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Cited by 402

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Large multiallelic copy number variations in humans

Handsaker, Robert E, Van Doren, Vanessa, Berman, Jennifer R, Genovese, Giulio, Kashin, Seva, Boettger, Linda M, McCarroll, Steven A·2015·Nature Genetics
DOI 10.1038/ng.3200PMC PMC4405206
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Research works printed but not linked: 36

  1. Bochukova, E.G. et al. Large, rare chromosomal deletions associated with severe early-onset obesity. Nature 463, 666–670 (2010). · DOI · Paper page
  2. McCarroll, S.A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166–1174 (2008). · DOI · Paper page
  3. de Cid, R. et al. Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat. Genet. 41, 211–215 (2009). · DOI
  4. McCarroll, S.A. et al. Donor-recipient mismatch for common gene deletion polymorphisms in graft-versus-host disease. Nat. Genet. 41, 1341–1344 (2009). · DOI
  5. Willer, C.J. et al. Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat. Genet. 41, 25–34 (2009). · DOI · Paper page
  6. McCarroll, S.A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet. 40, 1107–1112 (2008). · DOI · Paper page
  7. Handsaker, R.E., Korn, J.M., Nemesh, J. & McCarroll, S.A. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat. Genet. 43, 269–276 (2011). · DOI
  8. Hollox, E.J., Armour, J.A. & Barber, J.C. Extensive normal copy number variation of a β-defensin antimicrobial-gene cluster. Am. J. Hum. Genet. 73, 591–600 (2003). · DOI
  9. Perry, G.H. et al. Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39, 1256–1260 (2007). · DOI
  10. Perry, G.H. et al. The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet. 82, 685–695 (2008). · DOI
  11. Gu, W., Zhang, F. & Lupski, J.R. Mechanisms for human genomic rearrangements. Pathogenetics 1, 4 (2008). · DOI
  12. Sudmant, P.H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641–646 (2010). · DOI · Paper page
  13. Yoon, S., Xuan, Z., Makarov, V., Ye, K. & Sebat, J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586–1592 (2009). · DOI
  14. 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 Res. 21, 974–984 (2011). · DOI · Paper page
  15. Bellos, E., Johnson, M.R. & Coin, L.J. cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data. Genome Biol. 13, R120 (2012). · DOI
  16. Koren, A. et al. Genetic variation in human DNA replication timing. Cell 159, 1015–1026 (2014). · DOI
  17. Wang, Y., Lu, J., Yu, J., Gibbs, R.A. & Yu, F. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res. 23, 833–842 (2013). · DOI
  18. DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011). · DOI
  19. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011). · DOI
  20. Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333–i339 (2012). · DOI
  21. Boettger, L.M., Handsaker, R.E., Zody, M.C. & McCarroll, S.A. Structural haplotypes and recent evolution of the human 17q21.31 region. Nat. Genet. 44, 881–885 (2012). · DOI
  22. Su, S.Y. et al. Inferring combined CNV/SNP haplotypes from genotype data. Bioinformatics 26, 1437–1445 (2010). · DOI
  23. Kato, M., Nakamura, Y. & Tsunoda, T. An algorithm for inferring complex haplotypes in a region of copy-number variation. Am. J. Hum. Genet. 83, 157–169 (2008). · DOI
  24. Assaad, F.F., Tucker, K.L. & Signer, E.R. Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Mol. Biol. 22, 1067–1085 (1993). · DOI
  25. Dorer, D.R. & Henikoff, S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 77, 993–1002 (1994). · DOI
  26. Dorer, D.R. & Henikoff, S. Transgene repeat arrays interact with distant heterochromatin and cause silencing in cis and trans. Genetics 147, 1181–1190 (1997). · DOI
  27. Abu Bakar, S., Hollox, E.J. & Armour, J.A. Allelic recombination between distinct genomic locations generates copy number diversity in human β-defensins. Proc. Natl. Acad. Sci. USA 106, 853–858 (2009). · DOI
  28. Dennis, M.Y. et al. Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149, 912–922 (2012). · DOI · Paper page
  29. Smith, A.B., Esko, J.D. & Hajduk, S.L. Killing of trypanosomes by the human haptoglobin-related protein. Science 268, 284–286 (1995). · DOI
  30. Harrington, J.M., Howell, S. & Hajduk, S.L. Membrane permeabilization by trypanosome lytic factor, a cytolytic human high density lipoprotein. J. Biol. Chem. 284, 13505–13512 (2009). · DOI
  31. Genovese, G. et al. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 329, 841–845 (2010). · DOI · Paper page
  32. Genovese, G., Friedman, D.J. & Pollak, M.R. APOL1 variants and kidney disease in people of recent African ancestry. Nat. Rev. Nephrol. 9, 240–244 (2013). · DOI
  33. Moffatt, M.F. et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448, 470–473 (2007). · DOI
  34. Zanda, M. et al. A genome-wide assessment of the role of untagged copy number variants in type 1 diabetes. PLoS Genet. 10, e1004367 (2014). · DOI
  35. Hollox, E.J. et al. Psoriasis is associated with increased β-defensin genomic copy number. Nat. Genet. 40, 23–25 (2008). · DOI
  36. Steinberg, K.M. et al. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nat. Genet. 44, 872–880 (2012). · DOI

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Metadata

Authors
Handsaker, R. E., Van Doren, V., Berman, J. R., Genovese, G., Kashin, S., Boettger, L. M., & McCarroll, S. A.
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2015-01-26
Volume
47
Issue
3
Pages
296-303
ISSN
  • 1061-4036
  • 1546-1718
DOI
10.1038/ng.3200
PMC
PMC4405206
Cited by
402
References
17
Language
en
Licence
www.springer.com/tdm (tdm)

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CoChat. (2026). Citation check: Large multiallelic copy number variations in humans. https://app.cochat.ai/papers/10.1038/ng.3200
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Handsaker, R. E., Van Doren, V., Berman, J. R., Genovese, G., Kashin, S., Boettger, L. M., & McCarroll, S. A. (2015). Large multiallelic copy number variations in humans. Nature Genetics. https://doi.org/10.1038/ng.3200