Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization release_yaasb4tk3rgebhmmu26qkd5d4u

by Osman Ugur Sezerman, Ege Ulgen, Nogayhan Seymen, Ilknur Melis Durasi

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{'index': 1, 'target_release_id': None, 'extra': {'doi': '10.14806/ej.17.1.200', 'unstructured': 'Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.Journal. 2011;17(1):10-12'}, 'key': 'ref=2', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 2, 'target_release_id': None, 'extra': {'doi': '10.1016/j.ygeno.2013.07.011', 'unstructured': 'Criscuolo A, Brisse S. AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics. 2013;102(5-6):500-506'}, 'key': 'ref=3', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 3, 'target_release_id': None, 'extra': {'doi': '10.1186/1471-2105-15-182', 'unstructured': 'Jiang H, Lei R, Ding SW, Zhu S. Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014;15:182'}, 'key': 'ref=4', 'year': None, 'container_name': None, 'title': None, 'locator': None}
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{'index': 7, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btp324', 'unstructured': 'Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-1760'}, 'key': 'ref=8', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 8, 'target_release_id': None, 'extra': {'doi': '10.1038/nmeth.1923', 'unstructured': 'Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9(4):357-359'}, 'key': 'ref=9', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 9, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=10', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 10, 'target_release_id': None, 'extra': {'doi': '10.1371/journal.pcbi.1005944', 'unstructured': 'Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. PLoS Computational Biology. 2018;14(1):e1005944'}, 'key': 'ref=11', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 11, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=12', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 12, 'target_release_id': None, 'extra': {'doi': '10.1101/gr.107524.110', 'unstructured': 'Mckenna A, Hanna M, Banks E, et al. The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. 2010;20(9):1297-1303'}, 'key': 'ref=13', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 13, 'target_release_id': None, 'extra': {'doi': '10.1038/srep43169', 'unstructured': 'Sandmann S, De graaf AO, Karimi M, et al. Evaluating variant calling tools for non-matched next-generation sequencing data. Scientific Reports. 2017;7:43169'}, 'key': 'ref=14', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 14, 'target_release_id': None, 'extra': {'doi': '10.1186/s12859-018-2440-7', 'unstructured': 'Bian X, Zhu B, Wang M, et al. Comparing the performance of selected variant callers using synthetic data and genome segmentation. BMC Bioinformatics. 2018;19(1):429'}, 'key': 'ref=15', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 15, 'target_release_id': None, 'extra': {'doi': '10.1016/j.csbj.2018.01.003', 'unstructured': 'Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Computational and Structural Biotechnology Journal. 2018;16:15-24. DOI: 10.1016/j.csbj.2018.01.003'}, 'key': 'ref=16', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 16, 'target_release_id': None, 'extra': {'doi': '10.1101/gr.088013.108', 'unstructured': 'Li R, Li Y, Fang X, et al. SNP detection for massively parallel whole-genome resequencing. Genome Research. 2009;19(6):1124-1132'}, 'key': 'ref=17', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 17, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btp352', 'unstructured': 'Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079'}, 'key': 'ref=18', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 18, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/bts271', 'unstructured': 'Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: Accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012;28(14):1811-1817'}, 'key': 'ref=19', 'year': None, 'container_name': None, 'title': None, 'locator': None}
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{'index': 20, 'target_release_id': None, 'extra': {'doi': '10.1038/ng.3036', 'unstructured': 'Rimmer A, Phan H, Mathieson I, et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics. 2014;46(8):912-918'}, 'key': 'ref=21', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 21, 'target_release_id': None, 'extra': {'doi': '10.1038/nbt.4235', 'unstructured': 'Poplin R, Chang P-C, Alexander D, et al. A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology. 2018;36(10):983-987. DOI: 10.1038/nbt.4235'}, 'key': 'ref=22', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 22, 'target_release_id': None, 'extra': {'doi': '10.4137/cin.s13779', 'unstructured': 'Bao R, Huang L, Andrade J, et al. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Informatics. 2014;13(Suppl 2):67-82'}, 'key': 'ref=23', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 23, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btq033', 'unstructured': 'Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-842'}, 'key': 'ref=24', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 24, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btv098', 'unstructured': 'Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: Fast processing of NGS alignment formats. Bioinformatics. 2015;31(12):2032-2034'}, 'key': 'ref=25', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 25, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=26', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 26, 'target_release_id': None, 'extra': {'doi': '10.1038/nbt.1754', 'unstructured': 'Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative genomics viewer. Nature Biotechnology. 2011;29(1):24-26'}, 'key': 'ref=27', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 27, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/29.1.308', 'unstructured': 'Sherry ST, Ward MH, Kholodov M, et al. dbSNP: The NCBI database of genetic variation. Nucleic Acids Research. 2001;29(1):308-311'}, 'key': 'ref=28', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 28, 'target_release_id': None, 'extra': {'doi': '10.1038/nature15393', 'unstructured': 'Auton A, Brooks LD, Durbin RM, et al. A global reference for human genetic variation. Nature. 2015;526(7571):68-74'}, 'key': 'ref=29', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 29, 'target_release_id': None, 'extra': {'doi': '10.1038/nature19057', 'unstructured': 'Lek M, Karczewski KJ, Minikel EV, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536(7616):285-291'}, 'key': 'ref=30', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 30, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=31', 'year': None, 'container_name': None, 'title': None, 'locator': None}
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{'index': 32, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkt1113', 'unstructured': 'Landrum MJ, Lee JM, Riley GR, et al. ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research. 2014;42(Database issue):D980-D985'}, 'key': 'ref=33', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 33, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkg509', 'unstructured': 'Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Research. 2003;31(13):3812-3814'}, 'key': 'ref=34', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 34, 'target_release_id': None, 'extra': {'doi': '10.1038/nmeth0410-248', 'unstructured': 'Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nature Methods. 2010;7(4):248-249'}, 'key': 'ref=35', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 35, 'target_release_id': None, 'extra': {'doi': '10.1101/gr.092619.109', 'unstructured': 'Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Research. 2009;19(9):1553-1561'}, 'key': 'ref=36', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 36, 'target_release_id': None, 'extra': {'doi': '10.1038/nmeth0810-575', 'unstructured': 'Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nature Methods. 2010;7:575-576'}, 'key': 'ref=37', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 37, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkr407', 'unstructured': 'Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: Application to cancer genomics. Nucleic Acids Research. 2011;39(17):e118'}, 'key': 'ref=38', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 38, 'target_release_id': None, 'extra': {'doi': '10.1002/humu.22225', 'unstructured': 'Shihab HA, Gough J, Cooper DN, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Human Mutation. 2013;34(1):57-65'}, 'key': 'ref=39', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 39, 'target_release_id': None, 'extra': {'doi': '10.1371/journal.pcbi.1001025', 'unstructured': 'Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Computational Biology. 2010;6(12):e1001025'}, 'key': 'ref=40', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 40, 'target_release_id': None, 'extra': {'doi': '10.1101/gr.097857.109', 'unstructured': 'Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Research. 2010;20(1):110-121'}, 'key': 'ref=41', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 41, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btp190', 'unstructured': 'Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics. 2009;25(12):i54-i62'}, 'key': 'ref=42', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 42, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btw222', 'unstructured': 'Tang H, Thomas PD. PANTHER-PSEP: Predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics. 2016;32(14):2230-2232'}, 'key': 'ref=43', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 43, 'target_release_id': None, 'extra': {'doi': '10.1016/j.ajhg.2011.03.004', 'unstructured': 'González-pérez A, López-bigas N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. American Journal of Human Genetics. 2011;88(4):440-449'}, 'key': 'ref=44', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 44, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gky1016', 'unstructured': 'Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M. CADD: Predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Research. 2019;47(D1):D886-D894'}, 'key': 'ref=45', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 45, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btr357', 'unstructured': 'Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R. CHASM and SNVBox: Toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics. 2011;27(15):2147-2148'}, 'key': 'ref=46', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 46, 'target_release_id': None, 'extra': {'doi': '10.1371/journal.pone.0077945', 'unstructured': 'Mao Y, Chen H, Liang H, Meric-bernstam F, Mills GB, Chen K. CanDrA: Cancer-specific driver missense mutation annotation with optimized features. PLoS One. 2013;8(10):e77945'}, 'key': 'ref=47', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 47, 'target_release_id': None, 'extra': {'doi': '10.1186/1471-2164-14-s3-s3', 'unstructured': 'Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R. Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics. 2013;14(3):1-16'}, 'key': 'ref=48', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 48, 'target_release_id': None, 'extra': {'unstructured': "O'leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Research. 2016;44(D1):D733-D745"}, 'key': 'ref=49', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 49, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkx1098', 'unstructured': 'Zerbino DR, Achuthan P, Akanni W, et al. Ensembl 2018. Nucleic Acids Research. 2018;46(D1):D754-D761'}, 'key': 'ref=50', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 50, 'target_release_id': None, 'extra': {'doi': '10.1186/gm543', 'unstructured': 'Mccarthy DJ, Humburg P, Kanapin A, et al. Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 2014;6(3):26'}, 'key': 'ref=51', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 51, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkq603', 'unstructured': 'Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from next-generation sequencing data. Nucleic Acids Research. 2010;38:e164'}, 'key': 'ref=52', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 52, 'target_release_id': None, 'extra': {'doi': '10.4161/fly.19695', 'unstructured': 'Cingolani P, Platts A, Wang le L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2):80-92'}, 'key': 'ref=53', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 53, 'target_release_id': None, 'extra': {'doi': '10.1186/s13059-016-0974-4', 'unstructured': 'Mclaren W, Gil L, Hunt SE, et al. The Ensembl variant effect predictor. Genome Biology. 2016;17(1):122'}, 'key': 'ref=54', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 54, 'target_release_id': None, 'extra': {'doi': '10.1371/journal.pcbi.1003153', 'unstructured': 'Paila U, Chapman BA, Kirchner R, Quinlan AR. GEMINI: Integrative exploration of genetic variation and genome annotations. PLoS Computational Biology. 2013;9(7):e1003153'}, 'key': 'ref=55', 'year': None, 'container_name': None, 'title': None, 'locator': None}
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{'index': 65, 'target_release_id': None, 'extra': {'doi': '10.1038/nature11017', 'unstructured': 'Stephens PJ et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486:400-404'}, 'key': 'ref=66', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 66, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btu338', 'unstructured': 'Wang W, Wang P, Xu F, Luo R, Wong MP, Lam T-W. FaSD-somatic: A fast and accurate somatic SNV detection algorithm for cancer genome sequencing data. Bioinformatics. 2014;30(17):2498-2500'}, 'key': 'ref=67', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 67, 'target_release_id': None, 'extra': {'doi': '10.1002/humu.22771', 'unstructured': 'Ramos AH, Lichtenstein L, Gupta M, Lawrence MS, Pugh TJ, Saksena G, et al. Oncotator: Cancer variant annotation tool. Human Mutation. 2015;36(4):E2423-E24E9. pmid: 25703262'}, 'key': 'ref=68', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 68, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btt017', 'unstructured': 'Douville C, Carter H, Kim R, et al. CRAVAT: Cancer-related analysis of variants toolkit. Bioinformatics. 2013;29(5):647-648'}, 'key': 'ref=69', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 69, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkw1121', 'unstructured': 'Forbes SA, Beare D, Boutselakis H, et al. COSMIC: Somatic cancer genetics at high-resolution. Nucleic Acids Research. 2016;45(D1):D777-D783'}, 'key': 'ref=70', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 70, 'target_release_id': None, 'extra': {'unstructured': 'Futreal PA, Andrew Futreal P, Coin L, Marshall M, Down T, Hubbard T, et al. A census of human cancer genes. Nature Reviews. Cancer. 2004;4:177-183'}, 'key': 'ref=71', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 71, 'target_release_id': None, 'extra': {'doi': '10.1038/nature11003', 'unstructured': 'Barretina J, Caponigro G, Stransky N, et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483(7391):603-607. Published 2012 Mar 28. DOI: 10.1038/nature11003'}, 'key': 'ref=72', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 72, 'target_release_id': None, 'extra': {'unstructured': 'Sijmons RH. Identifying Patients with Familial Cancer Syndromes. 2010 Feb 27 [Updated 2010 Feb 27]. In: Riegert-Johnson DL, Boardman LA, Hefferon T, et al., editors. Cancer Syndromes [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2009. Available from:'}, 'key': 'ref=73', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 73, 'target_release_id': None, 'extra': {'doi': '10.1186/1471-2105-14-s11-s1', 'unstructured': 'Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: Features and perspectives. BMC Bioinformatics. 2013;14(11):S1'}, 'key': 'ref=74', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 74, 'target_release_id': None, 'extra': {'doi': '10.1186/1471-2164-15-732', 'unstructured': 'Amarasinghe KC, Li J, Hunter SM, et al. Inferring copy number and genotype in tumour exome data. BMC Genomics. 2014;15:732'}, 'key': 'ref=75', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 75, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkn195', 'unstructured': 'Hooghe B, Hulpiau P, van Roy F, De Bleser P. ConTra: A promoter alignment analysis tool for identification of transcription factor binding sites across species. Nucleic Acids Research. 2008;36:W128-W132'}, 'key': 'ref=76', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 76, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gks003', 'unstructured': 'Klambauer G, Schwarzbauer K, Mayr A, et al. cn.MOPS: Mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Research. 2012;40(9):e69'}, 'key': 'ref=77', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 77, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btr462', 'unstructured': 'Sathirapongsasuti JF, Lee H, Horst BA, et al. Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics. 2011;27(19):2648-2654'}, 'key': 'ref=78', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 78, 'target_release_id': None, 'extra': {'doi': '10.1186/s13059-017-1193-3', 'unstructured': 'Silva GO, Siegel MB, Mose LE, et al. SynthEx: A synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling. Genome Biology. 2017;18(1):66'}, 'key': 'ref=79', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 79, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btr670', 'unstructured': 'Boeva V, Popova T, Bleakley K, et al. Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics. 2012;28(3):423-425'}, 'key': 'ref=80', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 80, 'target_release_id': None, 'extra': {'doi': '10.1186/s12859-016-1174-7', 'unstructured': 'Yu Z, Li A, Wang M. CloneCNA: Detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data. BMC Bioinformatics. 2016;17:310'}, 'key': 'ref=81', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 81, 'target_release_id': None, 'extra': {'doi': '10.12688/f1000research.12516.1', 'unstructured': 'Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM. Tools for annotation and comparison of structural variation. F1000Res. 2017;6:1795'}, 'key': 'ref=82', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 82, 'target_release_id': None, 'extra': {'doi': '10.1002/0471250953.bi1506s45', 'unstructured': 'Fan X, Abbott TE, Larson D, Chen K. BreakDancer: Identification of genomic structural variation from paired-end read mapping. Current Protocols in Bioinformatics. 2014;45:15.6.1-15.611'}, 'key': 'ref=83', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 83, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/18.3.492', 'unstructured': 'Tesler G. GRIMM: Genome rearrangements web server. Bioinformatics. 2002;18(3):492-493'}, 'key': 'ref=84', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 84, 'target_release_id': None, 'extra': {'doi': '10.1186/gb-2014-15-6-r84', 'unstructured': 'Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: A probabilistic framework for structural variant discovery. Genome Biology. 2014;15(6):R84'}, 'key': 'ref=85', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 85, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gku1211', 'unstructured': 'Abo RP, Ducar M, Garcia EP, et al. BreaKmer: Detection of structural variation in targeted massively parallel sequencing data using kmers. Nucleic Acids Research. 2014;43(3):e19'}, 'key': 'ref=86', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 86, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkv605', 'unstructured': 'Zhao H, Zhao F. BreakSeek: A breakpoint-based algorithm for full spectral range INDEL detection. Nucleic Acids Research. 2015;43(14):6701-6713'}, 'key': 'ref=87', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 87, 'target_release_id': None, 'extra': {'doi': '10.1038/nmeth.1628', 'unstructured': 'Wang J, Mullighan CG, Easton J, et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nature Methods. 2011;8(8):652-654. Published 2011 Jun 12. DOI: 10.1038/nmeth.1628'}, 'key': 'ref=88', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 88, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/bts378', 'unstructured': 'Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO. DELLY: Structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):i333-i339'}, 'key': 'ref=89', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 89, 'target_release_id': None, 'extra': {'doi': '10.1177/0272989x8700700106', 'unstructured': 'Miller PL, Blumenfrucht SJ, Rose JR, et al. HYDRA: A knowledge acquisition tool for expert systems that critique medical workup. Medical Decision Making. 1987;7(1):12-21'}, 'key': 'ref=90', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 90, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btu714', 'unstructured': 'Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics. 2014;30(24):3458-3466'}, 'key': 'ref=91', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 91, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btp394', 'unstructured': 'Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865-2871'}, 'key': 'ref=92', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 92, 'target_release_id': None, 'extra': {'doi': '10.1371/journal.pone.0083356', 'unstructured': 'Hart SN, Sarangi V, Moore R, et al. SoftSearch: Integration of multiple sequence features to identify breakpoints of structural variations. PLoS One. 2013;8(12):e83356'}, 'key': 'ref=93', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 93, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btq293', 'unstructured': 'Zeitouni B, Boeva V, Janoueix-Lerosey I, et al. SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics. 2010;26(15):1895-1896'}, 'key': 'ref=94', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 94, 'target_release_id': None, 'extra': {'doi': '10.1101/gr.162883.113', 'unstructured': 'Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. TIGRA: A targeted iterative graph routing assembler for breakpoint assembly. Genome Research. 2014;24(2):310-317'}, 'key': 'ref=95', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 95, 'target_release_id': None, 'extra': {'doi': '10.1016/j.ymeth.2016.01.020', 'unstructured': 'Guan P, Sung WK. Structural variation detection using next-generation sequencing data: A comparative technical review. Methods. 2016;102:36-49'}, 'key': 'ref=96', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 96, 'target_release_id': None, 'extra': {'doi': '10.4274/tjh.2016.0149', 'unstructured': 'Sayitoğlu M. Clinical interpretation of genomic variations. Turkish Journal of Haematology. 2016;33(3):172-179'}, 'key': 'ref=97', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 97, 'target_release_id': None, 'extra': {'doi': '10.1002/humu.23348', 'unstructured': 'Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R. VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions. Human Mutation. 2017;39(1):61-68'}, 'key': 'ref=98', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 98, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/30.1.52', 'unstructured': 'Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research. 2002;30(1):52-55'}, 'key': 'ref=99', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 99, 'target_release_id': None, 'extra': {'doi': '10.1038/sj.bjc.6601894', 'unstructured': 'Bamford S, Dawson E, Forbes S, et al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. British Journal of Cancer. 2004;91(2):355-358'}, 'key': 'ref=100', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 100, 'target_release_id': None, 'extra': {'doi': '10.1038/ng.3774', 'unstructured': 'Griffith M, Spies NC, Krysiak K, et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics. 2017;49(2):170-174'}, 'key': 'ref=101', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 101, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=102', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 102, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=103', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 103, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=104', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 104, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkr1257', 'unstructured': 'Li MX, Gui HS, Kwan JS, Bao SY, Sham PC. A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic Acids Research. 2012;40(7):e53'}, 'key': 'ref=105', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 105, 'target_release_id': None, 'extra': {'doi': '10.1002/humu.22347', 'unstructured': 'Girdea M, Dumitriu S, Fiume M, et al. PhenoTips: Patient phenotyping software for clinical and research use. Human Mutation. 2013;34(8):1057-1065'}, 'key': 'ref=106', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 106, 'target_release_id': None, 'extra': {'doi': '10.1186/s12864-016-2722-2', 'unstructured': 'Stelzer G, Plaschkes I, Oz-levi D, et al. VarElect: The phenotype-based variation prioritizer of the GeneCards Suite. BMC Genomics. 2016;17(Suppl 2):444'}, 'key': 'ref=107', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 107, 'target_release_id': None, 'extra': {'doi': '10.1186/1755-8794-7-22', 'unstructured': 'Trakadis YJ, Buote C, Therriault JF, Jacques PÉ, Larochelle H, Lévesque S. PhenoVar: A phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes. BMC Medical Genomics. 2014;7:22. Published 2014 May 12. DOI: 10.1186/1755-8794-7-22'}, 'key': 'ref=108', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 108, 'target_release_id': None, 'extra': {'doi': '10.1016/j.ajhg.2017.01.004', 'unstructured': 'Li Q, Wang K. InterVar: Clinical interpretation of genetic variants by the 2015 ACMG-AMP guidelines. American Journal of Human Genetics. 2017;100(2):267-280'}, 'key': 'ref=109', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 109, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btr711', 'unstructured': 'Teer JK, Green ED, Mullikin JC, Biesecker LG. VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics. 2011;28(4):599-600'}, 'key': 'ref=110', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 110, 'target_release_id': None, 'extra': {'doi': '10.1038/nmeth.2656', 'unstructured': 'Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, Sakai R, Konings P, et al. eXtasy: Variant prioritization by genomic data fusion. Nature Methods. 2013;10(11):1083-1084. DOI: 10.1038/nmeth.2656'}, 'key': 'ref=111', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 111, 'target_release_id': None, 'extra': {'doi': '10.1038/nprot.2015.124', 'unstructured': 'Smedley D, Jacobsen JO, Jäger M, et al. Next-generation diagnostics and disease-gene discovery with the Exomiser. Nature Protocols. 2015;10(12):2004-2015'}, 'key': 'ref=112', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 112, 'target_release_id': None, 'extra': {'doi': '10.3389/fphys.2015.00383', 'unstructured': 'García-Campos MA, Espinal-Enríquez J, Hernández-Lemus E. Pathway analysis: State of the art. Frontiers in Physiology. 2015;6:383. doi: 10.3389/fphys.2015.00383'}, 'key': 'ref=113', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 113, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/bty271', 'unstructured': 'Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC. GSEA-InContext: Identifying novel and common patterns in expression experiments. Bioinformatics. 2018;34(13):i555-i564'}, 'key': 'ref=114', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 114, 'target_release_id': None, 'extra': {'doi': '10.1186/gb-2003-4-9-r60', 'unstructured': 'Dennis G, Sherman BT, Hosack DA, et al. DAVID: Database for annotation, visualization, and integrated discovery. Genome Biology. 2003;4(9):R60'}, 'key': 'ref=115', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 115, 'target_release_id': None, 'extra': {'doi': '10.3389/fncel.2016.00274', 'unstructured': 'Yu J, Gu X, Yi S. Ingenuity pathway analysis of gene expression profiles in distal Nerve stump following nerve injury: Insights into Wallerian degeneration. Frontiers in Cellular Neuroscience. 2016;10:274. Published 2016 Dec 6. DOI: 10.3389/fncel.2016.00274'}, 'key': 'ref=116', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 116, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btn577', 'unstructured': 'Tarca AL, Draghici S, Khatri P, et al. A novel signaling pathway impact analysis. Bioinformatics. 2008;25(1):75-82'}, 'key': 'ref=117', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 117, 'target_release_id': None, 'extra': {'doi': '10.1101/272450', 'unstructured': 'Ulgen E, Ozisik O, Sezerman OU. pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv. 2018'}, 'key': 'ref=118', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 118, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkw377', 'unstructured': 'Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016;44(W1):W90-W97'}, 'key': 'ref=119', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 119, 'target_release_id': None, 'extra': {'doi': '10.1039/c5mb00663e', 'unstructured': 'Yu G, HeReactomePA Q-Y. An R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016;12:477-479'}, 'key': 'ref=120', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 120, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=121', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 121, 'target_release_id': None, 'extra': {'doi': '10.1371/journal.pcbi.1004085', 'unstructured': 'Kutmon M, Van iersel MP, Bohler A, et al. PathVisio 3: An extendable pathway analysis toolbox. PLoS Computational Biology. 2015;11(2):e1004085'}, 'key': 'ref=122', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 122, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/28.1.27', 'unstructured': 'Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research. 2000;28(1):27-30'}, 'key': 'ref=123', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 123, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkq1018', 'unstructured': "Croft D, O'Kelly G, Wu G, et al. Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Research. 2010;39(Database issue):D691-D697"}, 'key': 'ref=124', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 124, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkr1074', 'unstructured': 'Kelder T, van Iersel MP, Hanspers K, et al. WikiPathways: Building research communities on biological pathways. Nucleic Acids Research. 2011;40(Database issue):D1301-D1307'}, 'key': 'ref=125', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 125, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btr260', 'unstructured': 'Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27(12):1739-1740'}, 'key': 'ref=126', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 126, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkw937', 'unstructured': 'Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: Quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Research. 2016;45(D1):D362-D368'}, 'key': 'ref=127', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 127, 'target_release_id': None, 'extra': {'doi': '10.1093/nar/gkq1039', 'unstructured': 'Cerami EG, Gross BE, Demir E, et al. Pathway commons, a web resource for biological pathway data. Nucleic Acids Research. 2010;39(Database issue):D685-D690'}, 'key': 'ref=128', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 128, 'target_release_id': None, 'extra': {'unstructured': 'Available from:'}, 'key': 'ref=129', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 129, 'target_release_id': None, 'extra': {'doi': '10.1093/bioinformatics/btg290', 'unstructured': 'Nikitin A, Egorov S, Daraselia N, Mazo I. Pathway studio—The analysis and navigation of molecular networks. Bioinformatics. 2003;19(16):2155-2157'}, 'key': 'ref=130', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 130, 'target_release_id': None, 'extra': {'doi': '10.1007/s10545-018-0146-7', 'unstructured': 'Rodenburg RJ. The functional genomics laboratory: Functional validation of genetic variants. Journal of Inherited Metabolic Disease. 2018;41(3):297-307'}, 'key': 'ref=131', 'year': None, 'container_name': None, 'title': None, 'locator': None}
{'index': 131, 'target_release_id': None, 'extra': {'doi': '10.1111/cts.12500', 'unstructured': 'Austin CP, Cutillo CM, Lau LPL, et al. Future of rare diseases research 2017–2027: An IRDiRC perspective. Clinical and Translational Science. 2018;11(1):21-27'}, 'key': 'ref=132', 'year': None, 'container_name': None, 'title': None, 'locator': None}
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release_date 2019-06-14
release_stage published
release_type chapter
release_year 2019
title Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization
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Extra Metadata (raw JSON)

container_name Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations [Working Title]
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crossref.type book-chapter