High-throughput RNA isoform sequencing using programmed cDNA concatenation

被引：76

作者：

Al'Khafaji, Aziz M. ^{[1
]}

Smith, Jonathan T. ^{[1
]}

Garimella, Kiran V. ^{[1
]}

Babadi, Mehrtash ^{[1
]}

Popic, Victoria ^{[1
]}

Sade-Feldman, Moshe ^{[1
,2
]}

Gatzen, Michael ^{[1
]}

Sarkizova, Siranush ^{[1
]}

Schwartz, Marc A. ^{[1
,3
,4
,5
]}

Blaum, Emily M. ^{[1
,2
]}

Day, Allyson ^{[1
]}

Costello, Maura ^{[1
]}

Bowers, Tera ^{[1
]}

Gabriel, Stacey ^{[1
]}

Banks, Eric ^{[1
]}

Philippakis, Anthony A. ^{[1
]}

Boland, Genevieve M. ^{[6
]}

Blainey, Paul C. ^{[1
,7
,8
]}

Hacohen, Nir ^{[1
,2
,9
,10
]}

机构：

[1] Broad Inst MIT & Harvard, Cambridge 02142, MA USA

[2] Massachusetts Gen Hosp, Ctr Canc Res, Dept Med, Boston, MA 02114 USA

[3] Harvard Med Sch, Dept Pediat, Boston, MA USA

[4] Boston Childrens Hosp, Div Hematol Oncol, Boston, MA USA

[5] Dana Farber Canc Inst, Dept Pediat Oncol, Boston, MA USA

[6] Harvard Med Sch, Massachusetts Gen Hosp, Div Surg Oncol, Boston, MA USA

[7] MIT, Dept Biol Engn, Cambridge, MA 02139 USA

[8] MIT, Koch Inst Integrat Canc Res, Cambridge, MA 02139 USA

[9] Harvard Med Sch, Boston, MA 02115 USA

[10] Massachusetts Gen Hosp, Ctr Immunol & Inflammatory Dis, Charlestown, MA 02129 USA

来源：

NATURE BIOTECHNOLOGY | 2024年 / 42卷 / 04期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1038/s41587-023-01815-7

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Full-length RNA-sequencing methods using long-read technologies can capture complete transcript isoforms, but their throughput is limited. We introduce multiplexed arrays isoform sequencing (MAS-ISO-seq), a technique for programmably concatenating complementary DNAs (cDNAs) into molecules optimal for long-read sequencing, increasing the throughput >15-fold to nearly 40 million cDNA reads per run on the Sequel IIe sequencer. When applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq demonstrated a 12- to 32-fold increase in the discovery of differentially spliced genes. Programmable concatenation of cDNA molecules increases the throughput of PacBio sequencing about 15-fold.

引用

页码：582 / 586

页数：16

共 36 条

[1] DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer [J].

Baid, Gunjan ;

Cook, Daniel E. ;

Shafin, Kishwar ;

Yun, Taedong ;

Llinares-Lopez, Felipe ;

Berthet, Quentin ;

Belyaeva, Anastasiya ;

Topfer, Armin ;

Wenger, Aaron M. ;

Rowell, William J. ;

Yang, Howard ;

Kolesnikov, Alexey ;

Ammar, Waleed ;

Vert, Jean-Philippe ;

Vaswani, Ashish ;

McLean, Cory Y. ;

Nattestad, Maria ;

Chang, Pi-Chuan ;

Carroll, Andrew .

NATURE BIOTECHNOLOGY, 2023, 41 (02) :232-+

[2] Alternative splicing as a regulator of development and tissue identity [J].

Baralle, Francisco E. ;

Giudice, Jimena .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2017, 18 (07) :437-451

[3]

Bio-Rad, 2023, MIN REV CD45 CHAR IS

[4] Levenshtein error-correcting barcodes for multiplexed DNA sequencing [J].

Buschmann, Tilo ;

Bystrykh, Leonid V. .

BMC BIOINFORMATICS, 2013, 14

[5]

CCS Docs, 2022, WHAT IS READS BAM

[6]

Durbin R., 1998, BIOL SEQUENCE ANAL P

[7] RNA splicing factors as oncoproteins and tumour suppressors [J].

Dvinge, Heidi ;

Kim, Eunhee ;

Abdel-Wahab, Omar ;

Bradley, Robert K. .

NATURE REVIEWS CANCER, 2016, 16 (07) :413-430

[8] GENCODE 2021 [J].

Frankish, Adam ;

Diekhans, Mark ;

Jungreis, Irwin ;

Lagarde, Julien ;

Loveland, Jane E. ;

Mudge, Jonathan M. ;

Sisu, Cristina ;

Wright, James C. ;

Armstrong, Joel ;

Barnes, If ;

Berry, Andrew ;

Bignell, Alexandra ;

Boix, Carles ;

Carbonell Sala, Silvia ;

Cunningham, Fiona ;

Di Domenico, Tomas ;

Donaldson, Sarah ;

Fiddes, Ian T. ;

Giron, Carlos Garcia ;

Gonzalez, Jose Manuel ;

Grego, Tiago ;

Hardy, Matthew ;

Hourlier, Thibaut ;

Howe, Kevin L. ;

Hunt, Toby ;

Izuogu, Osagie G. ;

Johnson, Rory ;

Martin, Fergal J. ;

Martinez, Laura ;

Mohanan, Shamika ;

Muir, Paul ;

Navarro, Fabio C. P. ;

Parker, Anne ;

Pei, Baikang ;

Pozo, Fernando ;

Riera, Ferriol Calvet ;

Ruffier, Magali ;

Schmitt, Bianca M. ;

Stapleton, Eloise ;

Suner, Marie-Marthe ;

Sycheva, Irina ;

Uszczynska-Ratajczak, Barbara ;

Wolf, Maxim Y. ;

Xu, Jinuri ;

Yang, Yucheng T. ;

Yates, Andrew ;

Zerbino, Daniel ;

Zhang, Yan ;

Choudhary, Jyoti S. ;

Gerstein, Mark .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D916-D923

[9]

Garbe W., 2012, SYMSPELL COMPUTER SO

[10]

Garbe W., 2012, 1000x, faster spelling correction algorithm

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