Dwarf koa (Desmanthus virgatus)

This is the final version. It was first published by BioMed Central at http://www.biomedcentral.com/1471-2164/16/473.Background: Mobile elements are active in the human genome, both in the germline and cancers, where they can\ud mutate driver genes.\ud Results: While analysing whole genome paired-end sequencing of oesophageal adenocarcinomas to find genomic\ud rearrangements, we identified three ways in which new mobile element insertions appear in the data, resembling\ud translocation or insertion junctions: inserts where unique sequence has been transduced by an L1 (Long interspersed\ud element 1) mobile element; novel inserts that are confidently, but often incorrectly, mapped by alignment software to\ud L1s or polyA tracts in the reference sequence; and a combination of these two ways, where different sequences within\ud one insert are mapped to different loci. We identified nine unique sequences that were transduced by neighbouring\ud L1s, both L1s in the reference genome and L1s not present in the reference. Many of the resulting inserts were small\ud fragments that include little or no recognisable mobile element sequence. We found 6 loci in the reference genome to\ud which sequence reads from inserts were frequently mapped, probably erroneously, by alignment software: these were\ud either L1 sequence or particularly long polyA runs. Inserts identified from such apparent rearrangement junctions\ud averaged 16 inserts/tumour, range 0?153 insertions in 43 tumours. However, many inserts would not be detected by\ud mapping the sequences to the reference genome, because they do not include sufficient mappable sequence. To\ud estimate total somatic inserts we searched for polyA sequences that were not present in the matched normal or other\ud normals from the same tumour batch, and were not associated with known polymorphisms. Samples of these candidate\ud inserts were verified by sequencing across them or manual inspection of surrounding reads: at least 85 % were somatic\ud and resembled L1-mediated events, most including L1Hs sequence. Approximately 100 such inserts were detected per\ud tumour on average (range zero to approximately 700).\ud Conclusions: Somatic mobile elements insertions are abundant in these tumours, with over 75 % of cases having a\ud number of novel inserts detected. The inserts create a variety of problems for the interpretation of paired-end\ud sequencing data.Funding\ud was primarily from Cancer Research UK program grants to RCF and ST\ud (C14478/A15874 and C14303/A17197), with additional support awarded to\ud RCF from UK Medical Research Council, NHS National Institute for Health\ud Research (NIHR), the Experimental Cancer Medicine Centre Network and\ud the NIHR Cambridge Biomedical Research Centre, and Cancer Research UK\ud Project grant C1023/A14545 to PAWE. JMJW was funded by a Wellcome\ud Trust Translational Medicine and Therapeutics grant

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A

Despite the approval of numerous molecular targeted drugs, long-term antiproliferative efficacy is rarely achieved and therapy resistance remains a central obstacle of cancer care. Combined inhibition of multiple cancer-driving pathways promises to improve antiproliferative efficacy. HIF-1 is a driver of gastric cancer and considered to be an attractive target for therapy. We noted that gastric cancer cells are able to functionally compensate the stable loss of HIF-1α. Via transcriptomics we identified a group of upregulated genes in HIF-1α-deficient cells and hypothesized that these genes confer survival upon HIF-1α loss. Strikingly, simultaneous knock-down of HIF-1α and Annexin A1 (ANXA1), one of the identified genes, resulted in complete cessation of proliferation. Using stable isotope-resolved metabolomics, oxidative and reductive glutamine metabolism was found to be significantly impaired in HIF-1α/ANXA1-deficient cells, potentially explaining the proliferation defect. In summary, we present a conceptually novel application of stable gene inactivation enabling in-depth deconstruction of resistance mechanisms. In theory, this experimental approach is applicable to any cancer-driving gene or pathway and promises to identify various new targets for combination therapies

Genomic mapping by anchoring random clones: a mathematical analysis

A complete physical map of the DNA of an organism, consisting of overlapping clones spanning the genome, is an extremely useful tool for genomic analysis. Various methods for the construction of such physical maps are available. One approach is to assemble the physical map by “fingerprinting” a large number of random clones and inferring overlap between clones with sufficiently similar fingerprints. E. S. Lander and M. S. Waterman (1988, Ge-nomic ~ 2:231-239) have recently provided a mathematical analysis of such physical mapping schemes, useful for planning such a project. Another approach is to assemble the physical map by “anchoring ” a large number of random clones-that is, by taking random short regions called anchors and identifying the clones containing each anchor. Here, we provide a mathematical analysis of such a physical mapping scheme. Q lee1 Academic Press, Ino. 1

Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis

This is the final version. It was first published by BioMed Central at http://www.biomedcentral.com/1471-2164/16/473.Background: Mobile elements are active in the human genome, both in the germline and cancers, where they can\ud mutate driver genes.\ud Results: While analysing whole genome paired-end sequencing of oesophageal adenocarcinomas to find genomic\ud rearrangements, we identified three ways in which new mobile element insertions appear in the data, resembling\ud translocation or insertion junctions: inserts where unique sequence has been transduced by an L1 (Long interspersed\ud element 1) mobile element; novel inserts that are confidently, but often incorrectly, mapped by alignment software to\ud L1s or polyA tracts in the reference sequence; and a combination of these two ways, where different sequences within\ud one insert are mapped to different loci. We identified nine unique sequences that were transduced by neighbouring\ud L1s, both L1s in the reference genome and L1s not present in the reference. Many of the resulting inserts were small\ud fragments that include little or no recognisable mobile element sequence. We found 6 loci in the reference genome to\ud which sequence reads from inserts were frequently mapped, probably erroneously, by alignment software: these were\ud either L1 sequence or particularly long polyA runs. Inserts identified from such apparent rearrangement junctions\ud averaged 16 inserts/tumour, range 0?153 insertions in 43 tumours. However, many inserts would not be detected by\ud mapping the sequences to the reference genome, because they do not include sufficient mappable sequence. To\ud estimate total somatic inserts we searched for polyA sequences that were not present in the matched normal or other\ud normals from the same tumour batch, and were not associated with known polymorphisms. Samples of these candidate\ud inserts were verified by sequencing across them or manual inspection of surrounding reads: at least 85 % were somatic\ud and resembled L1-mediated events, most including L1Hs sequence. Approximately 100 such inserts were detected per\ud tumour on average (range zero to approximately 700).\ud Conclusions: Somatic mobile elements insertions are abundant in these tumours, with over 75 % of cases having a\ud number of novel inserts detected. The inserts create a variety of problems for the interpretation of paired-end\ud sequencing data.Funding\ud was primarily from Cancer Research UK program grants to RCF and ST\ud (C14478/A15874 and C14303/A17197), with additional support awarded to\ud RCF from UK Medical Research Council, NHS National Institute for Health\ud Research (NIHR), the Experimental Cancer Medicine Centre Network and\ud the NIHR Cambridge Biomedical Research Centre, and Cancer Research UK\ud Project grant C1023/A14545 to PAWE. JMJW was funded by a Wellcome\ud Trust Translational Medicine and Therapeutics grant