References
- Jones LK, Saha V. Philadelphia positive acute lymphoblastic leukemia of childhood. Br J Haematol. 2005;130:489–500.
- Fielding AK, Rowe JM, Richards SM, et al. Prospective outcome data on 267 unselected adult patients with Philadelphia chromosome-positive acute lymphoblastic leukemia confirms superiority of allogeneic transplantation over chemotherapy in the pre-imatinib era: results from the International ALL Trial MRC UKALLXII/ECOG2993. Blood. 2009;113:4489–4496.
- Schultz KR, Bowman WP, Aledo A, et al. Improved early event-free survival with imatinib in Philadelphia chromosome-positive acute lymphoblastic leukemia: a children’s oncology group study. J Clin Oncol. 2009;27:5175–5181.
- Mullighan CG, Su X, Zhang J, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009;360:470–480.
- Den Boer ML, van Slegtenhorst M, De Menezes RX, et al. A subtype of childhood acute lymphoblastic leukemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol. 2009;10:125–134.
- Roberts KG, Li Y, Payne-Turner D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371:1005–1015.
- Roberts K, Payne-Turner D, McCastlain KK, et al. High frequency and poor outcome of Ph-like acute lymphoblastic leukemia in adults. Blood. 2015;126:2618.
- Roberts KG, Morin RD, Zhang J, et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012;22:153–166.
- Lengline E, Beldjord K, Dombret H, et al. Successful tyrosine kinase inhibitor therapy in a refractory B-cell precursor acute lymphoblastic leukemia with EBF1-PDGFRB fusion. Haematologica. 2013;98:e146–e148.
- Weston BW, Hayden MA, Roberts KG, et al. Tyrosine kinase inhibitor therapy induces remission in a patient with refractory EBF1-PDGFRB-positive acute lymphoblastic leukemia. J Clin Oncol. 2013;31:e413–e416.
- Mustjoki S, Hernesniemi S, Rauhala A, et al. A novel dasatinib-sensitive RCSD1-ABL1 fusion transcript in chemotherapy-refractory adult pre-B lymphoblastic leukemia with t(1;9)(q24;q34). Haematologica. 2009;94:1469–1471.
- Maher CA, Kumar-Sinha C, Cao X, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009;458:97–101.
- Zheng Z, Liebers M, Zhelyazkova B, et al. Anchored multiplex PCR for targeted next-generation sequencing. Nat Med. 2014;20:1479–1484.
- Zhao Q, Caballero OL, Levy S, et al. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci USA. 2009;106:1886–1891.
- Kamran S, Raca G, Nazir K. RCSD1-ABL1 translocation associated with IKZF1 gene deletion in B-cell acute lymphoblastic leukemia. Case Rep Hematol. 2015;2015:353247.
- Raca G, Gurbuxani S, Zhang Z, et al. RCSD1-ABL2 fusion resulting from a complex chromosomal rearrangement in high-risk B-cell acute lymphoblastic leukemia. Leuk Lymphoma. 2015;56:1145–1147.
- Nicorici D, Satalan M, Edgren H, et al. FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data. bioRxiv. 2014; doi: http://dx.doi.org/10.1101/011650.
- Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
- McKenna A, Hanna M, Banks E, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–1303.
- DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–498.
- Van der Auwera GA, Carneiro MO, Hartl C, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1-33.
- Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015;10:1556–1566.
- Lek M, Karczewski K, Minikel E, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–291.
- Tennessen JA, Bigham AW, O’Connor TD, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012;337:64–69.
- Abecasis GR, Auton A, Genomes Project C, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56–65.
- Sherry ST, Ward MH, Kholodov M, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–311.
- Chiaretti S, Brugnoletti F, Messina M, et al. CRLF2 overexpression identifies an unfavorable subgroup of adult B-cell precursor acute lymphoblastic leukemia lacking recurrent genetic abnormalities. Leuk Res. 2016;41:36–42.
- Harvey RC, Kang H, Roberts KG, et al. Development and validation of a highly sensitive and specific gene expression classifier to prospectively screen and identify B-precursor acute lymphoblastic leukemia (ALL) patients with a Philadelphia chromosome-like (“Ph-like” or “BCR-ABL1-Like”) signature for therapeutic targeting and clinical intervention. Blood. 2013;122:826.
- Stransky N, Cerami E, Schalm S, et al. The landscape of kinase fusions in cancer. Nat Commun. 2014;5:4846.
- Stadt UZ, Escherich G, Indenbirken D, et al. Rapid capture next-generation sequencing in clinical diagnostics of kinase pathway aberrations in B-cell precursor ALL. Pediatr Blood Cancer. 2016;63:1283–1286.
- Moorman AV, Schwab C, Ensor HM, et al. IGH@ translocations, CRLF2 deregulation, and microdeletions in adolescents and adults with acute lymphoblastic leukemia. J Clin Oncol. 2012;30:3100–3108.
- Russell LJ, Capasso M, Vater I, et al. Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia. Blood. 2009;114:2688–2698.
- Piskol R, Ramaswami G, Li JB. Reliable identification of genomic variants from RNA-seq data. Am J Hum Genet. 2013;93:641–651.
- Cirulli ET, Singh A, Shianna KV, et al. Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol. 2010;11:R57.
- Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127:2391–2405.