Clinical detection of deletion structural variants in whole-genome sequences

npj Genomic Medicine

Volumn 1, Issue , 2016, Pages

  Noll, Aaron C ^a,b,c   Miller, Neil A ^a   Smith, Laurie D ^a,b,d   Yoo, Byunggil ^a   Fiedler, Stephanie ^c   Cooley, Linda D ^c,d   Willig, Laurel K ^a,c,d   Petrikin, Josh E ^a,c,d   Cakici, Julie ^e   Lesko, John ^a   Newton, Angela ^a   Detherage, Kali ^a   Thiffault, Isabelle ^a,c,d   Saunders, Carol J ^a,c,d   Farrow, Emily G ^a,c,d   Kingsmore, Stephen F ^b,e  

^a Center for Pediatric Genomic Medicine   (United States)

^b UNIVERSITY OF KANSAS MEDICAL CENTER   (United States)

^c University of Missouri Kansas City ^*  (United States)

^d UNIVERSITY OF MISSOURI KANSAS CITY SCHOOL OF MEDICINE   (United States)

^e RADY CHILDREN S INSTITUTE FOR GENOMIC MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85017031375     PISSN: None     EISSN: 20567944     Source Type: Journal    
DOI: 10.1038/npjgenmed.2016.26     Document Type: Article

References (62)

1. McCandless, S. E., Brunger, J. W. & Cassidy, S. B. The burden of genetic disease on inpatient care in a children's hospital. Am. J. Hum. Genet. 74, 121-127 (2004).
2. Dye, D. E. et al. The impact of single gene and chromosomal disorders on hospital admissions of children and adolescents: A population-based study. Public Health Genomics 14, 153-161 (2011).
3. Kumar, P., Radhakrishnan, J., Chowdhary, M. A. & Giampietro, P. F. Prevalence and patterns of presentation of genetic disorders in a pediatric emergency department. Mayo Clin. Proc. 76, 777-783 (2001).
4. Lander, E. S. Initial impact of the sequencing of the human genome. Nature 470, 187-197 (2011).
5. Hauck, F. R., Tanabe, K. O. & Moon, R. Y. Racial and ethnic disparities in infant mortality. Semin. Perinatol. 35, 209-220 (2011).
6. Lynberg, M. C. & Khoury, M. J. Contribution of birth defects to infant mortality among racial/ethnic minority groups United States 1983. MMWR CDC Surveill. Summ. 39, 1-12 (1990).
7. Kochanek, K. D., Kirmeyer, S. E., Martin, J. A., Strobino, D. M. & Guyer, B. Annual summary of vital statistics: 2009. Pediatrics 129, 338-348 (2012).
8. Saunders, C. J. et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci. Transl. Med. 4, 154ra135 (2012).
9. Willig, L. K. et al. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: A retrospective analysis of diagnostic and clinical findings. Lancet Respir. Med. 3, 377-387 (2015).
10. Soden, S. E. et al. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci. Transl. Med. 6, 265ra168 (2014).
11. Lu, X. Y. et al. Genomic imbalances in neonates with birth defects: high detection rates by using chromosomal microarray analysis. Pediatrics 122, 1310-1318 (2008).
12. Buchanan, J. A. & Scherer, S. W. Contemplating effects of genomic structural variation. Genet. Med. 10, 639-647 (2008).
13. Park, H. et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat. Genet. 42, 400-405 (2010).
14. Abecasis, G. R. et al. An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65 (2012).
15. Zhang, F., Gu, W., Hurles, M. E. & Lupski, J. R. Copy number variation in human health disease and evolution. Annu. Rev. Genomics Hum. Genet. 10, 451-481 (2009).
16. Gonzaga-Jauregui, C., Lupski, J. R. & Gibbs, R. A. Human genome sequencing in health and disease. Annu. Rev. Med. 63, 35-61 (2012).
17. Kondrashov, A. S. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Hum. Mutat. 21, 12-27 (2003).
18. Park, J. H., Lee, S., Yu, H. G., Kim, J. I. & Seo, J. S. Copy number variation of age-related macular degeneration relevant genes in the Korean population. PLoS ONE 7, e31243 (2012).
19. Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38, 75-81 (2006).
20. Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl Acad. Sci. USA 104, 20007-20012 (2007).
21. Wood, L. D. et al. The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-1113 (2007).
22. Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2010).
23. Lupski, J. R. Genomic rearrangements and sporadic disease. Nat. Genet. 39, S43-S47 (2007).
24. Turner, D. J. et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat. Genet. 40, 90-95 (2008).
25. Zhang, F., Gu, W., Hurles, M. E. & Lupski, J. R. Copy number variation in human health, disease, and evolution. Annu. Rev. Genomics Hum. Genet. 10, 451-481 (2009).
26. Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007).
27. International Schizophrenia Consortium. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature 455, 237-241 (2008).
28. Cooper, G. M., Zerr, T., Kidd, J. M., Eichler, E. E. & Nickerson, D. A. Systematic assessment of copy number variant detection via genome-wide SNP genotyping. Nat. Genet. 40, 1199-1203 (2008).
29. Alkan, C., Coe, B. P. & Eichler, E. E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363-376 (2011).
30. Teo, S. M., Pawitan, Y., Ku, C. S., Chia, K. S. & Salim, A. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics 28, 2711-2718 (2012).
31. 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).
32. Li, H. et al. Genome Project Data Processing. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
33. Zhao, M., Wang, Q., Wang, Q., Jia, P. & Zhao, Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 14, S1 (2013).
34. Miller, N. A. et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med. 7, 100 (2015).
35. International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007).
36. Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010).
37. Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246-251 (2014).
38. Lehmann, C. et al. Application and comparison of classification algorithms for recognition of Alzheimer's disease in electrical brain activity (EEG). J. Neurosci. Methods 161, 342-350 (2007).
39. Maroco, J. et al. Data mining methods in the prediction of Dementia: A real-data comparison of the accuracy sensitivity and specificity of linear discriminant analysis logistic regression neural networks support vector machines classification trees and random forests. BMC Res. Notes 4, 299 (2011).
40. Mills, R. E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65 (2011).
41. Layer, R. M., Chiang, C., Quinlan, A. R. & Hall, I. M. LUMPY: A probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).
42. Spies, N., Zook, J. M., Salit, M. & Sidow, A. Svviz: A read viewer for validating structural variants. Bioinformatics 31, 3994-3996 (2015).
43. Marchenko, G. N., Marchenko, N. D. & Strongin, A. Y. The structure and regulation of the human and mouse matrix metalloproteinase-21 gene and protein. Biochem. J. 372, 503-515 (2003).
44. Guimier, A. et al. MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates. Nat Genet. 47, 1260-1263 (2015).
45. Kang, S. H. et al. Identification of proximal 1p36 deletions using array-CGH: A possible new syndrome. Clin. Genet. 72, 329-338 (2007).
46. Rudnik-Schöneborn, S. et al. A new case of proximal monosomy 1p36 extending the phenotype. Am. J. Med. Genet. A 146A, 2891-2897 (2008).
47. Shimojima, K., Páez, M. T., Kurosawa, K. & Yamamoto, T. The most proximal microdeletion identified on a dysmorphic and mentally retarded patient with inv (3)(p14.1q26.2). Brain Dev. 31, 629-633 (2009).
48. Rosenfeld, J. A. et al. Refinement of causative genes in monosomy 1p36 through clinical and molecular cytogenetic characterization of small interstitial deletions. Am. J. Med. Genet. A 152A, 1951-1959 (2010).
49. Nicoulaz, A. et al. Contiguous ~ 16 Mb 1p36 deletion: Dominant features of classical distal 1p36 monosomy with haplo-lethality. Am. J. Med. Genet. A 155A, 1964-1968 (2011).
50. McKenna, A. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
51. Trask, B. J. et al. Large multi-chromosomal duplications encompass many members of the olfactory receptor gene family in the human genome. Hum. Mol. Genet. 7, 2007-2020 (1998).
52. Köhler, S. et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42, D966-D974 (2014).
53. Wu, T. D. & Nacu, S. Fast and SNP-Tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
54. Quinlan, A. R. & Hall, I. M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
55. Valsesia, A., Mace, A., Jacquemont, S., Beckmann, J. S. & Kutalik, Z. The growing importance of CNVs: new insights for detection and clinical interpretation. Front. Genet. 4, 92 (2013).
56. Zhang D. et al. Accuracy of CNV detection from GWAS data. PLoS ONE 2011; 6: E14511.
57. Sudmant, P. H. et al. An integrated map of structural variation in 2, 504 human genomes. Nature 526, 75-81 (2015).
58. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
59. Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0. Available at http://www.repeatmasker.org. Accessed on 1 February 2016.
60. Benson, G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580 (1999).
61. Morgulis, A., Gertz, E. M., Schaffer, A. A. & Agarwala, R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 13, 1028-1040 (2006).
62. Flicek, P. et al. Ensembl 2014. Nucleic Acids Res. 42, D749-D755 (2014).