{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["Illumina HiSeq 2000"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000852"],"host":["EGA"],"description":["EGA study EGAS00001000852"],"dataset_title":["Benchmark and validation of whole exome sequencing of a trio and singleton for mobile element detection."],"repository":["EGA"],"category":["restricted"],"pubmed_abstract":["Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rateand high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster."],"pubmed_title":["Mobster: accurate detection of mobile element  insertions in next generation sequencing data."],"pubmed_authors":["Thung Djie Tjwan DT, de Ligt Joep J, Vissers Lisenka E M LE, Steehouwer Marloes M, Kroon Mark M, de Vries Petra P, Slagboom Eline P EP, Ye Kai K, Veltman Joris A JA, Hehir-Kwa Jayne Y JY"],"description_synonyms":["whole exome, TRIO, BamF, bim, biml, Edg, BamC, M89, bam, CG9208, 1386/06, aligned to, ham, paired-end tag (PET) library, BOD, aligned, UNC-73/Trio, fs(3)neo61, CG10422, 0368/10, element., bim-beta7, atomo, atomus, l(3)S138606, bod, DmelCG10422, l(3)S036810, atome, END, bimel, l(3)trio, ARHGEF23, BEST:LD36950, Element, HCAP, bim-beta6, l(3)036810, INS, atoms, tgat, mate-paired library, l(3)S137203, alpha, CDLS3, CG18214, BMH, l(3)S095914, Trio, DmelCG18214, 1372/03, l(3)S[1386/06], BIM, Bam-C, DTrio, BAM, l(3)S[1372/3], l(3)6D104, Bam, 0959/14, SMC3L1, elements, ORW1, CSPG6, HHT1, atom"],"pubmed_title_synonyms":["element., atomo, atomus, Element, elements, atome, anatomical unit, atom, body organ, atoms"],"name_synonyms":["l(3)trio, TRIO, ARHGEF23, WES, Complete Transcriptome, Complete, Complete Transcriptome Sequencing, Exome Sequencings, BEST:LD36950, Complete Exome Sequencings, Complete Exome, Complete Exome Sequencing, Whole Transcriptome Sequencing, l(3)036810, M89, Exome, tgat, CG9208, 1386/06, l(3)S137203, CG18214, Sequencing, l(3)S095914, Trio, DmelCG18214, 1372/03, Exome Sequencing, Whole Exome, l(3)S[1386/06], UNC-73/Trio., 0368/10, Whole, DTrio, Whole Exome Sequencing, l(3)S[1372/3], l(3)6D104, 0959/14, Whole Transcriptome, Transcriptome Sequencing, l(3)S138606, l(3)S036810, Transcriptome Sequencings"],"pubmed_abstract_synonyms":["AW488255, other disease, whole exome, False, NetrinA, D430049E23Rik, Development, Repetitive Sequence, element, netrin, Repetitive Sequences, diseases, Hek6, Alu Repetitive Sequence, Consensus, disease or disorder, Cek6, diseases and disorders, Low, ENSMUSG00000074119., ERP, APUDoma, Erp, human disease, me75, Elkh, F, Elements, Tyrosine-protein kinase receptor EPH-2, EK6, SAP-2, Sap-2, D17Mit170, T1, non-neoplastic, neuroendocrine tumour, 2.7.10.1, Solute carrier family 6 member 2, anatomical unit, Etrp, body organ, CT27014, NET1, SLC6A5, disorder, Homo sapiens disease, Consensus Development, NAT1, elements, netA, Family, atom, NET, Net, Alu-Like Repetitive Sequence, Elk, ELK, Alu Families, C130099E04Rik, cou, Alu, Neuronally-expressed EPH-related tyrosine kinase, disorders, EPH tyrosine kinase 2, SAP2, medical condition, 9330129L11, neuroendocrine tumor, Tl3, Alu Repetitive, Tl2, net, neuroendocrine neoplasm, Sequences, read, Lr, Norepinephrine transporter, Sequence, Alu Repetitive Sequences, Algorithm, Diseases, condition, EPH-like kinase 6, atomo, atomus, atome, Element, atoms, Alu Element, whole genome, hEK6, CG18657, disease, DmelCG18657, Alu Family, EPHT2, Families, Bra, netrin A"],"additional_accession":[]},"is_claimable":false,"name":"Benchmark and validation of whole exome sequencing of a trio and singleton","description":"Whole exome paired-end sequencing data was obtained for a trio and a fourth unrelated individual sequenced to high depth (95x) using a paired-end library with the Illumina HiSeq platform and aligned by BWA 0.5.9. The bam files were analysed and experimentally vaidated for the novel insertion of mobile elements.","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAS00001000852","cross_references":{"TAXONOMY":["9606"],"pubmed":["25348035"],"EGA":["EGAD00001000883","EGAC00001000076"]}}