A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism
Autoři:
Reuben M. Buckley aff001; Brian W. Davis aff002; Wesley A. Brashear aff002; Fabiana H. G. Farias aff003; Kei Kuroki aff005; Tina Graves aff006; LaDeana W. Hillier aff006; Milinn Kremitzki aff006; Gang Li aff002; Rondo P. Middleton aff007; Patrick Minx aff008; Chad Tomlinson aff006; Leslie A. Lyons aff001; William J. Murphy aff002; Wesley C. Warren aff009
Působiště autorů:
Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
aff001; Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
aff002; Department of Psychiatry, Washington University, St. Louis, Missouri, United States of America
aff003; NeuroGenomics and Informatics, Washington University, St. Louis, Missouri, United States of America
aff004; Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
aff005; McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
aff006; Nestlé Purina Research, Saint Louis, Missouri, United States of America
aff007; Donald Danforth Plant Science, St Louis, Missouri, United States of America
aff008; Division of Animal Sciences, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
aff009
Vyšlo v časopise:
A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 16(10): e32767. doi:10.1371/journal.pgen.1008926
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008926
Souhrn
The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBio long sequence reads that significantly improve sequence representation and assembly contiguity. The whole genome sequences of 54 domestic cats were aligned to the reference to identify single nucleotide variants (SNVs) and structural variants (SVs). Across all cats, 16 SNVs predicted to have deleterious impacts and in a singleton state were identified as high priority candidates for causative mutations. One candidate was a stop gain in the tumor suppressor FBXW7. The SNV is found in cats segregating for feline mediastinal lymphoma and is a candidate for inherited cancer susceptibility. SV analysis revealed a complex deletion coupled with a nearby potential duplication event that was shared privately across three unrelated cats with dwarfism and is found within a known dwarfism associated region on cat chromosome B1. This SV interrupted UDP-glucose 6-dehydrogenase (UGDH), a gene involved in the biosynthesis of glycosaminoglycans. Importantly, UGDH has not yet been associated with human dwarfism and should be screened in undiagnosed patients. The new high-quality cat genome reference and the compilation of sequence variation demonstrate the importance of these resources when searching for disease causative alleles in the domestic cat and for identification of feline biomedical models.
Klíčová slova:
Alleles – Cats – Domestic animals – Genome annotation – Mammalian genomics – Pets and companion animals – Sequence alignment – Dwarfism
Zdroje
1. Mauler DA, Gandolfi B, Reinero CR, O'Brien DP, Spooner JL, Lyons LA, et al. Precision Medicine in Cats: Novel Niemann-Pick Type C1 Diagnosed by Whole-Genome Sequencing. J Vet Intern Med. 2017;31(2):539–44. doi: 10.1111/jvim.14599 28233346; PubMed Central PMCID: PMC5354023.
2. Fang H, Wu Y, Yang H, Yoon M, Jiménez-Barrón LT, Mittelman D, et al. Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. BMC medical genomics. 2017;10(1):10. doi: 10.1186/s12920-017-0246-5 28228131
3. Wise AL, Manolio TA, Mensah GA, Peterson JF, Roden DM, Tamburro C, et al. Genomic medicine for undiagnosed diseases. The Lancet. 2019.
4. Shendure J, Findlay GM, Snyder MW. Genomic medicine–progress, pitfalls, and promise. Cell. 2019;177(1):45–57. doi: 10.1016/j.cell.2019.02.003 30901547
5. Moses L, Niemi S, Karlsson E. Pet genomics medicine runs wild. Nature Publishing Group; 2018.
6. Nicholas FW. Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals. Nucleic acids research. 2003;31(1):275–7. doi: 10.1093/nar/gkg074 12520001
7. Online Mendelian Inheritance in Animals (OMIA). Sydney School of Veterinary Science, 03/12/2019. World Wide Web URL: http://omia.org/. Available from: http://omia.org/.
8. Lyons LA. DNA mutations of the cat: the good, the bad and the ugly. J Feline Med Surg. 2015;17(3):203–19. Epub 2015/02/24. doi: 10.1177/1098612X15571878 25701860.
9. Kittleson MD, Meurs KM, Harris SP. The genetic basis of hypertrophic cardiomyopathy in cats and humans. J Vet Cardiol. 2015;17 Suppl 1:S53–73. Epub 2016/01/19. doi: 10.1016/j.jvc.2015.03.001 26776594; PubMed Central PMCID: PMC5909964.
10. Menotti-Raymond M, David VA, Schäffer AA, Stephens R, Wells D, Kumar-Singh R, et al. Mutation in CEP290 discovered for cat model of human retinal degeneration. Journal of Heredity. 2007;98(3):211–20. doi: 10.1093/jhered/esm019 17507457
11. Lyons LA, Biller DS, Erdman CA, Lipinski MJ, Young AE, Roe BA, et al. Feline polycystic kidney disease mutation identified in PKD1. J Am Soc Nephrol. 2004;15(10):2548–55. Epub 2004/10/07. doi: 10.1097/01.ASN.0000141776.38527.BB 15466259.
12. Wang P, Mazrier H, Caverly Rae J, Raj K, Giger U. A GNPTAB nonsense variant is associated with feline mucolipidosis II (I-cell disease). BMC Vet Res. 2018;14(1):416. Epub 2018/12/29. doi: 10.1186/s12917-018-1728-1 30591066; PubMed Central PMCID: PMC6307278.
13. Spycher M, Bauer A, Jagannathan V, Frizzi M, De Lucia M, Leeb T. A frameshift variant in the COL5A1 gene in a cat with Ehlers-Danlos syndrome. Anim Genet. 2018;49(6):641–4. Epub 2018/09/25. doi: 10.1111/age.12727 30246406.
14. Jaffey JA, Reading NS, Giger U, Abdulmalik O, Buckley RM, Johnstone S, et al. Clinical, metabolic, and genetic characterization of hereditary methemoglobinemia caused by cytochrome b5 reductase deficiency in cats. Journal of veterinary internal medicine. 2019.
15. Hug P, Kern P, Jagannathan V, Leeb T. A TAC3 Missense Variant in a Domestic Shorthair Cat with Testicular Hypoplasia and Persistent Primary Dentition. Genes. 2019;10(10):806.
16. Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, et al. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (Bethesda). 2016;6(6):1607–16. doi: 10.1534/g3.116.028746 27172201; PubMed Central PMCID: PMC4889657.
17. Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, et al. Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun. 2019;10(1):260. Epub 2019/01/18. doi: 10.1038/s41467-018-08260-0 30651564; PubMed Central PMCID: PMC6335429.
18. Ananthasayanam S, Kothandaraman H., Nayee N, Saha S., Baghel D.S., Gopalakrishnan K., Peddamma S., Singh R.B., Schatz M. First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis). bioRxiv. 2019;(April 26).
19. Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, et al. Long-read sequence assembly of the gorilla genome. Science. 2016;352(6281):aae0344. Epub 2016/04/02. doi: 10.1126/science.aae0344 27034376; PubMed Central PMCID: PMC4920363.
20. Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat Genet. 2017;49(4):643–50. Epub 2017/03/07. doi: 10.1038/ng.3802 28263316; PubMed Central PMCID: PMC5909822.
21. Ontiveros ES, Ueda Y, Harris SP, Stern JA, 99 Lives Consortium. Precision medicine validation: identifying the MYBPC 3 A31P variant with whole-genome sequencing in two Maine Coon cats with hypertrophic cardiomyopathy. Journal of feline medicine and surgery. 2018:1098612X18816460.
22. Oh A, Pearce JW, Gandolfi B, Creighton EK, Suedmeyer WK, Selig M, et al. Early-onset progressive retinal atrophy associated with an IQCB1 variant in African black-footed cats (Felis nigripes). Scientific reports. 2017;7:43918. doi: 10.1038/srep43918 28322220
23. Aberdein D, Munday JS, Gandolfi B, Dittmer KE, Malik R, Garrick DJ, et al. A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats. Mamm Genome. 2017;28(1–2):47–55. Epub 2016/10/23. doi: 10.1007/s00335-016-9668-1 27770190.
24. Genova F, Longeri M, Lyons LA, Bagnato A, 99 Lives Consortium, Strillacci MG. First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics. 2018;19(1):895. Epub 2018/12/12. doi: 10.1186/s12864-018-5297-2 30526495; PubMed Central PMCID: PMC6288940.
25. Smit A, Hubley R, Green P. 2013–2015. RepeatMasker Open-4.0. 2013.
26. Gandolfi B, Alhaddad H, Abdi M, Bach LH, Creighton EK, Davis BW, et al. Applications and efficiencies of the first cat 63K DNA array. Sci Rep. 2018;8(1):7024. Epub 2018/05/08. doi: 10.1038/s41598-018-25438-0 29728693; PubMed Central PMCID: PMC5935720.
27. Lyons LA, Fox DB, Chesney KL, Britt LG, Buckley RM, Coates JR, et al. Localization of a feline autosomal dominant dwarfism locus: a novel model of chondrodysplasia. bioRxiv. 2019:687210.
28. Lipinski MJ, Froenicke L, Baysac KC, Billings NC, Leutenegger CM, Levy AM, et al. The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations. Genomics. 2008;91(1):12–21. Epub 2007/12/07. doi: 10.1016/j.ygeno.2007.10.009 18060738; PubMed Central PMCID: PMC2267438.
29. McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. Epub 2016/06/09. doi: 10.1186/s13059-016-0974-4 27268795; PubMed Central PMCID: PMC4893825.
30. Dewey FE, Murray MF, Overton JD, Habegger L, Leader JB, Fetterolf SN, et al. Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR study. Science. 2016;354(6319):aaf6814. doi: 10.1126/science.aaf6814 28008009
31. Yeh CH, Bellon M, Nicot C. FBXW7: a critical tumor suppressor of human cancers. Mol Cancer. 2018;17(1):115. Epub 2018/08/09. doi: 10.1186/s12943-018-0857-2 30086763; PubMed Central PMCID: PMC6081812.
32. TICA. Munchkin 2015 [October 26, 2015].
33. Wen Y, Li J, Wang L, Tie K, Magdalou J, Chen L, et al. UDP-glucose dehydrogenase modulates proteoglycan synthesis in articular chondrocytes: its possible involvement and regulation in osteoarthritis. Arthritis Res Ther. 2014;16(6):484. Epub 2014/12/04. doi: 10.1186/s13075-014-0484-2 25465897; PubMed Central PMCID: PMC4298080.
34. Clarkin CE, Allen S, Kuiper NJ, Wheeler BT, Wheeler-Jones CP, Pitsillides AA. Regulation of UDP-glucose dehydrogenase is sufficient to modulate hyaluronan production and release, control sulfated GAG synthesis, and promote chondrogenesis. J Cell Physiol. 2011;226(3):749–61. Epub 2010/08/19. doi: 10.1002/jcp.22393 20717929.
35. Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, et al. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A. 2014;111(48):17230–5. doi: 10.1073/pnas.1410083111 25385592; PubMed Central PMCID: PMC4260561.
36. Yu Y, Grahn RA, Lyons LA. Mocha tyrosinase variant: a new flavour of cat coat coloration. Anim Genet. 2019;50(2):182–6. Epub 2019/02/05. doi: 10.1111/age.12765 30716167.
37. Yu Y, Shumway KL, Matheson JS, Edwards ME, Kline TL, Lyons LA. Kidney and cystic volume imaging for disease presentation and progression in the cat autosomal dominant polycystic kidney disease large animal model. BMC Nephrology. 2019;20(1):259. doi: 10.1186/s12882-019-1448-1 31299928
38. Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brondum RF, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014;46(8):858–65. Epub 2014/07/16. doi: 10.1038/ng.3034 25017103.
39. Bai B, Zhao WM, Tang BX, Wang YQ, Wang L, Zhang Z, et al. DoGSD: the dog and wolf genome SNP database. Nucleic Acids Res. 2015;43(Database issue):D777–83. Epub 2014/11/19. doi: 10.1093/nar/gku1174 25404132; PubMed Central PMCID: PMC4383968.
40. Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, et al. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell. 2013;154(3):691–703. Epub 2013/07/31. doi: 10.1016/j.cell.2013.06.040 23890820; PubMed Central PMCID: PMC3732391.
41. Hermsen R, de Ligt J, Spee W, Blokzijl F, Schafer S, Adami E, et al. Genomic landscape of rat strain and substrain variation. BMC Genomics. 2015;16:357. Epub 2015/05/07. doi: 10.1186/s12864-015-1594-1 25943489; PubMed Central PMCID: PMC4422378.
42. Teng H, Zhang Y, Shi C, Mao F, Cai W, Lu L, et al. Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species. Mol Biol Evol. 2017;34(9):2214–28. Epub 2017/05/10. doi: 10.1093/molbev/msx157 28482038; PubMed Central PMCID: PMC5850741.
43. Yang J, Li WR, Lv FH, He SG, Tian SL, Peng WF, et al. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments. Mol Biol Evol. 2016;33(10):2576–92. Epub 2016/07/13. doi: 10.1093/molbev/msw129 27401233; PubMed Central PMCID: PMC5026255.
44. Chen ZH, Zhang M, Lv FH, Ren X, Li WR, Liu MJ, et al. Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species. Genome Biol Evol. 2018;10(5):1282–97. Epub 2018/05/24. doi: 10.1093/gbe/evy085 29790980; PubMed Central PMCID: PMC5963296.
45. Choi JW, Chung WH, Lee KT, Cho ES, Lee SW, Choi BH, et al. Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds. DNA Res. 2015;22(4):259–67. Epub 2015/06/29. doi: 10.1093/dnares/dsv011 26117497; PubMed Central PMCID: PMC4535618.
46. Jagannathan V, Gerber V, Rieder S, Tetens J, Thaller G, Drogemuller C, et al. Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses. Anim Genet. 2019;50(1):74–7. Epub 2018/12/14. doi: 10.1111/age.12753 30525216.
47. Bimber BN, Ramakrishnan R, Cervera-Juanes R, Madhira R, Peterson SM, Norgren RB Jr, et al. Whole genome sequencing predicts novel human disease models in rhesus macaques. Genomics. 2017;109(3–4):214–20. doi: 10.1016/j.ygeno.2017.04.001 28438488
48. Xue C, Raveendran M, Harris RA, Fawcett GL, Liu X, White S, et al. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res. 2016;26(12):1651–62. Epub 2016/12/10. doi: 10.1101/gr.204255.116 27934697; PubMed Central PMCID: PMC5131817.
49. The 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526(7571):68–74. Epub 2015/10/04. doi: 10.1038/nature15393 26432245; PubMed Central PMCID: PMC4750478.
50. Ottoni C, Van Neer W, De Cupere B, Daligault J, Guimaraes S, Peters J, et al. The palaeogenetics of cat dispersal in the ancient world. Nature Ecology & Evolution. 2017;1(7):0139.
51. Vigne J-D, Guilaine J, Debue K, Haye L, Gérard P. Early taming of the cat in Cyprus. Science. 2004;304(5668):259-. doi: 10.1126/science.1095335 15073370
52. Van Neer W, Linseele V, Friedman R, De Cupere B. More evidence for cat taming at the Predynastic elite cemetery of Hierakonpolis (Upper Egypt). Journal of Archaeological Science. 2014;45:103–11.
53. Driscoll CA, Menotti-Raymond M, Roca AL, Hupe K, Johnson WE, Geffen E, et al. The Near Eastern origin of cat domestication. Science. 2007;317(5837):519–23. Epub 2007/06/30. doi: 10.1126/science.1139518 17600185; PubMed Central PMCID: PMC5612713.
54. Kurushima JD, Lipinski MJ, Gandolfi B, Froenicke L, Grahn JC, Grahn RA, et al. Variation of cats under domestication: genetic assignment of domestic cats to breeds and worldwide random-bred populations. Anim Genet. 2013;44(3):311–24. Epub 2012/11/23. doi: 10.1111/age.12008 23171373; PubMed Central PMCID: PMC3594446.
55. Festing MF. Inbred strains should replace outbred stocks in toxicology, safety testing, and drug development. Toxicologic pathology. 2010;38(5):681–90. doi: 10.1177/0192623310373776 20562325
56. Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, et al. Predicting the clinical impact of human mutation with deep neural networks. Nat Genet. 2018;50(8):1161–70. Epub 2018/07/25. doi: 10.1038/s41588-018-0167-z 30038395; PubMed Central PMCID: PMC6237276.
57. Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nature Reviews Genetics. 2009;10(4):241. doi: 10.1038/nrg2554 19293820
58. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536(7616):285–91. Epub 2016/08/19. doi: 10.1038/nature19057 27535533; PubMed Central PMCID: PMC5018207.
59. Gudbjartsson DF, Helgason H, Gudjonsson SA, Zink F, Oddson A, Gylfason A, et al. Large-scale whole-genome sequencing of the Icelandic population. Nat Genet. 2015;47(5):435–44. Epub 2015/03/26. doi: 10.1038/ng.3247 25807286.
60. The 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. A map of human genome variation from population-scale sequencing. Nature. 2010;467(7319):1061–73. Epub 2010/10/29. doi: 10.1038/nature09534 20981092; PubMed Central PMCID: PMC3042601.
61. Gabor L, Malik R, Canfield P. Clinical and anatomical features of lymphosarcoma in 118 cats. Australian Veterinary Journal. 1998;76(11):725–32. doi: 10.1111/j.1751-0813.1998.tb12300.x 9862061
62. Louwerens M, London CA, Pedersen NC, Lyons LA. Feline lymphoma in the post-feline leukemia virus era. J Vet Intern Med. 2005;19(3):329–35. Epub 2005/06/16. doi: 10.1892/0891-6640(2005)19[329:flitpl]2.0.co;2 15954547.
63. Fabrizio F, Calam AE, Dobson JM, Middleton SA, Murphy S, Taylor SS, et al. Feline mediastinal lymphoma: a retrospective study of signalment, retroviral status, response to chemotherapy and prognostic indicators. J Feline Med Surg. 2014;16(8):637–44. Epub 2013/12/25. doi: 10.1177/1098612X13516621 24366846.
64. Tetzlaff MT, Yu W, Li M, Zhang P, Finegold M, Mahon K, et al. Defective cardiovascular development and elevated cyclin E and Notch proteins in mice lacking the Fbw7 F-box protein. Proc Natl Acad Sci U S A. 2004;101(10):3338–45. Epub 2004/02/10. doi: 10.1073/pnas.0307875101 14766969; PubMed Central PMCID: PMC373463.
65. Tsunematsu R, Nakayama K, Oike Y, Nishiyama M, Ishida N, Hatakeyama S, et al. Mouse Fbw7/Sel-10/Cdc4 is required for notch degradation during vascular development. J Biol Chem. 2004;279(10):9417–23. Epub 2003/12/16. doi: 10.1074/jbc.M312337200 14672936.
66. Mao JH, Perez-Losada J, Wu D, Delrosario R, Tsunematsu R, Nakayama KI, et al. Fbxw7/Cdc4 is a p53-dependent, haploinsufficient tumour suppressor gene. Nature. 2004;432(7018):775–9. Epub 2004/12/14. doi: 10.1038/nature03155 15592418.
67. Perez-Losada J, Wu D, DelRosario R, Balmain A, Mao JH. Allele-specific deletions in mouse tumors identify Fbxw7 as germline modifier of tumor susceptibility. PLoS One. 2012;7(2):e31301. Epub 2012/02/22. doi: 10.1371/journal.pone.0031301 22348067; PubMed Central PMCID: PMC3278431.
68. Maser RS, Choudhury B, Campbell PJ, Feng B, Wong KK, Protopopov A, et al. Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature. 2007;447(7147):966–71. Epub 2007/05/23. doi: 10.1038/nature05886 17515920; PubMed Central PMCID: PMC2714968.
69. Roversi G, Picinelli C, Bestetti I, Crippa M, Perotti D, Ciceri S, et al. Constitutional de novo deletion of the FBXW7 gene in a patient with focal segmental glomerulosclerosis and multiple primitive tumors. Sci Rep. 2015;5:15454. Epub 2015/10/21. doi: 10.1038/srep15454 26482194; PubMed Central PMCID: PMC4612309.
70. Mahamdallie S, Yost S, Poyastro-Pearson E, Holt E, Zachariou A, Seal S, et al. Identification of new Wilms tumour predisposition genes: an exome sequencing study. Lancet Child Adolesc Health. 2019;3(5):322–31. Epub 2019/03/20. doi: 10.1016/S2352-4642(19)30018-5 30885698; PubMed Central PMCID: PMC6472290.
71. Havrilla JM, Pedersen BS, Layer RM, Quinlan AR. A map of constrained coding regions in the human genome.
72. Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21(6):974–84. Epub 2011/02/18. doi: 10.1101/gr.114876.110 21324876; PubMed Central PMCID: PMC3106330.
73. Klambauer G, Schwarzbauer K, Mayr A, Clevert DA, Mitterecker A, Bodenhofer U, 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 Res. 2012;40(9):e69. Epub 2012/02/04. doi: 10.1093/nar/gks003 22302147; PubMed Central PMCID: PMC3351174.
74. Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):i333–i9. doi: 10.1093/bioinformatics/bts378 22962449; PubMed Central PMCID: PMC3436805.
75. Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 2014;15(6):R84. doi: 10.1186/gb-2014-15-6-r84 24970577; PubMed Central PMCID: PMC4197822.
76. Kosugi S, Momozawa Y, Liu X, Terao C, Kubo M, Kamatani Y. Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing. Genome Biol. 2019;20(1):117. Epub 2019/06/05. doi: 10.1186/s13059-019-1720-5 31159850; PubMed Central PMCID: PMC6547561.
77. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun. 2019;10(1):1784. Epub 2019/04/18. doi: 10.1038/s41467-018-08148-z 30992455; PubMed Central PMCID: PMC6467913.
78. Horton WA, Hall JG, Hecht JT. Achondroplasia. Lancet. 2007;370(9582):162–72. Epub 2007/07/17. doi: 10.1016/S0140-6736(07)61090-3 17630040.
79. Foldynova-Trantirkova S, Wilcox WR, Krejci P. Sixteen years and counting: the current understanding of fibroblast growth factor receptor 3 (FGFR3) signaling in skeletal dysplasias. Hum Mutat. 2012;33(1):29–41. Epub 2011/11/03. doi: 10.1002/humu.21636 22045636; PubMed Central PMCID: PMC3240715.
80. Alhamoudi KM, Bhat J, Nashabat M, Alharbi M, Alyafee Y, Asiri A, et al. A Missense Mutation in the UGDH Gene Is Associated With Developmental Delay and Axial Hypotonia. Front Pediatr. 2020;8:71. Epub 2020/03/17. doi: 10.3389/fped.2020.00071 32175296; PubMed Central PMCID: PMC7056728.
81. Hengel H, Bosso-Lefevre C, Grady G, Szenker-Ravi E, Li H, Pierce S, et al. Loss-of-function mutations in UDP-Glucose 6-Dehydrogenase cause recessive developmental epileptic encephalopathy. Nat Commun. 2020;11(1):595. Epub 2020/02/01. doi: 10.1038/s41467-020-14360-7 32001716; PubMed Central PMCID: PMC6992768.
82. Garcia-Garcia MJ, Anderson KV. Essential role of glycosaminoglycans in Fgf signaling during mouse gastrulation. Cell. 2003;114(6):727–37. Epub 2003/09/25. doi: 10.1016/s0092-8674(03)00715-3 14505572.
83. Choksi SP, Babu D, Lau D, Yu X, Roy S. Systematic discovery of novel ciliary genes through functional genomics in the zebrafish. Development. 2014;141(17):3410–9. Epub 2014/08/21. doi: 10.1242/dev.108209 25139857; PubMed Central PMCID: PMC4199137.
84. Pontius JU, Mullikin JC, Smith DR, Agencourt Sequencing T, Lindblad-Toh K, Gnerre S, et al. Initial sequence and comparative analysis of the cat genome. Genome Res. 2007;17(11):1675–89. Epub 2007/11/03. doi: 10.1101/gr.6380007 17975172; PubMed Central PMCID: PMC2045150.
85. Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32(14):2103–10. Epub 2016/05/07. doi: 10.1093/bioinformatics/btw152 27153593; PubMed Central PMCID: PMC4937194.
86. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963. doi: 10.1371/journal.pone.0112963 25409509; PubMed Central PMCID: PMC4237348.
87. Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nature biotechnology. 2012;30(8):771. doi: 10.1038/nbt.2303 22797562
88. Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Kallberg M, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220–2. doi: 10.1093/bioinformatics/btv710 26647377.
89. Kent WJ. BLAT—the BLAST-like alignment tool. Genome Res. 2002;12(4):656–64. Epub 2002/04/05. doi: 10.1101/gr.229202 11932250; PubMed Central PMCID: PMC187518.
90. Small C, Bassham S, Catchen J, Amores A, Fuiten A, Brown R, et al. The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome biology. 2016;17(1):258. doi: 10.1186/s13059-016-1126-6 27993155
91. Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 2012;40(Database issue):D130–5. Epub 2011/11/29. doi: 10.1093/nar/gkr1079 22121212; PubMed Central PMCID: PMC3245008.
92. Thibaud-Nissen F, Souvorov A, Murphy T, DiCuccio M, Kitts P. Eukaryotic genome annotation pipeline. The NCBI Handbook [Internet] 2nd edition: National Center for Biotechnology Information (US); 2013.
93. Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, et al. Ensembl 2018. Nucleic Acids Res. 2018;46(D1):D754–D61. Epub 2017/11/21. doi: 10.1093/nar/gkx1098 29155950; PubMed Central PMCID: PMC5753206.
94. Visser M, Weber KL, Lyons LA, Rincon G, Boothe DM, Merritt DA. Identification and quantification of domestic feline cytochrome P450 transcriptome across multiple tissues. J Vet Pharmacol Ther. 2019;42(1):7–15. Epub 2018/09/02. doi: 10.1111/jvp.12708 30171610; PubMed Central PMCID: PMC6322962.
95. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. Epub 2010/07/21. doi: 10.1101/gr.107524.110 20644199; PubMed Central PMCID: PMC2928508.
96. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11 0 1–33. Epub 2014/11/29. doi: 10.1002/0471250953.bi1110s43 25431634; PubMed Central PMCID: PMC4243306.
97. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:13033997. 2013.
98. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. Epub 2009/06/10. doi: 10.1093/bioinformatics/btp352 19505943; PubMed Central PMCID: PMC2723002.
99. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature genetics. 2011;43(5):491. doi: 10.1038/ng.806 21478889
100. Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, et al. Scaling accurate genetic variant discovery to tens of thousands of samples. BioRxiv. 2018:201178.
101. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. doi: 10.1093/bioinformatics/btr330 21653522; PubMed Central PMCID: PMC3137218.
102. Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. BioRxiv. 2019:531210.
103. Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, et al. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Methods. 2015;12(10):966–8. doi: 10.1038/nmeth.3505 26258291; PubMed Central PMCID: PMC4589466.
104. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang 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. Epub 2012/06/26. doi: 10.4161/fly.19695 22728672; PubMed Central PMCID: PMC3679285.
105. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6. Epub 2011/01/12. doi: 10.1038/nbt.1754 21221095; PubMed Central PMCID: PMC3346182.
Článek vyšel v časopise
PLOS Genetics
2020 Číslo 10
- Případ Bulovka: Jak postupují jiné nemocnice, aby podobným tragédiím zabránily?
- Jak často se u masových střelců vyskytují duševní choroby?
- Zvoní budík? Přispěte si ještě chvilku, bude vám to myslet rychleji!
- FDA varuje před selfmonitoringem cukru pomocí chytrých hodinek. Jak je to v Česku?
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
Nejčtenější v tomto čísle
- Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies
- RNA-directed DNA Methylation
- The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations
- Correction: Molecular predictors of brain metastasis-related microRNAs in lung adenocarcinoma