Publications by authors named "Stephen Espy"

2 Publications

  • Page 1 of 1

CONSERTING: integrating copy-number analysis with structural-variation detection.

Nat Methods 2015 Jun 4;12(6):527-30. Epub 2015 May 4.

1] Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. [2] Pediatric Cancer Genome Project, St. Jude Children's Research Hospital and Washington University School of Medicine, Memphis, Tennessee, USA.

We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), an algorithm for detecting somatic copy-number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation on the basis of changes in read depth and the detection of localized structural variations, with high accuracy and sensitivity. Analysis of 43 cancer genomes from both pediatric and adult patients revealed novel oncogenic CNAs, complex rearrangements and subclonal CNAs missed by alternative approaches.
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http://dx.doi.org/10.1038/nmeth.3394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4591043PMC
June 2015

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia.

Nature 2012 Jan 11;481(7380):157-63. Epub 2012 Jan 11.

Department of Computational Biology and Bioinformatics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.

Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.
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http://dx.doi.org/10.1038/nature10725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3267575PMC
January 2012