A gradient-boosting approach for filtering de novo mutations in parent-offspring trios

Bioinformatics

Volumn 30, Issue 13, 2014, Pages 1830-1836

  Liu, Yongzhuang ^a,b   Li, Bingshan ^c   Tan, Renjie ^a,b   Zhu, Xiaolin ^b   Wang, Yadong ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b DUKE UNIVERSITY   (United States)

^c VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTIFICIAL INTELLIGENCE; COMPUTER PROGRAM; EXOME; FEMALE; GENOME; HUMAN; MUTATION;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; EXOME; FEMALE; GENOME; HUMANS; MUTATION; SOFTWARE;

EID: 84903708021     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu141     Document Type: Article

References (31)

1. Breiman, L. (2001) Random forests. Mach. Learn., 45, 5-32
2. Challis, D. et al. (2012) An integrative variant analysis suite for whole exome nextgeneration sequencing data. BMC Bioinform., 13, 8
3. Chiara, M. et al. (2012) SVM2: An improved paired-end-based tool for the detection of small genomic structural variations using high-Throughput single-genome resequencing data. Nucleic Acids Res., 40, e145
4. Chipman, H.A. et al. (2010) Bart: Bayesian additive regression trees. Ann. Appl. Stat., 4, 266-298
5. Conrad, D.F. et al. (2011) Variation in genome-wide mutation rates within and between human families. Nature genetics, 43, 712-714
6. de Ligt, J. et al. (2012) Diagnostic exome sequencing in persons with severe intellectual disability. New England J. Med., 367, 1921-1929
7. DePristo, M.A. et al. (2011) A framework for variation Discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498
8. Ding, J. et al. (2012) Feature-based classifiers for somatic mutation Detection in tumour-normal paired sequencing data. Bioinformatics, 28, 167-175
9. Epi4K Consortium & Epilepsy Phenome/Genome Project. (2013) De novo mutations in epileptic encephalopathies. Nature, 501, 217-221
10. Friedman, J.H. (2001) Greedy function approximation: A gradient boosting machine. Ann. Stat., 29, 1189-1232
11. Friedman, J.H. (2002) Stochastic gradient boosting. Comput. Stat. Data An., 38, 367-378
12. Girard, S.L. et al. (2011) Increased exonic de novo mutation rate in individuals with schizophrenia. Nat. Genet., 43, 860-863
13. Hastie, T. et al. (2009) The Elements of Statistical Learnin. Springer, New York
14. Koboldt, D.C. et al. (2012) VarScan 2: Somatic mutation and copy number alteration Discovery in cancer by exome sequencing. Genome Res., 22, 568-576
15. Le, S.Q. and Durbin, R. (2011) SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res., 21, 952-960
16. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760
17. Li, B. et al. (2012) A likelihood-based framework for variant calling and de novo mutation Detection in families. PLoS Genet., 8, e1002944
18. Meacham, F. et al. (2011) Identification and correction of systematic error in highthroughput sequence data. BMC Bioinform., 12, 451
19. Michaelson, J.J. and Sebat, J. (2012) forestSV: Structural variant discovery through statistical learning. Nat. Methods, 9, 819-821
20. Michaelson, J.J. et al. (2012) Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell, 151, 1431-1442
21. Neale, B.M. et al. (2012) Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature, 485, 242-245
22. Nielsen, R. et al. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451
23. O'Fallon, B.D. et al. (2013) A support vector machine for identification of singlenucleotide polymorphisms from next-generation sequencing data. Bioinformatics, 29, 1361-1366
24. O'Roak, B.J. et al. (2012) Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature, 485, 246-250
25. Ramu, A. et al. (2013) DeNovoGear: De novo indel and point mutation Discovery and phasing. Nat. Methods, 10, 985-987
26. Robinson, J.T. et al. (2011) Integrative genomics viewer. Nat. Biotechnol., 29, 24-26
27. Rauch, A. et al. (2012) Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: An exome sequencing study. Lancet, 380, 1674-1682
28. Sanders, S.J. et al. (2012) De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature, 485, 237-241
29. Veltman, J.A. and Brunner, H.G. (2012) De novo mutations in human genetic disease. Nat. Rev. Genet., 13, 565-575
30. Xu, B. et al. (2012) De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat. Genet., 44, 1365-1369
31. Xu, B. et al. (2011) Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat. Genet., 43, 864-868.