WGS Simulation of DUF1220 Regions
Revision as of 21:03, 5 February 2026 by Lorikrammer (talk | contribs)
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"name": "WGS Simulation of DUF1220 Regions",
"version": "4.0",
"license": "https://opensource.org/licenses/MIT",
"created": "2020-08-30T11:30:52.000Z",
"modified": "2024-11-17T14:18:09.680Z",
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"Olduvai protein domains (formerly \"DUF1220\") are the most duplicated protein coding sequence in the human genome (https://doi.org/10.1371/journal.pbio.0020207). They are expressed in many tissues, including strongly in the brain (https://doi.org/10.1126/science.1127980). The copy number of Olduvai domains has been linked to increased brain size (https://doi.org/10.1007/s00429-014-0814-9), and performance on IQ tests (https://doi.org/10.1007/s00439-014-1489-2), as well as neurodiverse states like autism (https://doi.org/10.1371/journal.pgen.1004241).",
"Precise evaluation of copy number in humans has been difficult to achieve, as ratiometric approaches fail to identify small changes when the total number is in the ~300 range, as in humans. Read depth approaches using short read WGS data are promising, but most existing pipelines mask repeats altogether (potentially including these sequences), and those that do measure copy number do it relative to the gene. However, Olduvai domains are known to exist in different number and kind within a family of genes, rendering this approach inoperative. The pipeline described here is used to identify the copy number of genetic sequences independent of the genes in which they occur, and with higher fidelity than existing methods, designed specifically with Olduvai copy number in mind.",
"Approximately 25 individuals were randomly chosen from each of the American (Utah -- Northern and Western European ancestry; CEU), Nigerian (Yoruba; YRI), Han Chinese (Beijing; CHB), Japanese (Tokyo; JPT), Mexican-American (Los Angeles; MXL), Colombian (Medellin; CLM), Puerto Rican (Puerto Rico; PUR), African-American (Southwest US; ASW), Luhya (Webuye, Kenya; LWK), Han Chinese (South China; CHS), Tuscan (Toscana, Italia; TSI), Spanish (Iberian populations; IBS), Finnish (Finland; FIN), and BGR populations for a total of 324 individuals. Where domains were more than 1 kb apart, the boundaries of the domains were extended up to 250 bp to allow the possibility of capturing unique sequence directly adjacent to the domain. No intermediate files were generated because the commands were run executed as a pipe at the command line, so uuids were used for the file IOs in the Description Domain. Relative file paths refer to the local machine on which this pipeline was run. This pipeline was created based on the work of Astling et al. doi: 10.1186/s12864-017-3976-z"
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