I recently completed a GWAS job and found some genetic regions of interest. But when I was doing gene annotation, I found that when the version of the cattle reference genome (UMD3.1.1 or ARS-UCD1.2) is different, different results will be produced. e.g. position of DGAT1 in ARS-UCD1.2 (BTA 14: 603981..614153))and in UMD3.1.1.(BTA 14: 1795425..1804838)(1795425..1804838)
My SNP chip data comes from many versions of the chip (for historical reasons), and I took out a common location for use. But now I am very confused, which one should I use? I found a similar question and their answer is ARS-UCD1.2. (Researchgate.net/post/UMD311_or_ARS-UCD12_Can_we_make_an_analysis_of_snp_data_with_different_references_genomes)
If you know of any good ways or options to deal with this problem, please let me know. Thanks!
Hi Yansen
I see your problem. you can deal with several versions of genomes to produce files that will rely on only one of these.
regarding genomic positons, I suggest you to use one of the tools produced by the UCSC database (http://genome.ucsc.edu/cgi-bin/hgLiftOver) and update all your data on the last genome, which will display the most possible annotations.
all the best (select cow as original genome and cow/UMD3.1.1 for destination.
all the best
fred
Frederic Lepretre Thank you for your reply, this tool is very good. But I found my original SNP data from BovineSNP50_v1-BovineSNP50_v3. So I finally chose UMD3.1 annotations. But now I think one other question is after we finish the GWAS analysis, do we choose the corresponding reference genome version for annotation? Or transfer the results to a new reference genome (ARS-UCD1.2) position, and then annotate with the new reference genome (ARS-UCD1.2)?
I personally think that the latest reference genome should be used for candidate gene annotation, but because my result is a genetic region, I will try the above two and finally compare.
What do you think?
Hi Yansen,
working on the last version of the genome will allow you to get access to more information. yes, it's better to do this way in your case.
take care when managing files and genomes, just this point to carry.
all the best
fred
Hi Frederic Lepretre
Here I give the results of the test I just used tools produced by the UCSC database. Our idea is feasible for most. I tested 19 sets of data (different chromosomes), and 4 sets were not successfully transformed. This means that if your results can be converted, you can use the new reference genome (ARS-UCD1.2, released in 2018), but if not, then you have to continue using the old reference genome (I currently have no good other ideas). An important result of my own results is that I can only use the reference genome (UMD3.1, released in 2014). The following are the reasons given by the website that cannot be converted:
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Deleted in new: Sequence intersects no chains Partially deleted in new: Sequence insufficiently intersects one chain Split in new: Sequence insufficiently intersects multiple chains Duplicated in new: Sequence sufficiently intersects multiple chains Boundary problem: Missing start or end base in an exon
``````````````````
Kind regards,
Yansen
Check https://www.nature.com/articles/s41598-021-87078-1?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=JRCN_1_LW01_CN_SCIREP_article_paid_XMOL
Hi Dr Yansen Chen . I hope the following link could help: https://www.nature.com/articles/s41598-021-87078-1?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=JRCN_1_LW01_CN_SCIREP_article_paid_XMOL
See the following link that might help: Article Sequence-based genome-wide association study of individual m...
Kindly see the following link too: Article Genome-wide association studies for tick resistance in Bos t...
Hi Aref Wazwaz Chinaza Godswill Awuchi
Thank you for your suggestions. I also think it is a good way to fill in the chip data as sequencing data and screen out the variants of the new version of the reference genome. But for the Abanda et al. (2021) papers that you all gave, I didn't get a method suitable for my problem. would you like to explain it in detail?
Check on this paper from Benin,
https://www.mdpi.com/2076-2615/11/10/2833/pdf
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