YMAP: A pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Genome Medicine

Volumn 6, Issue , 2014, Pages 1-15

  Abbey, Darren A ^a   Funt, Jason ^b   Lurie Weinberger, Mor N ^c   Thompson, Dawn A ^b   Regev, Aviv ^b   Myers, Chad L ^d   Berman, Judith ^a,c  

^a UNIVERSITY OF MINNESOTA   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

^d University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANDIDA ALBICANS; CENTROMERE; CHROMOSOME NUMBER; COPY NUMBER VARIATION; DIPLOIDY; DNA BASE COMPOSITION; DNA MICROARRAY; DNA SEQUENCE; EUKARYOTE; FUNGAL STRAIN; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENOME; GENOME ANALYSIS; HAPLOTYPE MAP; HETEROZYGOSITY LOSS; HUMAN; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; RESTRICTION FRAGMENT; RESTRICTION SITE; SEGMENTAL DUPLICATION; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84925731610     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-014-0100-8     Document Type: Article

References (47)

1. Selmecki A, Forche A, Berman J: Aneuploidy and isochromosome formation in drug-resistant Candida albicans . Science 2006, 313:367-370.
2. Selmecki A, Gerami-Nejad M, Paulson C, Forche A, Berman J: An isochromosome confers drug resistance in vivo by amplification of two genes, ERG11 and TAC1. Mol Microbiol 2008, 68:624-641.
3. Kobayashi T, Heck DJ, Nomura M, Horiuchi T: Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev 1998, 12:3821-3830.
4. Ketel C, Wang HSW, McClellan M, Bouchonville K, Selmecki A, Lahav T, Gerami-Nejad M, Berman J: Neocentromeres form efficiently at multiple possible loci in Candida albicans . PLoS Genet 2009, 5:e1000400.
5. Baum M, Sanyal K, Mishra PK, Thaler N, Carbon J: Formation of functional centromeric chromatin is specified epigenetically in Candida albicans . Proc Natl Acad Sci U S A 2006, 103:14877-14882.
6. McEachern MJ, Hicks JB: Unusually large telomeric repeats in the yeast Candida albicans . Mol Cell Biol 1993, 13:551-560.
7. van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT: Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 2007, 8:R52.
8. Anderson MZ, Baller JA, Dulmage K, Wigen L, Berman J: The three clades of the telomere-associated TLO gene family of Candida albicans have different splicing, localization, and expression features. Eukaryot Cell 2012, 11:1268-1275.
9. Rustchenko EP, Curran TM, Sherman F: Variations in the number of ribosomal DNA units in morphological mutants and normal strains of Candida albicans and in normal strains of Saccharomyces cerevisiae. J Bacteriol 1993, 175:7189-7199.
10. Lephart PR, Chibana H, Magee PT: Effect of the major repeat sequence on chromosome loss in Candida albicans . Eukaryot Cell 2005, 4:733-741.
11. Janbon G, Sherman F, Rustchenko E: Monosomy of a specific chromosome determines L-sorbose utilization: a novel regulatory mechanism in Candida albicans . Proc Natl Acad Sci U S A 1998, 95:5150-5155.
12. Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z: A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform 2014, 15:256-278.
13. Dolled-Filhart MP, Lee M, Ou-Yang C-W, Haraksingh RR, Lin JC-H: Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing. Sci World J 2013, 2013:730210.
14. Naquin D, D'Aubenton-Carafa Y, Thermes C, Silvain M: CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data. BMC Bioinformatics 2014, 15:198.
15. Qi J, Zhao F: inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res 2011, 39:W567-W575.
16. O'Brien TM, Ritz AM, Raphael BJ, Laidlaw DH: Gremlin: an interactive visualization model for analyzing genomic rearrangements. IEEE Trans Vis Comput Graph 2010, 16:918-926.
17. Straver R, Sistermans EA, Holstege H, Visser A, Oudejans CBM, Reinders MJT: WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme. Nucleic Acids Res 2014, 42:e31-e31.
18. Kinde I, Papadopoulos N, Kinzler KW, Vogelstein B: FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing. PLoS One 2012, 7:e41162.
19. Myers CL, Dunham MJ, Kung SY, Troyanskaya OG: Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 2004, 20:3533-3543.
20. Piazza R, Magistroni V, Pirola A, Redaelli S, Spinelli R, Redaelli S, Galbiati M, Valletta S, Giudici G, Cazzaniga G, Gambacorti-Passerini C: CEQer: a graphical tool for copy number and allelic imbalance detection from whole-exome sequencing data. PLoS One 2013, 8:e74825.
21. Sathirapongsasuti JF, Lee H, Horst BAJ, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF: Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics 2011, 27:2648-2654.
22. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol 2011, 29:24-26.
23. Thorvaldsdóttir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013, 14:178-192.
24. Legrand M, Forche A, Selmecki A, Chan C, Kirkpatrick DT, Berman J: Haplotype mapping of a diploid non-meiotic organism using existing and induced aneuploidies. PLoS Genet 2008, 4:e1.
25. Abbey D, Hickman M, Gresham D, Berman J: High-resolution SNP/CGH microarrays reveal the accumulation of loss of heterozygosity in commonly used Candida albicans strains. G3 (Bethesda) 2011, 1:523-530.
26. Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL, May P, Huang AA, Dudley AM, Fay JC: Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda) 2013, 3:2163-2171.
27. MAP pipeline website. [ http://lovelace.cs.umn.edu/Ymap/ ]
28. Ymap Source code hosted at Sourceforge. [ https://sourceforge.net/projects/ymap/ ]
29. Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359.
30. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
31. Wysokar A, Tibbetts K, McCown M, Homer N, Fennell T. Picard: A set of tools for working with next generation sequencing data in BAM format. [ http://broadinstitute.github.io/picard/ ]
32. Andrews S. FastQC: A quality control tool for high throughput sequence data. [ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ]
33. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20:1297-1303.
34. Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H: The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Res 2012, 40:D64-D70.
35. Miller MG, Johnson AD: White-opaque switching in Candida albicans is controlled by mating-type locus homeodomain proteins and allows efficient mating. Cell 2002, 110:293-302.
36. Noble SM, Johnson AD: Strains and strategies for large-scale gene deletion studies of the diploid human fungal pathogen Candida albicans . Eukaryot Cell 2005, 4:298-309.
37. Cleveland WS: Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc 1978, 74:829-836.
38. Arlot S, Celisse A: A survey of cross-validation procedures for model selection. Stat Surveys 2010, 4:40-79.
39. NCBI Resource Coordinators: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2014, 42:D7-D17.
40. Butler G, Rasmussen MD, Lin MF, Santos MAS, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJP, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PWJ, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, et al: Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 2009, 459:657-662.
41. Hickman MA, Zeng G, Forche A, Hirakawa MP, Abbey D, Harrison BD, Wang Y-M, Su C-H, Bennett RJ, Wang Y, Berman J: The 'obligate diploid' Candida albicans forms mating-competent haploids. Nature 2013, 494:55-59.
42. Muzzey D, Schwartz K, Weissman JS, Sherlock G: Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biol 2013, 14:R97.
43. Forche A, Alby K, Schaefer D, Johnson AD, Berman J, Bennett RJ: The parasexual cycle in Candida albicans provides an alternative pathway to meiosis for the formation of recombinant strains. PLoS Biol 2008, 6:e110.
44. Kozinn PJ, Taschdjian CL, Burchall JJ, Wiener H: Transmission of P32-Labeled Candida Albicans to Newborn Mice at Birth. AMA Am J Dis Child 1960, 99:31-34.
45. Marr KA, White TC, van Burik JA, Bowden RA: Development of fluconazole resistance in Candida albicans causing disseminated infection in a patient undergoing marrow transplantation. Clin Infect Dis 1997, 25:908-910.
46. Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G: The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. Nucleic Acids Res 2005, 33:D358-D363.
47. The MIT license (MIT) at The Open Source website. [ http://opensource.org/licenses/MIT ]