Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data

Bioinformatics

Volumn 31, Issue 1, 2015, Pages 116-118

  Chiba, Kenichi ^a   Shiraishi, Yuichi ^a   Nagata, Yasunobu ^b   Yoshida, Kenichi ^b   Imoto, Seiya ^a   Ogawa, Seishi ^b   Miyano, Satoru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CD135 ANTIGEN; FLT3 PROTEIN, HUMAN;

BIOLOGY; EXOME; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; LEUKEMIA, MYELOID, ACUTE; MUTATION; NUCLEOTIDE SEQUENCE; PROCEDURES; TANDEM REPEAT;

COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; EXOME; FMS-LIKE TYROSINE KINASE 3; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA, MYELOID, ACUTE; MUTATION; TANDEM REPEAT SEQUENCES;

EID: 84922374171     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu593     Document Type: Article

References (8)

1. Corbacioglu,S. et al. (2006) Newly identified c-KIT receptor tyrosine kinase ITD in childhood AML induces ligand-independent growth and is responsive to a synergistic effect of imatinib and rapamycin. Blood, 108, 3504-3513.
2. Kindler,T. et al. (2010) FLT3 as a therapeutic target in AML: still challenging after all these years. Blood, 116, 5089-5102.
3. Ley,T.J. et al. (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med., 368, 2059-2074.
4. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics, 25, 1754-1760.
5. Lin,L.I. et al. (2005) Characterization of CEBPA mutations in acute myeloid leukemia: most patients with CEBPA mutations have biallelic mutations and show a distinct immunophenotype of the leukemic cells. Clin. Cancer. Res., 11, 1372-1379.
6. Robinson,J.T. et al. (2011) Integrative genomics viewer. Nat. Biotechnol., 29, 24-26.
7. Shiraishi,Y. et al. (2013) An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res., 41, e89.
8. Ye,K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-2871.