The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants
Open accessAbstract
We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.
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Cites
A map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877
The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Global variation in copy number in the human genome
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., et al. (2006) · Nature · doi:10.1038/nature05329 · Cited by 4,288
Self-citationDetection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
Self-citationMiller, D. T., Adam, M. P., Aradhya, S., Biesecker, L. G., Brothman, A. R., Carter, N. P., Church, D. M., Crolla, J. A., Eichler, E. E., Epstein, C. J., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.006 · Cited by 2,882
Self-citationLarge-scale copy number polymorphism in the human genome
Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., et al. (2004) · Science · doi:10.1126/science.1098918 · Cited by 2,557
Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W.-L., Chen, C., Zhai, Y., et al. (1998) · Nature Genetics · doi:10.1038/2524 · Cited by 2,240
Tackling the widespread and critical impact of batch effects in high-throughput data
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K., & Irizarry, R. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2825 · Cited by 2,196
Functional impact of global rare copy number variation in autism spectrum disorders
Pinto, D., Pagnamenta, A. T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T. R., Correia, C., Abrahams, B. S., et al. (2010) · Nature · doi:10.1038/nature09146 · Cited by 2,013 · cited 1×
“and analysis of data from genome-wide association studie”
MethodSelf-citationOrigins and functional impact of copy number variation in the human genome
The Wellcome Trust Case Control Consortium, Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T. D., Barnes, C., et al. (2010) · Nature · doi:10.1038/nature08516 · Cited by 1,970
Self-citation
Cited by
Convergence of genes and cellular pathways dysregulated in autism spectrum disorders
Pinto, D., Delaby, E., Merico, D., Barbosa, M., Merikangas, A., Klei, L., Thiruvahindrapuram, B., Xu, X., Ziman, R., Wang, Z., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.03.018 · Cited by 969
Self-citationA copy number variation map of the human genome
Zarrei, M., MacDonald, J. R., Merico, D., & Scherer, S. W. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3871 · Cited by 921
Self-citationKirov, G., Pocklington, A. J., Holmans, P., Ivanov, D., Ikeda, M., Ruderfer, D., Moran, J., Chambert, K., Toncheva, D., Georgieva, L., et al. (2012) · Molecular Psychiatry · doi:10.1038/mp.2011.154 · Cited by 844
“28 However, relative enrichment for de novos among cases was similar for large de novos > 500 kb (2.1% vs 0.8%, P = 0.0014) as it was for small de novos 200 kb (2.3% vs 0.9%, P = 0.0035), and the overall size distribution of case de novos was not shifted towards smaller CNVs (Figure 2 and…”
MethodResultInfluentialSoldner, F., Laganière, J., Cheng, A. W., Hockemeyer, D., Gao, Q., Alagappan, R., Khurana, V., Golbe, L. I., Myers, R. H., Lindquist, S., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.019 · Cited by 728
Fu, J. M., Satterstrom, F. K., Peng, M., Brand, H., Collins, R. L., Dong, S., Wamsley, B., Klei, L., Wang, L., Hao, S. P., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01104-0 · Cited by 640
Self-citation
Metadata
- Authors
- Pinto, D., Darvishi, K., Shi, X., Rajan, D., Rigler, D., Fitzgerald, T., Lionel, A. C., Thiruvahindrapuram, B., MacDonald, J. R., Mills, R., Prasad, A., Noonan, K., Gribble, S., Prigmore, E., Donahoe, P. K., Smith, R. S., Park, J. H., Hurles, M. E., Carter, N. P., Lee, C., Scherer, S. W., & Feuk, L.
- Venue
- Nature Biotechnology
- Published
- 2011-05-08
- Volume
- 29
- Issue
- 6
- Pages
- 512-520
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2044823121
- Cited by
- 403
- References
- 48
- FWCI
- 28.69
- Type
- journal article
- Language
- en
- Open access
- green
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- Pinto, D., Darvishi, K., Shi, X., Rajan, D., Rigler, D., Fitzgerald, T., Lionel, A. C., Thiruvahindrapuram, B., MacDonald, J. R., Mills, R., Prasad, A., Noonan, K., Gribble, S., Prigmore, E., Donahoe, P. K., Smith, R. S., Park, J. H., Hurles, M. E., Carter, N. P., . . . Feuk, L. (2011). Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nature Biotechnology. https://doi.org/10.1038/nbt.1852
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