Investigation of copy number variation in Baluchi sheep genome using comparative analysis of PennCNV and QuantiSNP algorithms

Document Type : Research Paper

Authors

1 Ph.D Student, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

2 Assistant Professor, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

3 Assistant Professor, Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran

4 Professor, Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

Abstract

Copy number variation (CNV), one of the most important structural changes in the genome, has been known as an important source of genetic and phenotypic variations. The purpose of this study was to compare the two different algorithms in CNV detection consisting PennCNV and QuantiSNP in Baluchi sheep.Data analysis was performed using the Illumina OvineSNP50k BeadChip on 96 Baluchi sheep.After CNV calling, the copy number variation regions (CNVRs) were determined using the CNVRuler program.91 CNVRs with a length range of 18.75 up to 511.7 kbp were identified by the PennCNV algorithm, covering 0.46% of whole sheep genome.Also, 316 CNVRs with the length range of 7.5 up to 1280 kbp were obtained using QuantiSNP algorithm, covering 1.33% of whole sheep genome. The number of loss events was about five and three times more than the number of gain events for QuantiSNP and PennCNV algorithms, respectively.Also, the number of CNVs detected by QuantiSNP was about four times higherthan PennCNV.Also, 86.6% of total CNVs (174 CNVs with average length of 12.62 kb) identified by PennCNV were common with CNVs detected by QuantiSNP. In general, the results showed that the use of several algorithms could improve the accuracy for detecting the structural variation in the genome and led to a better understanding of the sheep genome. 

Keywords

Main Subjects

References

Bae J. S., Cheong H. S., Kim L. H., NamGung S., Park T. J., Chun J. Y. and Shin H. D. 2010. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics, 11(1): 232.
Baumbusch L. O., Aarøe J., Johansen F. E., Hicks J., Sun H., Bruhn L. and Børresen-Dale A. L. 2008. Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics, 9(1): 379.
Bhanuprakash V., Chhotaray S., Pruthviraj D. R., Rawat C., Karthikeyan A. and Panigrahi M. 2018. Copy number variation in livestock: A mini review. Veterinary World, 11(4): 535-541.
Carter N. P. 2007. Methods and strategies for analyzing copy number variation using DNA microarrays. Nature Genetics, 39(7s), S16.
Clop A., Vidal O. and Amills M .2012. Copy number variation in the genomes of domestic animals. Animal Genetics, 43(5): 503-517.
Colella S., Yau C., Taylor J. M., Mirza G., Butler H., Clouston P. and Ragoussis J. 2007. QuantiSNP: An Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research, 35(6): 2013-2025.
Craddock N. J. and Jones I. R. J. N. 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447: 661-678.
Dathe K., Kjaer K. W., Brehm A., Meinecke P., Nürnberg P., Neto J. C. and Seemann P. 2009. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. The American Journal of Human Genetics, 84(4): 483-492.
de Lemos M. V. A., Berton M. P., de Camargo G. M. F., Peripolli E., de Oliveira Silva R. M., Olivieri B. F. and Tonhati H. 2018. Copy number variation regions in Nellore cattle: evidences of environment adaptation. Livestock Science, 207: 51-58.
Dermitzakis E. T. and Stranger B. E. 2006. Genetic variation in human gene expression. Mammalian Genome, 17(6): 503-508.
Diskin S. J., Li M., Hou C., Yang S., Glessner J., Hakonarson H. and Wang K. 2008. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Research, 36(19): e126-e126.
Fadista J., Thomsen B., Holm L. E. and Bendixen C. 2010. Copy number variation in the bovine genome. BMC Genomics, 11(1): 284.
Feuk L., Carson, A. R. and Scherer S. W. 2006. Structural variation in the human genome. Nature Reviews Genetics, 7(2): 85.
Fontanesi L., Beretti F., Riggio V., González E. G., Dall’Olio S., Davoli R. and Portolano B. 2009. Copy number variation and missense mutations of the agouti signaling protein (ASIP) gene in goat breeds with different coat colors. Cytogenetic and Genome Research, 126(4): 333-347.
Fontanesi L., Martelli P. L., Beretti F., Riggio V., Dall'Olio S., Colombo M. and Portolano B. 2010. An initial comparative map of copy number variations in the goat (Capra hircus) genome. BMC Genomics, 11(1): 639.
Fontanesi L., Beretti F., Martelli P. L., Colombo M., Dall'Olio S., Occidente M. and Russo V. 2011. A first comparative map of copy number variations in the sheep genome. Genomics, 97(3): 158-165.
Freeman J. L., Perry G. H., Feuk L., Redon R., McCarroll S. A., Altshuler D. M. and Carter N. P. 2006. Copy number variation: new insights in genome diversity. Genome Research, 16(8): 949-961.
Giuffra E., Törnsten A., Marklund S., Bongcam-Rudloff E., Chardon P., Kijas J. M. and Andersson L. 2002. A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mammalian Genome, 13(10): 569-577.
Hastings P. J., Lupski J. R., Rosenberg S. M. and Ira G. 2009. Mechanisms of change in gene copy number. Nature Reviews Genetics, 10(8): 551.
Hester S. D., Reid L., Nowak N., Jones W. D., Parker J. S., Knudtson K. and Denslow N. D. 2009. Comparison of comparative genomic hybridization technologies across microarray platforms. Journal of Biomolecular Techniques, 20(2): 135.
Hou C. L., Meng F. H., Wang W., Wang S. Y., Xing Y. P., Cao J. W. and Zhou H. M. 2015. Genome-wide analysis of copy number variations in Chinese sheep using array comparative genomic hybridization. Small Ruminant Research, 128: 19-26.
Hou Y., Liu G. E., Bickhart D. M., Cardone M. F., Wang K., Kim E. S. and Sonstegard T. S. 2011. Genomic characteristics of cattle copy number variations. BMC Genomics, 12(1): 127.
Hou Y., Bickhart D. M., Hvinden M. L., Li C., Song J., Boichard D. A. and Sonstegard T. S. 2012. Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array. BMC Genomics, 13(1): 376.
Jenkins G. M., Goddard M. E., Black M. A., Brauning R., Auvray B., Dodds K. G. and McEwan J. C. 2016. Copy number variants in the sheep genome detected using multiple approaches. BMC Genomics, 17(1): 441.
Jiang L., Jiang J., Wang J., Ding X., Liu J. and Zhang Q. 2012. Genome-wide identification of copy number variations in Chinese Holstein. PLoS One, 7(11):e48732.
Karimi K., Esmailizadeh A., Wu D. D. and Gondro C. 2018. Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set. Animal Production Science, 58(7): 1192-1200.
Kim J. H., Hu H. J., Yim S. H., Bae J. S., Kim S. Y. and Chung Y. J. 2012. CNVRuler: a copy number variation-based case–control association analysis tool. Bioinformatics, 28(13): 1790-1792.
Kim S. Y., Kim J. H. and Chung Y. J. 2012. Effect of combining multiple CNV defining algorithms on the reliability of CNV calls from SNP genotyping data. Genomics & Informatics, 10(3): 194.
Korn J. M., Kuruvilla F. G., McCarroll S. A., Wysoker A., Nemesh J., Cawley S. and Lee C. 2008. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nature Genetics, 40(10): 1253.
Lai W. R., Johnson M. D., Kucherlapati R. and Park P. J. 2005. Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21(19): 3763-3770.
Lin P., Hartz S. M., Wang J. C., Krueger R. F., Foroud T. M., Edenberg H. J. and Webb B. T. 2011. Copy number variation accuracy in genome-wide association studies. Human Heredity, 71(3): 141-147.
Liu G. E., Hou Y., Zhu B., Cardone M. F., Jiang L., Cellamare A. and Gasbarre L. C. 2010. Analysis of copy number variations among diverse cattle breeds. Genome Research, 20(5): 693-703.
Liu J., Ulloa A., Perrone-Bizzozero N., Yeo R., Chen J. and Calhoun V. D. 2012. A pilot study on collective effects of 22q13. 31 deletions on gray matter concentration in schizophrenia. PloS ONE, 7(12): 52865.
Liu J., Calhoun V. D., Chen J., Claus E. D. and Hutchison K. E. 2013. Effect of homozygous deletions at 22q13. 1 on alcohol dependence severity and cue‐elicited BOLD response in the precuneus. Addiction Biology, 18(3):548-558.
Liu J., Zhang L., Xu L., Ren H., Lu J., Zhang X. and Du L. 2013. Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array. BMC Genomics, 14(1): 229.
Ma Y., Zhang Q., Lu Z., Zhao X. and Zhang Y. 2015. Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep. Genomics, 106(5): 295-300.
Marioni J. C., Thorne N. P. Valsesia A., Fitzgerald T., Redon R., Fiegler H. and Carter N. P. 2007. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biology, 8(10): R228.
Metzger J., Philipp U., Lopes M. S., da Camara Machado A., Felicetti M., Silvestrelli M. and Distl O. 2013. Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics, 14(1): 487.
Norris B. J. and Whan V. A. 2008. A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep. Genome Research, 18(8): 1282-1293.
Park R. W., Kim T. M., Kasif S. and Park P. J. 2015. Identification of rare germline copy number variations over-represented in five human cancer types. Molecular Cancer, 14(1): 25.
Peiffer D. A., Le J. M., Steemers F. J., Chang W., Jenniges T., Garcia F. and Cheung S. W. 2006. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Research, 16(9): 1136-1148.
Pinkel D., Segraves R., Sudar D., Clark S., Poole I., Kowbel D. and Dairkee S. H. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics, 20(2): 207.
Pinto D., Darvishi K., Shi X., Rajan D., Rigler D., Fitzgerald T. and Prasad A. 2011. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nature Biotechnology, 29(6): 512.
Pongpanich M., Sullivan P. F. and Tzeng J.-Y. J. B .2010. A quality control algorithm for filtering SNPs in genome-wide association studies. Bioinformatics, 26(14): 1731-1737.
Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M. A., Bender D. and Sham P. C. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3): 559-575.
Reymond A., Henrichsen C. N., Harewood L. and Merla G. 2007. Side effects of genome structural changes. Current Opinion in Genetics & Development, 17(5): 381-386.
Salomón-Torres R., González-Vizcarra V. M., Medina-Basulto G. E., Montaño-Gómez M. F., Mahadevan P., Yaurima-Basaldúa V. H. and Villa-Angulo R. 2015. Genome-wide identification of copy number variations in Holstein cattle from Baja California, Mexico, using high-density SNP genotyping arrays. Genetics and Molecular Research, 14(4): 11848-11859.
Stranger B. E., Forrest M. S., Dunning M., Ingle C. E., Beazley C., Thorne N. and Tyler-Smith C. 2007. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science, 315(5813): 848-853.
Teo Y. Y., Fry A. E., Clark T. G., Tai E. S. and Seielstad M. 2007. On the usage of HWE for identifying genotyping errors. Annals of Human Genetics, 71(5): 701-703.
Wain L. V., Armour J. A. and Tobin M. D. 2009. Genomic copy number variation, human health, and disease. The Lancet, 374(9686): 340-350.
Wang K., Li M., Hadley D., Liu R., Glessner J., Grant S. F. and Bucan M. 2007. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research, 17(11): 1665-1674.
Wang X., Nahashon S., Feaster T. K., Bohannon-Stewart A. and Adefope N. 2010. An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics, 11(1): 351.
Winchester L., Yau C. and Ragoussis J. 2009. Comparing CNV detection methods for SNP arrays. Briefings in Functional Genomics and Proteomics, 8(5): 353-366.
Wright D., Boije H., Meadows J. R., Bed'Hom B., Gourichon D., Vieaud, A. and Andersson L. 2009. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genetics, 5(6): 1000512.
Xi R., Hadjipanayis A. G., Luquette L. J., Kim T. M., Lee E., Zhang J. and Kucherlapati R. 2011. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proceedings of the National Academy of Sciences, 108(46): 1128-1136.
Xu L., Hou Y., Bickhart D., Song J. and Liu G. 2013. Comparative analysis of CNV calling algorithms: literature survey and a case study using bovine high-density SNP data. Microarrays, 2(3): 171-185.
Yan J., Blair H. T., Liu M., Li W., He S., Chen L. and Dukkipati V. S. 2017. Genome-wide detection of autosomal copy number variants in several sheep breeds using Illumina OvineSNP50 BeadChips. Small Ruminant Research, 155: 24-32.
Yang L., Xu L., Zhou Y., Liu M., Wang L., Kijas J. W. and Liu G. E. 2018. Diversity of copy number variation in a worldwide population of sheep. Genomics, 110(3): 143-148.
Yeo R. A., Gangestad S. W., Liu J., Calhoun V. D. and Hutchison K. E. 2011. Rare copy number deletions predict individual variation in intelligence. PloS ONE, 6(1): 16339.
Yuan Z., Liu E., Liu Z., Kijas J. W., Zhu C., Hu S. and Wei C. 2017. Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Animal Genetics, 48(1): 55-66.
Zhang F., GU W., Hurles M. E. and Lupski J. R. 2009. Copy number variation in human health, disease, and evolution Annual Review of Genomics and Human Genetics, 10: 451-481.
Zhang X., Du R., Li S., Zhang F., Jin L. and Wang H. 2014. Evaluation of copy number variation detection for a SNP array platform. BMC Bioinformatics, 15(1): 50.
Zhao M., Wang Q., Wang Q., Jia P. and Zhao Z. 2013. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics, 14(11): S1.
Zhu C., Fan H., Yuan Z., Hu S., Ma X., Xuan J. and Zhao F. 2016. Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays. Scientific Reports, 6: 27822.
Animal Production Research
Volume 9, Issue 1
June 2020
Pages 29-44

Files

Share

How to cite

Statistics