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Method: Polishing copy number variant calls on exome sequencing data via deep learning
- Furkan Özden,
- Can Alkan,
- and A. Ercüment Çiçek
Genome Res. June 2022 32: 1170-1182; Published in Advance June 13, 2022, doi:10.1101/gr.274845.120
...are shown with respect to varied confidence threshold (DEL, DUP, and overall precision); 6832 CNV calls made by XHMM on our test data set (the 1000 Genomes Project WES data set test samples) are used. The ground truth is the CNV calls made by CNVnator on the corresponding WGS samples. The last panel shows...
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Research: Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
- Eric R. Lucas,
- Alistair Miles,
- Nicholas J. Harding,
- Chris S. Clarkson,
- Mara K.N. Lawniczak,
- Dominic P. Kwiatkowski,
- David Weetman,
- Martin J. Donnelly,
- and The Anopheles gambiae 1000 Genomes Consortium
Genome Res. August 2019 29: 1250-1261; Published in Advance July 25, 2019, doi:10.1101/gr.245795.118
...-caught mosquitoes collected from 16 populations between 2000 and 2012 and sequenced with a mean coverage of 32×. We then focus on five regions of particular interest for metabolic insecticide resistance to investigate whether CNVs in these regions are under positive selection.ResultsGenome-wide CNV discovery...
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Research: Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia
- Sanchita Bhattacharya,
- Jian Li,
- Alexandra Sockell,
- Matthew J. Kan,
- Felice A. Bava,
- Shann-Ching Chen,
- María C. Ávila-Arcos,
- Xuhuai Ji,
- Emery Smith,
- Narges B. Asadi,
- Ralph S. Lachman,
- Hugo Y.K. Lam,
- Carlos D. Bustamante,
- Atul J. Butte,
- and Garry P. Nolan
Genome Res. April 2018 28: 423-431; Published in Advance March 22, 2018, doi:10.1101/gr.223693.117
...526: 68–74. ↵Abyzov A, Urban AE, Snyder M, Gerstein M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population sequencing. Genome Res 21: 974–984. ↵Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS...
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
..., selective pressures, and adaption.DiscussionDespite its wide usage and impact on biomedical research, K562's genomic sequence and structural features have never been comprehensively characterized, beyond its karyotype (Selden et al. 1983; Wu et al. 1995; Gribble et al. 2000; Naumann et al. 2001) and SNPs...
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Resource: Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing
- Thomas Zichner,
- David A. Garfield,
- Tobias Rausch,
- Adrian M. Stütz,
- Enrico Cannavó,
- Martina Braun,
- Eileen E.M. Furlong,
- and Jan O. Korbel
Genome Res. March 2013 23: 568-579; Published in Advance December 6, 2012, doi:10.1101/gr.142646.112
...discovery To discover deletions and tandem duplications we applied the SV detection methods DELLY (Rausch et al. 2012b), Pindel (Ye et al. 2009) v0.2.4d, and CNVnator (Abyzov et al. 2011) v0.2.2 on each sample. We further used Genome STRiP (Handsaker et al. 2011) v1.0.4 to perform simultaneous population...
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Resource: The genome of the vervet (Chlorocebus aethiops sabaeus)
- Wesley C. Warren,
- Anna J. Jasinska,
- Raquel García-Pérez,
- Hannes Svardal,
- Chad Tomlinson,
- Mariano Rocchi,
- Nicoletta Archidiacono,
- Oronzo Capozzi,
- Patrick Minx,
- Michael J. Montague,
- Kim Kyung,
- LaDeana W. Hillier,
- Milinn Kremitzki,
- Tina Graves,
- Colby Chiang,
- Jennifer Hughes,
- Nam Tran,
- Yu Huang,
- Vasily Ramensky,
- Oi-wa Choi,
- Yoon J. Jung,
- Christopher A. Schmitt,
- Nikoleta Juretic,
- Jessica Wasserscheid,
- Trudy R. Turner,
- Roger W. Wiseman,
- Jennifer J. Tuscher,
- Julie A. Karl,
- Jörn E. Schmitz,
- Roland Zahn,
- David H. O'Connor,
- Eugene Redmond,
- Alex Nisbett,
- Béatrice Jacquelin,
- Michaela C. Müller-Trutwin,
- Jason M. Brenchley,
- Michel Dione,
- Martin Antonio,
- Gary P. Schroth,
- Jay R. Kaplan,
- Matthew J. Jorgensen,
- Gregg W.C. Thomas,
- Matthew W. Hahn,
- Brian J. Raney,
- Bronwen Aken,
- Rishi Nag,
- Juergen Schmitz,
- Gennady Churakov,
- Angela Noll,
- Roscoe Stanyon,
- David Webb,
- Francoise Thibaud-Nissen,
- Magnus Nordborg,
- Tomas Marques-Bonet,
- Ken Dewar,
- George M. Weinstock,
- Richard K. Wilson,
- and Nelson B. Freimer
Genome Res. December 2015 25: 1921-1933; Published in Advance September 16, 2015, doi:10.1101/gr.192922.115
...bp to 2 Mb size (Supplemental Table S8). To identify a high-confidence set of deletions, we used CNVnator (Abyzov et al. 2011), which relies on sequence depth, and LUMPY (Layer et al. 2014), which relies on split and pairedend sequence discordance. Among the VRC monkeys, we found 556 unique deletions...
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Research: Characteristics of de novo structural changes in the human genome
- Wigard P. Kloosterman,
- Laurent C. Francioli,
- Fereydoun Hormozdiari,
- Tobias Marschall,
- Jayne Y. Hehir-Kwa,
- Abdel Abdellaoui,
- Eric-Wubbo Lameijer,
- Matthijs H. Moed,
- Vyacheslav Koval,
- Ivo Renkens,
- Markus J. van Roosmalen,
- Pascal Arp,
- Lennart C. Karssen,
- Bradley P. Coe,
- Robert E. Handsaker,
- Eka D. Suchiman,
- Edwin Cuppen,
- Djie Tjwan Thung,
- Mitch McVey,
- Michael C. Wendl,
- Genome of the Netherlands Consortium,
- André Uitterlinden,
- Cornelia M. van Duijn,
- Morris A. Swertz,
- Cisca Wijmenga,
- GertJan B. van Ommen,
- P. Eline Slagboom,
- Dorret I. Boomsma,
- Alexander Schönhuth,
- Evan E. Eichler,
- Paul I.W. de Bakker,
- Kai Ye,
- and Victor Guryev
Genome Res. June 2015 25: 792-801; Published in Advance April 16, 2015, doi:10.1101/gr.185041.114
.... 2013]); and read depth analysis (CNVnator [Abyzov et al. 2011], DWACseq [http://tools.s.nl/dwac-seq.html], FACADE [Coe et al. 2010]). In addition, Mobster was used to call de novo mobile element insertions (MEIs) (Thung et al. 2014). For each algorithm , variant calls confined to offspring of a single...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...), as described at http://creativecommons.org/licenses/by/4.0/.References ↵Abyzov A, Urban AE, Snyder M, Gerstein M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population sequencing. Genome Res 21: 974–984. ↵Alexandrov A, Colognori D, Shu M...
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Research: Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor
- Brennan Decker,
- Brian W. Davis,
- Maud Rimbault,
- Adrienne H. Long,
- Eric Karlins,
- Vidhya Jagannathan,
- Rebecca Reiman,
- Heidi G. Parker,
- Cord Drögemüller,
- Jason J. Corneveaux,
- Erica S. Chapman,
- Jeffery M. Trent,
- Tosso Leeb,
- Matthew J. Huentelman,
- Robert K. Wayne,
- Danielle M. Karyadi,
- and Elaine A. Ostrander
Genome Res. November 2015 25: 1646-1655; Published in Advance July 31, 2015, doi:10.1101/gr.190314.115
..., or preparation of the manuscript. References Abyzov A, Urban AE, Snyder M, Gerstein M. 2011. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population sequencing. Genome Res 21: 974–984. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
...to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show...
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