My background is in non-linear Mathematics, in particular mathematical modeling of fluid flow in porous media via numerical simulation, in which I gained my phD. I then moved into Meteorology, spending 7 years working in the computational aspects of modeling UK scale weather events. In 2000 I had a shift in applications area, moving into Cancer Genomics at the Sanger Institute, and spent 7 years working in sequence variant detection. In 2008 I moved into my current position at the Strangeways Research Laboratory where I am an analyst developer in sequence variant detection.
My main area of work is the development of a software pipeline for the automated analysis and variant calling from Next Generation Sequencing (NGS) data. The targeted gene pipeline addresses all aspects of the workflow, from automated primer design and multiplexing, through sequence read demultiplexing and alignment, culminating in variant calling, annotation and verification. Key enhancements of variant calling have been improved raw call filtering resulting in increased sensitivity. Recent advancements include a novel analysis (unpublished) to detect intermediate sized insertions and deletions in targeted gene data. I have also developed an
effective filtering strategy for raw exome data calls, validated by comparison with chip genotypes, and yielding high concordance/sensitivity.
Dicks E, Song H, Ramus S et al. Germline whole exome sequencing and large-scale replication identifies FANCM as a likely high grade serous ovarian cancer susceptibility gene. Submitted to Plos Genetics.
Song H, Cicek MS, Dicks E, et al. The contribution of deleterious germline mutations in BRCA1, BRCA2 and the mismatch repair genes to ovarian cancer in the population. Hum Mol Genet. 2014; 23(17):4703-9.
Song H, Dicks E, Ramus S, et al. Contribution of Germline Mutations in the RAD51B, RAD51C, and RAD51D Genes to Ovarian Cancer in the Population. J Clin Oncol. 2015; In Press.
Pharoah P, Song H, Dicks E, et al. PPM1D mosaic truncating variants in ovarian cancer cases may be treatment related somatic mutations. J Natl Cancer Inst. 2015; In Press.
Ramus S, Song H, Dicks E et al. Mutations In The BRIP1, BARD1, PALB2 And NBN Genes In Women With Ovarian Cancer. J Natl Cancer Inst. 2015; In Press.
Dicks E, Teague JW, Stephens P, Raine K, Yates A, Mattocks C, Tarpey P, Butler A, Menzies A, Richardson D, Jenkinson A, Davies H, Edkins S, Forbes S, Gray K, Greenman C, Shepherd R, Stratton M, Futreal P, Wooster R. AutoCSA, An Algorithm for High Throughput DNA Sequence Variant Detection in Cancer Genomes. Bioinformatics 2007; 23(13):1689-1691. (AutoCSA URL: www.sanger.ac.uk/resources/software/autocsa (link is external) )
Blow M, Grocock R, van Dongen S, Enright A, Dicks E, Futreal P, Wooster R, Stratton M. RNA editing of human microRNAs. Genome Biol. 2006; 7(4):R27.
Davies H, Dicks E, Stephens P, Cox C, Teague J, Greenman C, Bignell G, O’Meara S, Edkins S, Parker A, Stevens C, Menzies A, Blow M, Bottomley B, Dronsfield M, Futreal PA, Stratton MR, Wooster R. High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison. Genomics 2006; 87(3):427-32.