Corrigendum: Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control (BioMed Research International (2013) 2013 (915636) DOI: 10.1155/2013/915636);Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control

BioMed Research International

Volumn 2013, Issue , 2013, Pages

  Guo, Yan ^a   Sheng, Quanghu ^a   Samuels, David C ^b   Lehmann, Brian ^c   Bauer, Joshua A ^c   Pietenpol, Jennifer ^c   Shyr, Yu ^a  

^a VANDERBILT UNIVERSITY   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; CANCER CELL CULTURE; COMPARATIVE EFFECTIVENESS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; CONTROLLED STUDY; COPY NUMBER VARIATION; EXOME; FALSE POSITIVE RESULT; GENE PROBE; GENE SEQUENCE; HUMAN; HUMAN CELL; SENSITIVITY AND SPECIFICITY; ALGORITHM; BREAST TUMOR; EVALUATION STUDY; FEMALE; GENETICS; HUMAN GENOME; METHODOLOGY; STATISTICS; TUMOR CELL LINE;

CONIFEROPHYTA;

ALGORITHMS; BREAST NEOPLASMS; CELL LINE, TUMOR; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; EXOME; FEMALE; GENOME, HUMAN; HUMANS;

EID: 84888990872     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2017/7409598     Document Type: Erratum

References (28)

1. Ng S. B., Buckingham K. J., Lee C., Bigham A. W., Tabor H. K., Dent K. M., Huff C. D., Shannon P. T., Jabs E. W., Nickerson D. A., Shendure J., Bamshad M. J., Exome sequencing identifies the cause of a mendelian disorder. Nature Genetics 2010 42 1 30 35 2-s2.0-73349110071 10.1038/ng.499
2. Glessner J. T., Wang K., Cai G., Korvatska O., Kim C. E., Wood S., Zhang H., Estes A., Brune C. W., Bradfield J. P., Imielinski M., Frackelton E. C., Reichert J., Crawford E. L., Munson J., Sleiman P. M. A., Chiavacci R., Annaiah K., Thomas K., Hou C., Glaberson W., Flory J., Otieno F., Garris M., Soorya L., Klei L., Piven J., Meyer K. J., Anagnostou E., Sakurai T., Game R. M., Rudd D. S., Zurawiecki D., McDougle C. J., Davis L. K., Miller J., Posey D. J., Michaels S., Kolevzon A., Silverman J. M., Bernier R., Levy S. E., Schultz R. T., Dawson G., Owley T., McMahon W. M., Wassink T. H., Sweeney J. A., Nurnberger J. I., Coon H., Sutcliffe J. S., Minshew N. J., Grant S. F. A., Bucan M., Cook E. H., Buxbaum J. D., Devlin B., Schellenberg G. D., Hakonarson H., Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 2009 459 7246 569 572 2-s2.0-67349182343 10.1038/nature07953
3. Yang T. L., Guo Y., Shen H., Li J., Glessner J. T., Qiu C., Deng F. Y., Tian Q., Yu P., Liu Y. Z., Copy number variation on chromosome 10q26.3 for obesity identified by a genome-wide study. The Journal of Clinical Endocrinology & Metabolism 2013 98 1 E191 E195 10.1210/jc.2012-2751
4. Bergamaschi A., Kim Y. H., Wang P., Sørlie T., Hernandez-Boussard T., Lonning P. E., Tibshirani R., Børresen-Dale A.-L., Pollack J. R., Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes and Cancer 2006 45 11 1033 1040 2-s2.0-33748939380 10.1002/gcc.20366 (Pubitemid 44435537)
5. Moroni M., Veronese S., Benvenuti S., Marrapese G., Sartore-Bianchi A., Di Nicolantonio F., Gambacorta M., Siena S., Bardelli A., Gene copy number for epidermal growth factor receptor (EGFR) and clinical response to antiEGFR treatment in colorectal cancer: a cohort study. The Lancet Oncology 2005 6 5 279 286 2-s2.0-17844362179 10.1016/S1470-2045(05)70102-9 (Pubitemid 40590264)
6. Cappuzzo F., Ligorio C., Toschi L., Rossi E., Trisolini R., Paioli D., Magrini E., Finocchiaro G., Bartolini S., Cancellieri A., Hirsch F. R., Crino L., Varella-Garcia M., EGFR and HER2 gene copy number and response to first-line chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). Journal of Thoracic Oncology 2007 2 5 423 429 2-s2.0-34249862665 10.1097/01.JTO.0000268676.79872.9b (Pubitemid 47181697)
7. Vasson A., Leroux C., Orhant L., Boimard M., Toussaint A., Leroy C., Commere V., Ghiotti T., Deburgrave N., Saillour Y., Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes. European Journal of Human Genetics 2013 21 9 977 987 10.1038/ejhg.2012.279
8. Lybæk H., Meza-Zepeda L. A., Kresse S. H., Høysæter T., Steen V. M., Houge G., Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development. European Journal of Human Genetics 2008 16 11 1318 1328 2-s2.0-54549122445 10.1038/ejhg.2008.78
9. Schoumans J., Nielsen K., Jeppesen I., Anderlid B.-M., Blennow E., Brøndum-Nielsen K., Nordenskjöld M., A comparison of different metaphase CGH methods for the detection of cryptic chromosome aberrations of defined size. European Journal of Human Genetics 2004 12 6 447 454 2-s2.0-3142767622 10.1038/sj.ejhg.5201175 (Pubitemid 38923703)
10. Hashimoto K., Mori N., Tamesa T., Okada T., Kawauchi S., Oga A., Furuya T., Tangoku A., Oka M., Sasaki K., Analysis of DNA copy number aberrations in hepatitis C virus-associated hepatocellular carcinomas by conventional CGH and array CGH. Modern Pathology 2004 17 6 617 622 2-s2.0-2642580037 10.1038/modpathol.3800107 (Pubitemid 38715482)
11. Abyzov A., Urban A. E., Snyder M., Gerstein M., CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research 2011 21 6 974 984 2-s2.0-79951970227 10.1101/gr.114876.110
12. Boeva V., Popova T., Bleakley K., Chiche P., Cappo J., Schleiermacher G., Janoueix-Lerosey I., Delattre O., Barillot E., Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 2012 28 3 423 425 2-s2.0-84856561659 10.1093/bioinformatics/ btr670
13. Chiang D. Y., Getz G., Jaffe D. B., O'Kelly M. J. T., Zhao X., Carter S. L., Russ C., Nusbaum C., Meyerson M., Lander E. S., High-resolution mapping of copy-number alterations with massively parallel sequencing. Nature Methods 2009 6 1 99 103 2-s2.0-58149218240 10.1038/nmeth.1276
14. Magi A., Benelli M., Yoon S., Roviello F., Torricelli F., Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Research 2011 39 10, article e65 2-s2.0-79961202047 10.1093/nar/gkr068
15. Medvedev P., Fiume M., Dzamba M., Smith T., Brudno M., Detecting copy number variation with mated short reads. Genome Research 2010 20 11 1613 1622 2-s2.0-78649309503 10.1101/gr.106344.110
16. Miller C. A., Hampton O., Coarfa C., Milosavljevic A., ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS ONE 2011 6 1 2-s2.0-79551621409 10.1371/journal.pone.0016327 e16327
17. Waszak S. M., Hasin Y., Zichner T., Olender T., Keydar I., Khen M., Stütz A. M., Schlattl A., Lancet D., Korbel J. O., Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Computational Biology 2010 6 11 2-s2.0-78649646546 10.1371/journal.pcbi.1000988 e1000988
18. Sathirapongsasuti J. F., Lee H., Horst B. A. J., Brunner G., Cochran A. J., Binder S., Quackenbush J., Nelson S. F., Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics 2011 27 19 2648 2654 2-s2.0-80053446554 10.1093/bioinformatics/btr462
19. Krumm N., Sudmant P. H., Ko A., O'Roak B. J., Malig M., Coe B. P., Quinlan A. R., Nickerson D. A., Eichler E. E., Copy number variation detection and genotyping from exome sequence data. Genome Research 2012 22 8 1525 1532 10.1101/gr.138115.112
20. Klambauer G., Schwarzbauer K., Mayr A., Clevert D. A., Mitterecker A., Bodenhofer U., Hochreiter S., cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Research 2012 40 9, article e69
21. Love M. I., Myišičková A., Sun R., Kalscheuer V., Vingron M., Haas S. A., Modeling read counts for CNV detection in exome sequencing data. Statistical Applications in Genetics and Molecular Biology 2011 10 1, article 52 2-s2.0-82955184653 10.2202/1544-6115.1732
22. Plagnol V., Curtis J., Epstein M., Mok K. Y., Stebbings E., Grigoriadou S., Wood N. W., Hambleton S., Burns S. O., Thrasher A. J., A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 2012 28 21 2747 2754
23. Gusnanto A., Wood H. M., Pawitan Y., Rabbitts P., Berri S., Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics 2012 28 1 40 47 2-s2.0-84855185866 10.1093/bioinformatics/btr593
24. Li J., Lupat R., Amarasinghe K. C., Thompson E. R., Doyle M. A., Ryland G. L., Tothill R. W., Halgamuge S. K., Campbell I. G., Gorringe K. L., CONTRA: copy number analysis for targeted resequencing. Bioinformatics 2012 28 10 1307 1313 10.1093/bioinformatics/bts146
25. Li H., Durbin R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009 25 14 1754 1760 2-s2.0-67649884743 10.1093/bioinformatics/btp324
26. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., The sequence alignment/Map format and SAMtools. Bioinformatics 2009 25 16 2078 2079 2-s2.0-68549104404 10.1093/bioinformatics/ btp352
27. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M. A., The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 2010 20 9 1297 1303 2-s2.0-77956295988 10.1101/gr.107524.110
28. Cock P. J. A., Fields C. J., Goto N., Heuer M. L., Rice P. M., The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2009 38 6 1767 1771 2-s2.0-77951226627 10.1093/nar/gkp1137