Literature DB >> 35041928

Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence.

Christopher A Miller1, Jason R Walker2, Travis L Jensen3, William F Hooper3, Robert S Fulton2, Jeffrey S Painter4, Mikkael A Sekeres5, Timothy J Ley6, David H Spencer7, Johannes B Goll3, Matthew J Walter6.   

Abstract

The U2AF1 gene is a core part of mRNA splicing machinery and frequently contains somatic mutations that contribute to oncogenesis in myelodysplastic syndrome, acute myeloid leukemia, and other cancers. A change introduced in the GRCh38 version of the human reference build prevents detection of mutations in this gene, and others, by variant calling pipelines. This study describes the problem in detail and shows that a modified GRCh38 reference build with unchanged coordinates can be used to ameliorate the issue.
Copyright © 2022 Association for Molecular Pathology and American Society for Investigative Pathology. All rights reserved.

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Year:  2022        PMID： 35041928      PMCID： PMC8950341          DOI： 10.1016/j.jmoldx.2021.10.013

Source DB:  PubMed          Journal:  J Mol Diagn        ISSN： 1525-1578            Impact factor:   5.568


  19 in total

1.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.

Authors:  Daniel C Koboldt; Qunyuan Zhang; David E Larson; Dong Shen; Michael D McLellan; Ling Lin; Christopher A Miller; Elaine R Mardis; Li Ding; Richard K Wilson
Journal:  Genome Res       Date:  2012-02-02       Impact factor: 9.043

2.  Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo.

Authors:  Cara Lunn Shirai; James N Ley; Brian S White; Sanghyun Kim; Justin Tibbitts; Jin Shao; Matthew Ndonwi; Brian Wadugu; Eric J Duncavage; Theresa Okeyo-Owuor; Tuoen Liu; Malachi Griffith; Sean McGrath; Vincent Magrini; Robert S Fulton; Catrina Fronick; Michelle O'Laughlin; Timothy A Graubert; Matthew J Walter
Journal:  Cancer Cell       Date:  2015-05-11       Impact factor: 31.743

3.  Toward a Shared Vision for Cancer Genomic Data.

Authors:  Robert L Grossman; Allison P Heath; Vincent Ferretti; Harold E Varmus; Douglas R Lowy; Warren A Kibbe; Louis M Staudt
Journal:  N Engl J Med       Date:  2016-09-22       Impact factor: 91.245

Review 4.  The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers.

Authors:  Zbyslaw Sondka; Sally Bamford; Charlotte G Cole; Sari A Ward; Ian Dunham; Simon A Forbes
Journal:  Nat Rev Cancer       Date:  2018-11       Impact factor: 60.716

5.  Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes.

Authors:  Timothy A Graubert; Dong Shen; Li Ding; Theresa Okeyo-Owuor; Cara L Lunn; Jin Shao; Kilannin Krysiak; Christopher C Harris; Daniel C Koboldt; David E Larson; Michael D McLellan; David J Dooling; Rachel M Abbott; Robert S Fulton; Heather Schmidt; Joelle Kalicki-Veizer; Michelle O'Laughlin; Marcus Grillot; Jack Baty; Sharon Heath; John L Frater; Talat Nasim; Daniel C Link; Michael H Tomasson; Peter Westervelt; John F DiPersio; Elaine R Mardis; Timothy J Ley; Richard K Wilson; Matthew J Walter
Journal:  Nat Genet       Date:  2011-12-11       Impact factor: 38.330

6.  U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing.

Authors:  T Okeyo-Owuor; B S White; R Chatrikhi; D R Mohan; S Kim; M Griffith; L Ding; S Ketkar-Kulkarni; J Hundal; K M Laird; C L Kielkopf; T J Ley; M J Walter; T A Graubert
Journal:  Leukemia       Date:  2014-10-14       Impact factor: 11.528

7.  U2AF1 mutation types in primary myelofibrosis: phenotypic and prognostic distinctions.

Authors:  Ayalew Tefferi; Christy M Finke; Terra L Lasho; Curtis A Hanson; Rhett P Ketterling; Naseema Gangat; Animesh Pardanani
Journal:  Leukemia       Date:  2018-02-27       Impact factor: 11.528

8.  Impaired hematopoiesis and leukemia development in mice with a conditional knock-in allele of a mutant splicing factor gene U2af1.

Authors:  Dennis Liang Fei; Tao Zhen; Benjamin Durham; John Ferrarone; Tuo Zhang; Lisa Garrett; Akihide Yoshimi; Omar Abdel-Wahab; Robert K Bradley; Paul Liu; Harold Varmus
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-15       Impact factor: 11.205

9.  Curated variation benchmarks for challenging medically relevant autosomal genes.

Authors:  Chen-Shan Chin; Justin M Zook; Fritz J Sedlazeck; Justin Wagner; Nathan D Olson; Lindsay Harris; Jennifer McDaniel; Haoyu Cheng; Arkarachai Fungtammasan; Yih-Chii Hwang; Richa Gupta; Aaron M Wenger; William J Rowell; Ziad M Khan; Jesse Farek; Yiming Zhu; Aishwarya Pisupati; Medhat Mahmoud; Chunlin Xiao; Byunggil Yoo; Sayed Mohammad Ebrahim Sahraeian; Danny E Miller; David Jáspez; José M Lorenzo-Salazar; Adrián Muñoz-Barrera; Luis A Rubio-Rodríguez; Carlos Flores; Giuseppe Narzisi; Uday Shanker Evani; Wayne E Clarke; Joyce Lee; Christopher E Mason; Stephen E Lincoln; Karen H Miga; Mark T W Ebbert; Alaina Shumate; Heng Li
Journal:  Nat Biotechnol       Date:  2022-02-07       Impact factor: 68.164

10.  Clinical and biological implications of driver mutations in myelodysplastic syndromes.

Authors:  Elli Papaemmanuil; Moritz Gerstung; Luca Malcovati; Sudhir Tauro; Gunes Gundem; Peter Van Loo; Chris J Yoon; Peter Ellis; David C Wedge; Andrea Pellagatti; Adam Shlien; Michael John Groves; Simon A Forbes; Keiran Raine; Jon Hinton; Laura J Mudie; Stuart McLaren; Claire Hardy; Calli Latimer; Matteo G Della Porta; Sarah O'Meara; Ilaria Ambaglio; Anna Galli; Adam P Butler; Gunilla Walldin; Jon W Teague; Lynn Quek; Alex Sternberg; Carlo Gambacorti-Passerini; Nicholas C P Cross; Anthony R Green; Jacqueline Boultwood; Paresh Vyas; Eva Hellstrom-Lindberg; David Bowen; Mario Cazzola; Michael R Stratton; Peter J Campbell
Journal:  Blood       Date:  2013-09-12       Impact factor: 22.113
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  2 in total

1.  A complete reference genome improves analysis of human genetic variation.

Authors:  Sergey Aganezov; Stephanie M Yan; Daniela C Soto; Melanie Kirsche; Samantha Zarate; Pavel Avdeyev; Dylan J Taylor; Kishwar Shafin; Alaina Shumate; Chunlin Xiao; Justin Wagner; Jennifer McDaniel; Nathan D Olson; Michael E G Sauria; Mitchell R Vollger; Arang Rhie; Melissa Meredith; Skylar Martin; Joyce Lee; Sergey Koren; Jeffrey A Rosenfeld; Benedict Paten; Ryan Layer; Chen-Shan Chin; Fritz J Sedlazeck; Nancy F Hansen; Danny E Miller; Adam M Phillippy; Karen H Miga; Rajiv C McCoy; Megan Y Dennis; Justin M Zook; Michael C Schatz
Journal:  Science       Date:  2022-04-01       Impact factor: 63.714

2.  The complete sequence of a human genome.

Authors:  Sergey Nurk; Sergey Koren; Arang Rhie; Mikko Rautiainen; Andrey V Bzikadze; Alla Mikheenko; Mitchell R Vollger; Nicolas Altemose; Lev Uralsky; Ariel Gershman; Sergey Aganezov; Savannah J Hoyt; Mark Diekhans; Glennis A Logsdon; Michael Alonge; Stylianos E Antonarakis; Matthew Borchers; Gerard G Bouffard; Shelise Y Brooks; Gina V Caldas; Nae-Chyun Chen; Haoyu Cheng; Chen-Shan Chin; William Chow; Leonardo G de Lima; Philip C Dishuck; Richard Durbin; Tatiana Dvorkina; Ian T Fiddes; Giulio Formenti; Robert S Fulton; Arkarachai Fungtammasan; Erik Garrison; Patrick G S Grady; Tina A Graves-Lindsay; Ira M Hall; Nancy F Hansen; Gabrielle A Hartley; Marina Haukness; Kerstin Howe; Michael W Hunkapiller; Chirag Jain; Miten Jain; Erich D Jarvis; Peter Kerpedjiev; Melanie Kirsche; Mikhail Kolmogorov; Jonas Korlach; Milinn Kremitzki; Heng Li; Valerie V Maduro; Tobias Marschall; Ann M McCartney; Jennifer McDaniel; Danny E Miller; James C Mullikin; Eugene W Myers; Nathan D Olson; Benedict Paten; Paul Peluso; Pavel A Pevzner; David Porubsky; Tamara Potapova; Evgeny I Rogaev; Jeffrey A Rosenfeld; Steven L Salzberg; Valerie A Schneider; Fritz J Sedlazeck; Kishwar Shafin; Colin J Shew; Alaina Shumate; Ying Sims; Arian F A Smit; Daniela C Soto; Ivan Sović; Jessica M Storer; Aaron Streets; Beth A Sullivan; Françoise Thibaud-Nissen; James Torrance; Justin Wagner; Brian P Walenz; Aaron Wenger; Jonathan M D Wood; Chunlin Xiao; Stephanie M Yan; Alice C Young; Samantha Zarate; Urvashi Surti; Rajiv C McCoy; Megan Y Dennis; Ivan A Alexandrov; Jennifer L Gerton; Rachel J O'Neill; Winston Timp; Justin M Zook; Michael C Schatz; Evan E Eichler; Karen H Miga; Adam M Phillippy
Journal:  Science       Date:  2022-03-31       Impact factor: 63.714
  2 in total

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