Page 115 - GTM-2-3

Global Translational Medicine TEs link to Parkinson’s risk and progression

https://doi.org/10.1126/science.abk3112 37. Li H, Durbin R, 2009, Fast and accurate short read
alignment with Burrows-Wheeler transform. Bioinformatics,
26. Mills RE, Bennett EA, Iskow RC, et al., 2007, Which
transposable elements are active in the human genome? 25: 1754–1760.
Trends Genet, 23: 183–191. https://doi.org/10.1093/bioinformatics/btp324
https://doi.org/10.1016/j.tig.2007.02.006 38. DePristo MA, Banks E, Poplin R, et al., 2011, A framework
for variation discovery and genotyping using next-
27. Kazazian HH Jr., Wong C, Youssoufian H, et al., 1988, generation DNA sequencing data. Nat Genet, 43: 491–498.
Haemophilia A resulting from de novo insertion of L1
sequences represents a novel mechanism for mutation in https://doi.org/10.1038/ng.806
man. Nature, 332: 164–166. 39. Regier AA, Farjoun Y, Larson DE, et al., 2018, Functional
https://doi.org/10.1038/332164a0 equivalence of genome sequencing analysis pipelines
enables harmonized variant calling across human genetics
28. Payer LM, Steranka JP, Yang WR, et al., 2017, Structural projects. Nat Commun, 9: 4038.
variants caused by Alu insertions are associated with risks
for many human diseases. Proc Natl Acad Sci U S A, 114: https://doi.org/10.1038/s41467-018-06159-4
E3984–E3992. 40. Gardner EJ, Lam VK, Harris DN, et al., 2017, The mobile
https://doi.org/10.1073/pnas.1704117114 element locator tool (MELT): Population-scale mobile
element discovery and biology. Genome Res, 27: 1916–1929.
29. Payer LM, Burns KH, 2019, Transposable elements in
human genetic disease. Nat Rev Genet, 20: 760–772. https://doi.org/10.1101/gr.218032.116
https://doi.org/10.1038/s41576-019-0165-8 41. Sudmant PH, Rausch T, Gardner EJ, et al., 2015, An
integrated map of structural variation in 2,504 human
30. Burns KH, 2020, Our conflict with transposable elements and genomes. Nature, 526: 75–81.
its implications for human disease. Annu Rev Pathol, 15: 51–70.
https://doi.org/10.1038/nature15394
https://doi.org/10.1146/annurev-pathmechdis-012419-032633
42. Niu Y, Teng X, Zhou H, et al., 2022, Characterizing mobile
31. Ahmadi A, De Toma I, Vilor-Tejedor N, et al., 2020, element insertions in 5675 genomes. Nucleic Acids Res,
Transposable elements in brain health and disease. Ageing 50: 2493–2508.
Res Rev, 64: 101153.
https://doi.org/10.1093/nar/gkac128
https://doi.org/10.1016/j.arr.2020.101153
43. Danecek P, Auton A, Abecasis G, et al., 2011, The variant call
32. Pfaff AL, Bubb VJ, Quinn JP, et al., 2021, Reference SVA format and VCFtools. Bioinformatics, 27: 2156–2158.
insertion polymorphisms are associated with Parkinson’s
disease progression and differential gene expression. NPJ https://doi.org/10.1093/bioinformatics/btr330
Parkinsons Dis, 7: 44. 44. Purcell S, Neale B, Todd-Brown K, et al., 2007, PLINK:
https://doi.org/10.1038/s41531-021-00189-4 A tool set for whole-genome association and population-
based linkage analyses. Am J Hum Genet, 81: 559–575.
33. Koks S, Pfaff AL, Singleton LM, et al., 2022, Non-reference
genome transposable elements (TEs) have a significant https://doi.org/10.1086/519795
impact on the progression of the Parkinson’s disease. Exp 45. McLaren W, Gil L, Hunt SE, et al., 2016, The ensembl variant
Biol Med, 247: 1680–1690. effect predictor. Genome Biol, 17: 122.
https://doi.org/10.1177/15353702221117147 https://doi.org/10.1186/s13059-016-0974-4
34. Parkinson Progression Marker Initiative, 2011, The 46. Hubisz MJ, Pollard KS, Siepel A, 2011, PHAST and
Parkinson progression marker initiative (PPMI). Prog RPHAST: Phylogenetic analysis with space/time models.
Neurobiol, 95: 629–635. Brief Bioinform, 12: 41–51.
https://doi.org/10.1016/j.pneurobio.2011.09.005 https://doi.org/10.1093/bib/bbq072
35. Rosenthal LS, Drake D, Alcalay RN, et al., 2016, The NINDS 47. Pollard KS, Hubisz MJ, Rosenbloom KR, et al., 2010,
Parkinson’s disease biomarkers program. Mov Disord, Detection of nonneutral substitution rates on mammalian
31: 915–923. phylogenies. Genome Res, 20: 110–121.
https://doi.org/10.1002/mds.26438 https://doi.org/10.1101/gr.097857.109
36. Kang UJ, Goldman JG, Alcalay RN, et al., 2016, The BioFIND 48. Navarro Gonzalez J, Zweig AS, Speir ML, et al., 2021, The
study: Characteristics of a clinically typical Parkinson’s UCSC genome browser database: 2021 update. Nucleic Acids
disease biomarker cohort. Mov Disord, 31: 924–932. Res, 49: D1046–D1057.
https://doi.org/10.1002/mds.26613 https://doi.org/10.1093/nar/gkaa1070

Volume 2 Issue 3 (2023) 11 https://doi.org/10.36922/gtm.1583