TY - JOUR AU - Goodwin, S. AU - McPherson, J. D. AU - McCombie, W. R. PY - 2016 DA - 2016// TI - Coming of age: ten years of next-generation sequencing technologies JO - Nat Rev Genet. VL - 17 UR - https://doi.org/10.1038/nrg.2016.49 DO - 10.1038/nrg.2016.49 ID - Goodwin2016 ER - TY - JOUR AU - Bleidorn, C. PY - 2016 DA - 2016// TI - Third generation sequencing: technology and its potential impact on evolutionary biodiversity research JO - Syst Biodivers VL - 14 UR - https://doi.org/10.1080/14772000.2015.1099575 DO - 10.1080/14772000.2015.1099575 ID - Bleidorn2016 ER - TY - JOUR AU - Lee, H. AU - Deignan, J. L. AU - Dorrani, N. AU - Strom, S. P. AU - Kantarci, S. AU - Quintero-Rivera, F. PY - 2014 DA - 2014// TI - Clinical exome sequencing for genetic identification of rare Mendelian disorders JO - JAMA. VL - 312 UR - https://doi.org/10.1001/jama.2014.14604 DO - 10.1001/jama.2014.14604 ID - Lee2014 ER - TY - JOUR AU - Yang, Y. AU - Muzny, D. M. AU - Reid, J. G. AU - Bainbridge, M. N. AU - Willis, A. AU - Ward, P. A. PY - 2013 DA - 2013// TI - Clinical whole-exome sequencing for the diagnosis of Mendelian disorders JO - N Engl J Med VL - 369 UR - https://doi.org/10.1056/NEJMoa1306555 DO - 10.1056/NEJMoa1306555 ID - Yang2013 ER - TY - JOUR AU - Wright, C. F. AU - FitzPatrick, D. R. AU - Firth, H. V. PY - 2018 DA - 2018// TI - Paediatric genomics: diagnosing rare disease in children JO - Nat Rev Genet VL - 19 UR - https://doi.org/10.1038/nrg.2017.116 DO - 10.1038/nrg.2017.116 ID - Wright2018 ER - TY - JOUR AU - Deelen, P. AU - Dam, S. AU - Herkert, J. C. AU - Karjalainen, J. M. AU - Brugge, H. AU - Abbott, K. M. PY - 2019 DA - 2019// TI - Improving the diagnostic yield of exome- sequencing by predicting gene–phenotype associations using large-scale gene expression analysis JO - Nat Commun VL - 10 UR - https://doi.org/10.1038/s41467-019-10649-4 DO - 10.1038/s41467-019-10649-4 ID - Deelen2019 ER - TY - JOUR AU - Meienberg, J. AU - Bruggmann, R. AU - Oexle, K. AU - Matyas, G. PY - 2016 DA - 2016// TI - Clinical sequencing: is WGS the better WES? JO - Hum Genet VL - 135 UR - https://doi.org/10.1007/S00439-015-1631-9 DO - 10.1007/S00439-015-1631-9 ID - Meienberg2016 ER - TY - JOUR AU - Belkadi, A. AU - Bolze, A. AU - Itan, Y. AU - Cobat, A. AU - Vincent, Q. B. AU - Antipenko, A. PY - 2015 DA - 2015// TI - Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1418631112 DO - 10.1073/pnas.1418631112 ID - Belkadi2015 ER - TY - JOUR AU - Kosugi, S. AU - Momozawa, Y. AU - Liu, X. AU - Terao, C. AU - Kubo, M. AU - Kamatani, Y. PY - 2019 DA - 2019// TI - Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1720-5 DO - 10.1186/s13059-019-1720-5 ID - Kosugi2019 ER - TY - JOUR AU - Guan, P. AU - Sung, W. -. K. PY - 2016 DA - 2016// TI - Structural variation detection using next-generation sequencing data: a comparative technical review JO - Methods. VL - 102 UR - https://doi.org/10.1016/j.ymeth.2016.01.020 DO - 10.1016/j.ymeth.2016.01.020 ID - Guan2016 ER - TY - JOUR AU - Cameron, D. L. AU - Stefano, L. AU - Papenfuss, A. T. PY - 2019 DA - 2019// TI - Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software JO - Nat Commun VL - 10 UR - https://doi.org/10.1038/s41467-019-11146-4 DO - 10.1038/s41467-019-11146-4 ID - Cameron2019 ER - TY - JOUR AU - Amarillo, I. E. AU - Nievera, I. AU - Hagan, A. AU - Huchthagowder, V. AU - Heeley, J. AU - Hollander, A. PY - 2016 DA - 2016// TI - Integrated small copy number variations and epigenome maps of disorders of sex development JO - Hum Genome Var VL - 3 UR - https://doi.org/10.1038/hgv.2016.12 DO - 10.1038/hgv.2016.12 ID - Amarillo2016 ER - TY - JOUR AU - Jain, M. AU - Koren, S. AU - Miga, K. H. AU - Quick, J. AU - Rand, A. C. AU - Sasani, T. A. PY - 2018 DA - 2018// TI - Nanopore sequencing and assembly of a human genome with ultra-long reads JO - Nat Biotechnol VL - 36 UR - https://doi.org/10.1038/nbt.4060 DO - 10.1038/nbt.4060 ID - Jain2018 ER - TY - JOUR AU - Cretu Stancu, M. AU - Roosmalen, M. J. AU - Renkens, I. AU - Nieboer, M. M. AU - Middelkamp, S. AU - Ligt, J. PY - 2017 DA - 2017// TI - Mapping and phasing of structural variation in patient genomes using nanopore sequencing JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-017-01343-4 DO - 10.1038/s41467-017-01343-4 ID - Cretu Stancu2017 ER - TY - JOUR AU - Ebbert, M. T. W. AU - Jensen, T. D. AU - Jansen-West, K. AU - Sens, J. P. AU - Reddy, J. S. AU - Ridge, P. G. PY - 2019 DA - 2019// TI - Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1707-2 DO - 10.1186/s13059-019-1707-2 ID - Ebbert2019 ER - TY - JOUR AU - Zhou, A. AU - Lin, T. AU - Xing, J. PY - 2019 DA - 2019// TI - Evaluating nanopore sequencing data processing pipelines for structural variation identification JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1858-1 DO - 10.1186/s13059-019-1858-1 ID - Zhou2019 ER - TY - JOUR AU - Chaisson, M. J. P. AU - Sanders, A. D. AU - Zhao, X. AU - Malhotra, A. AU - Porubsky, D. AU - Rausch, T. PY - 2019 DA - 2019// TI - Multi-platform discovery of haplotype-resolved structural variation in human genomes JO - Nat Commun VL - 10 UR - https://doi.org/10.1038/s41467-018-08148-z DO - 10.1038/s41467-018-08148-z ID - Chaisson2019 ER - TY - JOUR AU - Levy-Sakin, M. AU - Ebenstein, Y. PY - 2013 DA - 2013// TI - Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy JO - Curr Opin Biotechnol VL - 24 UR - https://doi.org/10.1016/j.copbio.2013.01.009 DO - 10.1016/j.copbio.2013.01.009 ID - Levy-Sakin2013 ER - TY - JOUR AU - Levy-Sakin, M. AU - Pastor, S. AU - Mostovoy, Y. AU - Li, L. AU - Leung, A. K. Y. AU - McCaffrey, J. PY - 2019 DA - 2019// TI - Genome maps across 26 human populations reveal population-specific patterns of structural variation JO - Nat Commun VL - 10 UR - https://doi.org/10.1038/s41467-019-08992-7 DO - 10.1038/s41467-019-08992-7 ID - Levy-Sakin2019 ER - TY - STD TI - Hastie AR, Lam ET, Pang AWC, Zhang LX, Andrews W, Lee J, et al. Rapid Automated Large Structural Variation Detection in a Diploid Genome by NanoChannel Based Next-Generation Mapping. bioRxiv. 2017:102764. doi:https://doi.org/10.1101/102764. ID - ref20 ER - TY - JOUR AU - Bocklandt, S. AU - Hastie, A. AU - Cao, H. PY - 2019 DA - 2019// TI - Bionano genome mapping: high-throughput, ultra-long molecule genome analysis system for precision genome assembly and haploid-resolved structural variation discovery JO - Adv Exp Med Biol VL - 1129 UR - https://doi.org/10.1007/978-981-13-6037-4_7 DO - 10.1007/978-981-13-6037-4_7 ID - Bocklandt2019 ER - TY - JOUR AU - Leung, A. K. -. Y. AU - Kwok, T. -. P. AU - Wan, R. AU - Xiao, M. AU - Kwok, P. -. Y. AU - Yip, K. Y. PY - 2016 DA - 2016// TI - OMBlast: alignment tool for optical mapping using a seed-and-extend approach JO - Bioinformatics. VL - 33 UR - https://doi.org/10.1093/bioinformatics/btw620 DO - 10.1093/bioinformatics/btw620 ID - Leung2016 ER - TY - JOUR AU - Leung, A. K. -. Y. AU - Jin, N. AU - Yip, K. Y. AU - Chan, T. -. F. PY - 2017 DA - 2017// TI - OMTools: a software package for visualizing and processing optical mapping data JO - Bioinformatics. VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx317 DO - 10.1093/bioinformatics/btx317 ID - Leung2017 ER - TY - JOUR AU - Jaratlerdsiri, W. AU - Chan, E. K. F. AU - Petersen, D. C. AU - Yang, C. AU - Croucher, P. I. AU - Bornman, M. S. R. PY - 2017 DA - 2017// TI - Next generation mapping reveals novel large genomic rearrangements in prostate cancer JO - Oncotarget VL - 8 UR - https://doi.org/10.18632/oncotarget.15802 DO - 10.18632/oncotarget.15802 ID - Jaratlerdsiri2017 ER - TY - JOUR AU - Du, C. AU - Mark, D. AU - Wappenschmidt, B. AU - Böckmann, B. AU - Pabst, B. AU - Chan, S. PY - 2018 DA - 2018// TI - A tandem duplication of BRCA1 exons 1–19 through DHX8 exon 2 in four families with hereditary breast and ovarian cancer syndrome JO - Breast Cancer Res Treat VL - 172 UR - https://doi.org/10.1007/s10549-018-4957-x DO - 10.1007/s10549-018-4957-x ID - Du2018 ER - TY - JOUR AU - Dixon, J. R. AU - Xu, J. AU - Dileep, V. AU - Zhan, Y. AU - Song, F. AU - Le, V. T. PY - 2018 DA - 2018// TI - Integrative detection and analysis of structural variation in cancer genomes JO - Nat Genet VL - 50 UR - https://doi.org/10.1038/s41588-018-0195-8 DO - 10.1038/s41588-018-0195-8 ID - Dixon2018 ER - TY - JOUR AU - Barseghyan, H. AU - Tang, W. AU - Wang, R. T. AU - Almalvez, M. AU - Segura, E. AU - Bramble, M. S. PY - 2017 DA - 2017// TI - Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis JO - Genome Med VL - 9 UR - https://doi.org/10.1186/s13073-017-0479-0 DO - 10.1186/s13073-017-0479-0 ID - Barseghyan2017 ER - TY - STD TI - Dai Y, Li P, Wang Z, Liang F, Yang F, Fang L, et al. Single-molecule optical mapping enables accurate molecular diagnosis of facioscapulohumeral muscular dystrophy (FSHD). bioRxiv. 2018:286104. doi:https://doi.org/10.1101/286104. ID - ref28 ER - TY - JOUR AU - Sharim, H. AU - Grunwald, A. AU - Gabrieli, T. AU - Michaeli, Y. AU - Margalit, S. AU - Torchinsky, D. PY - 2019 DA - 2019// TI - Long-read single-molecule maps of the functional methylome JO - Genome Res VL - 29 UR - https://doi.org/10.1101/gr.240739.118 DO - 10.1101/gr.240739.118 ID - Sharim2019 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics. VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Li, B. AU - Dewey, C. N. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - MacDonald, J. R. AU - Ziman, R. AU - Yuen, R. K. C. AU - Feuk, L. AU - Scherer, S. W. PY - 2014 DA - 2014// TI - The database of genomic variants: a curated collection of structural variation in the human genome JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt958 DO - 10.1093/nar/gkt958 ID - MacDonald2014 ER - TY - JOUR AU - Firth, H. V. AU - Richards, S. M. AU - Bevan, A. P. AU - Clayton, S. AU - Corpas, M. AU - Rajan, D. PY - 2009 DA - 2009// TI - DECIPHER: database of chromosomal imbalance and phenotype in humans using Ensembl resources JO - Am J Hum Genet VL - 84 UR - https://doi.org/10.1016/j.ajhg.2009.03.010 DO - 10.1016/j.ajhg.2009.03.010 ID - Firth2009 ER - TY - STD TI - Bionano Genomics. Bionano solve theory of operation: variant annotation pipeline. 2018. https://bionanogenomics.com/wp-content/uploads/2018/04/30190-Bionano-Solve-Theory-of-Operation-Variant-Annotation-Pipeline.pdf. Accessed 19 Feb 2020. UR - https://bionanogenomics.com/wp-content/uploads/2018/04/30190-Bionano-Solve-Theory-of-Operation-Variant-Annotation-Pipeline.pdf ID - ref34 ER - TY - JOUR AU - Landrum, M. J. AU - Lee, J. M. AU - Benson, M. AU - Brown, G. R. AU - Chao, C. AU - Chitipiralla, S. PY - 2018 DA - 2018// TI - ClinVar: improving access to variant interpretations and supporting evidence JO - Nucleic Acids Res VL - 46 UR - https://doi.org/10.1093/nar/gkx1153 DO - 10.1093/nar/gkx1153 ID - Landrum2018 ER - TY - JOUR AU - Rubinstein, W. S. AU - Maglott, D. R. AU - Lee, J. M. AU - Kattman, B. L. AU - Malheiro, A. J. AU - Ovetsky, M. PY - 2012 DA - 2012// TI - The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1173 DO - 10.1093/nar/gks1173 ID - Rubinstein2012 ER - TY - STD TI - David J. Winter. Rentrez: an R package for the NCBI eUtils API. R J 2017;9:520--526. https://cran.r-project.org/web/packages/rentrez/citation.html. Accessed 1 Aug 2019. UR - https://cran.r-project.org/web/packages/rentrez/citation.html ID - ref37 ER - TY - JOUR AU - Cao, Z. AU - Wang, L. AU - Chen, Y. AU - Cai, R. AU - Lu, J. AU - Yu, Y. PY - 2017 DA - 2017// TI - VarfromPDB: an automated and integrated tool to mine disease-gene-variant relations from the public databases and literature JO - J Proteomics Bioinform VL - 10 UR - https://doi.org/10.4172/jpb.1000455 DO - 10.4172/jpb.1000455 ID - Cao2017 ER - TY - STD TI - Walker A. openxlsx: Read, Write and Edit XLSX Files. R package version 4.1.0. https://CRAN.R-project.org/package=openxlsx. 2018;:2018. https://cran.r-project.org/web/packages/openxlsx/index.html. Accessed 5 Aug 2019. UR - https://cran.r-project.org/web/packages/openxlsx/index.html ID - ref39 ER - TY - STD TI - Bionano Genomics. SMAP file format specification sheet. 2019. https://bionanogenomics.com/wp-content/uploads/2017/03/30041-SMAP-File-Format-Specification-Sheet.pdf. Accessed 25 Feb 2020. UR - https://bionanogenomics.com/wp-content/uploads/2017/03/30041-SMAP-File-Format-Specification-Sheet.pdf ID - ref40 ER - TY - STD TI - Hastie A, Liang T, Pham K, Saghbini M, Džakula Ž, Cao H. De novo assembly of the genome-in-a-bottle reference Ashkenazi trio, structural variation discovery and comparison with other individuals by next-generation mapping. In: ASHG. 2015. https://bionanogenomics.com/wp-content/uploads/2017/11/Bionano-Poster_ASHG2015_Alex_De-Novo-Assembly-Genome-in-a-Bottle-Reference-Ashkenazi-Trio.pdf. Accessed 24 Feb 2020. UR - https://bionanogenomics.com/wp-content/uploads/2017/11/Bionano-Poster_ASHG2015_Alex_De-Novo-Assembly-Genome-in-a-Bottle-Reference-Ashkenazi-Trio.pdf ID - ref41 ER - TY - JOUR AU - Yang, T. -. L. AU - Chen, X. -. D. AU - Guo, Y. AU - Lei, S. -. F. AU - Wang, J. -. T. AU - Zhou, Q. PY - 2008 DA - 2008// TI - Genome-wide copy-number-variation study identified a susceptibility gene, UGT2B17, for osteoporosis JO - Am J Hum Genet VL - 83 UR - https://doi.org/10.1016/j.ajhg.2008.10.006 DO - 10.1016/j.ajhg.2008.10.006 ID - Yang2008 ER - TY - JOUR AU - Mak, A. C. Y. AU - Lai, Y. Y. Y. AU - Lam, E. T. AU - Kwok, T. -. P. AU - Leung, A. K. Y. AU - Poon, A. PY - 2016 DA - 2016// TI - Genome-wide structural variation detection by genome mapping on Nanochannel arrays JO - Genetics. VL - 202 UR - https://doi.org/10.1534/genetics.115.183483 DO - 10.1534/genetics.115.183483 ID - Mak2016 ER - TY - JOUR AU - Weischenfeldt, J. AU - Symmons, O. AU - Spitz, F. AU - Korbel, J. O. PY - 2013 DA - 2013// TI - Phenotypic impact of genomic structural variation: insights from and for human disease JO - Nat Rev Genet. VL - 14 UR - https://doi.org/10.1038/nrg3373 DO - 10.1038/nrg3373 ID - Weischenfeldt2013 ER - TY - JOUR AU - Geoffroy, V. AU - Herenger, Y. AU - Kress, A. AU - Stoetzel, C. AU - Piton, A. AU - Dollfus, H. PY - 2018 DA - 2018// TI - AnnotSV: an integrated tool for structural variations annotation JO - Bioinformatics. VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty304 DO - 10.1093/bioinformatics/bty304 ID - Geoffroy2018 ER - TY - JOUR AU - Wang, K. AU - Li, M. AU - Hakonarson, H. PY - 2010 DA - 2010// TI - ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq603 DO - 10.1093/nar/gkq603 ID - Wang2010 ER - TY - JOUR AU - Brandler, W. M. AU - Antaki, D. AU - Gujral, M. AU - Kleiber, M. L. AU - Whitney, J. AU - Maile, M. S. PY - 2018 DA - 2018// TI - Paternally inherited cis-regulatory structural variants are associated with autism JO - Science. VL - 360 UR - https://doi.org/10.1126/science.aan2261 DO - 10.1126/science.aan2261 ID - Brandler2018 ER - TY - STD TI - Carlson M. org.Hs.eg.db: Genome wide annotation for Human. 2019. https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html. Accessed 1 Aug 2019. UR - https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html ID - ref48 ER - TY - JOUR AU - Richards, S. AU - Aziz, N. AU - Bale, S. AU - Bick, D. AU - Das, S. AU - Gastier-Foster, J. PY - 2015 DA - 2015// TI - Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology JO - Genet Med VL - 17 UR - https://doi.org/10.1038/gim.2015.30 DO - 10.1038/gim.2015.30 ID - Richards2015 ER -