, Jerome ;

de Bruijn, Ewart ;

Cuppen, Edwin ;

Talkowski, Michael E. ;

Marschall, Tobias ;

de Ridder, Jeroen ;

Kloosterman, Wigard P. .

NATURE COMMUNICATIONS, 2017, 8

[9] On 'three decades of nanopore sequencing' Reply [J].

Deamer, David ;

Akeson, Mark ;

Branton, Daniel .

NATURE BIOTECHNOLOGY, 2016, 34 (05) :482-482

[10] A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping [J].

Deschamps, Stephane ;

Zhang, Yun ;

Llaca, Victor ;

Ye, Liang ;

Sanyal, Abhijit ;

King, Matthew ;

May, Gregory ;

Lin, Haining .

NATURE COMMUNICATIONS, 2018, 9

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