Cypiripi: Exact genotyping of CYP2D6 using high-throughput sequencing data

Bioinformatics

Volumn 31, Issue 12, 2015, Pages i27-i34

  Numanagić, Ibrahim ^a   Malikić, Salem ^a   Pratt, Victoria M ^b   Skaar, Todd C ^b   Flockhart, David A ^b   Sahinalp, S Cenk ^a,c  

^a SIMON FRASER UNIVERSITY   (Canada)

^b INDIANA UNIVERSITY   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450 2D6;

ALLELE; CLASSIFICATION; COMPUTER PROGRAM; COPY NUMBER VARIATION; GENETIC POLYMORPHISM; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; PROCEDURES; PSEUDOGENE;

ALLELES; CYTOCHROME P-450 CYP2D6; DNA COPY NUMBER VARIATIONS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMORPHISM, GENETIC; PSEUDOGENES; SOFTWARE;

EID: 84931074003     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv232     Document Type: Conference Paper

References (18)

1. Genomes Project Consortium (2012) An integrated map of genetic variation from 1 092 human genomes. Nature, 491, 56-65
2. Alkan C., et al. (2009). Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-1067
3. Cavallari L.H. (2012). Tailoring drug therapy based on genotype. J. Pharm. Pract., 25, 413-416
4. Fang H., et al. (2014). Establishment of cyp2d6 reference samples by multiple validated genotyping platforms. Pharmacogenomics J., 14, 564-572
5. Gaedigk A., et al. (2007). The cyp2d6 activity score: translating genotype information into a qualitative measure of phenotype. Clin. Pharmacol. Ther., 83, 234-242
6. Gaedigk A., et al. (2010). Identification of novel cyp2d7-2d6 hybrids: non-functional and functional variants. Front. Pharmacol., 1, 121
7. Green R.C., et al. (2013). Clinical genome sequencing. Genomic Personalized Med., 1-2, 102-122
8. Hach F., et al. (2010). mrsfast: a cache-oblivious algorithm for short-read mapping. Nat. Methods, 7, 576-577
9. Hach F., et al. (2014). mrsfast-ultra: a compact, SNP-aware mapper for high performance sequencing applications. Nucleic Acids Res., 42, W494-W500
10. Ingelman-Sundberg M. (2004). Genetic polymorphisms of cytochrome p450 2d6 (cyp2d6): clinical consequences, evolutionary aspects and functional diversity. Pharmacogenomics J., 5, 6-13
11. Kent W.J. (2002). Blatthe blast-like alignment tool. Genome Res., 12, 656-664
12. Kimura S., et al. (1989). The human debrisoquine 4-hydroxylase (cyp2d) locus: sequence and identification of the polymorphic cyp2d6 gene, a related gene, and a pseudogene. Am. J. Hum. Genet., 45, 889
13. Kramer W.E., et al. (2009). Cyp2d6: novel genomic structures and alleles. Pharmacogenet. Genomics, 19, 813
14. Larkin M.A., et al. (2007). Clustal w and clustal x version 2.0. Bioinformatics, 23, 2947-2948
15. Ma Q. and Lu A.Y. (2011). Pharmacogenetics, pharmacogenomics, and individualized medicine. Pharmacol. Rev., 63, 437-459
16. Pratt V.M., et al. (2010). Characterization of 107 genomic DNA reference materials for CYP2D6, CYP2C19, CYP2C9, VKORC1, and UGT1A1: a GeT-RM and association for molecular pathology collaborative project. J. Mol. Diagn., 12, 835-846
17. Zhou S.-F. (2009). Polymorphism of human cytochrome p450 2d6 and its clinical significance. Clin. Pharmacokinet., 48, 761-804
18. Zook J.M., et al. (2014). Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotech., 32, 246-251