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Literature DB >> 31649132

RNAmut: robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing.

Muxin Gu^1,2, Maximillian Zwiebel^1,3, Swee Hoe Ong⁴, Nick Boughton⁵, Josep Nomdedeu^1,2,6, Faisal Basheer^1,2,7, Yasuhito Nannya⁸, Pedro M Quiros^1,2, Seishi Ogawa⁸, Mario Cazzola⁹, Roland Rad³, Adam P Butler⁴, M S Vijayabaskar^10,2, George S Vassiliou^11,2,7.

Abstract

Entities: Chemical

Mesh：

Substances：
RNA

Year: 2019 PMID： 31649132 PMCID： PMC7271607 DOI： 10.3324/haematol.2019.230821

Source DB: PubMed Journal: Haematologica ISSN： 0390-6078 Impact factor: 9.941

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17 in total

1. STAR: ultrafast universal RNA-seq aligner.

Authors: Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal: Bioinformatics Date: 2012-10-25 Impact factor: 6.937

2. RNA-sequencing analysis of core binding factor AML identifies recurrent ZBTB7A mutations and defines RUNX1-CBFA2T3 fusion signature.

Authors: Vincent-Philippe Lavallée; Sébastien Lemieux; Geneviève Boucher; Patrick Gendron; Isabel Boivin; Richard N Armstrong; Guy Sauvageau; Josée Hébert
Journal: Blood Date: 2016-03-11 Impact factor: 22.113

Review 3. Genomics of Acute Myeloid Leukemia Diagnosis and Pathways.

Authors: Lars Bullinger; Konstanze Döhner; Hartmut Döhner
Journal: J Clin Oncol Date: 2017-02-13 Impact factor: 44.544

4. Gene expression and risk of leukemic transformation in myelodysplasia.

Authors: Yusuke Shiozawa; Luca Malcovati; Anna Gallì; Andrea Pellagatti; Mohsen Karimi; Aiko Sato-Otsubo; Yusuke Sato; Hiromichi Suzuki; Tetsuichi Yoshizato; Kenichi Yoshida; Yuichi Shiraishi; Kenichi Chiba; Hideki Makishima; Jacqueline Boultwood; Eva Hellström-Lindberg; Satoru Miyano; Mario Cazzola; Seishi Ogawa
Journal: Blood Date: 2017-11-02 Impact factor: 22.113

5. VaDiR: an integrated approach to Variant Detection in RNA.

Authors: Lisa Neums; Seiji Suenaga; Peter Beyerlein; Sara Anders; Devin Koestler; Andrea Mariani; Jeremy Chien
Journal: Gigascience Date: 2018-02-01 Impact factor: 6.524

6. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

Authors: Timothy J Ley; Christopher Miller; Li Ding; Benjamin J Raphael; Andrew J Mungall; A Gordon Robertson; Katherine Hoadley; Timothy J Triche; Peter W Laird; Jack D Baty; Lucinda L Fulton; Robert Fulton; Sharon E Heath; Joelle Kalicki-Veizer; Cyriac Kandoth; Jeffery M Klco; Daniel C Koboldt; Krishna-Latha Kanchi; Shashikant Kulkarni; Tamara L Lamprecht; David E Larson; Ling Lin; Charles Lu; Michael D McLellan; Joshua F McMichael; Jacqueline Payton; Heather Schmidt; David H Spencer; Michael H Tomasson; John W Wallis; Lukas D Wartman; Mark A Watson; John Welch; Michael C Wendl; Adrian Ally; Miruna Balasundaram; Inanc Birol; Yaron Butterfield; Readman Chiu; Andy Chu; Eric Chuah; Hye-Jung Chun; Richard Corbett; Noreen Dhalla; Ranabir Guin; An He; Carrie Hirst; Martin Hirst; Robert A Holt; Steven Jones; Aly Karsan; Darlene Lee; Haiyan I Li; Marco A Marra; Michael Mayo; Richard A Moore; Karen Mungall; Jeremy Parker; Erin Pleasance; Patrick Plettner; Jacquie Schein; Dominik Stoll; Lucas Swanson; Angela Tam; Nina Thiessen; Richard Varhol; Natasja Wye; Yongjun Zhao; Stacey Gabriel; Gad Getz; Carrie Sougnez; Lihua Zou; Mark D M Leiserson; Fabio Vandin; Hsin-Ta Wu; Frederick Applebaum; Stephen B Baylin; Rehan Akbani; Bradley M Broom; Ken Chen; Thomas C Motter; Khanh Nguyen; John N Weinstein; Nianziang Zhang; Martin L Ferguson; Christopher Adams; Aaron Black; Jay Bowen; Julie Gastier-Foster; Thomas Grossman; Tara Lichtenberg; Lisa Wise; Tanja Davidsen; John A Demchok; Kenna R Mills Shaw; Margi Sheth; Heidi J Sofia; Liming Yang; James R Downing; Greg Eley
Journal: N Engl J Med Date: 2013-05-01 Impact factor: 91.245

7. Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia.

Authors: Yusuke Shiozawa; Luca Malcovati; Anna Gallì; Aiko Sato-Otsubo; Keisuke Kataoka; Yusuke Sato; Yosaku Watatani; Hiromichi Suzuki; Tetsuichi Yoshizato; Kenichi Yoshida; Masashi Sanada; Hideki Makishima; Yuichi Shiraishi; Kenichi Chiba; Eva Hellström-Lindberg; Satoru Miyano; Seishi Ogawa; Mario Cazzola
Journal: Nat Commun Date: 2018-09-07 Impact factor: 14.919

RNAmut: robust identification of somatic mutations in acute myeloid leukemia using RNA-sequencing.

1. STAR: ultrafast universal RNA-seq aligner.

2. RNA-sequencing analysis of core binding factor AML identifies recurrent ZBTB7A mutations and defines RUNX1-CBFA2T3 fusion signature.

Review 3. Genomics of Acute Myeloid Leukemia Diagnosis and Pathways.

4. Gene expression and risk of leukemic transformation in myelodysplasia.

5. VaDiR: an integrated approach to Variant Detection in RNA.

6. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

7. Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia.

8. Fast and accurate short read alignment with Burrows-Wheeler transform.

9. Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data.

10. A fast detection of fusion genes from paired-end RNA-seq data.

Review 1. Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia.

2. NPM1 gene mutations can be confidently identified in blood DNA months before de novo AML onset.

3. FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines.

4. The PML-RARA fusion is not detectable in historical blood samples of acute promyelocytic leukaemia patients.