SNP/Variant "Changing" chromosomes with LiftOver from mm6 to mm10 for Linux Command Line

[Benthal, Joseph T]

To UCSC Support,

 

I am currently using the LiftOver tool, which has been beneficial in my work so far. However, a specific variant of interest is changing chromosomes after LiftOver from mm6 to mm10 using the mm6ToMm10.chain.gz file. Specifically, it is changing from chromosome 3 to chromosome 5, while most variants in my .bed file seem to stay on the same chromosome after LiftOver. Is this behavior erroneous, or is this an expected behavior? Out of the 732 SNPs that were input, only one SNP was exhibiting this behavior.

 

Thank you,

 

Joe

 

Joseph Benthal

PhD Candidate

Southard-Smith Lab

Human Genetics Program

Vanderbilt University

 

[Luis Nassar]

Hello, Joe.

Thanks for your interest in the Genome Browser.

There could be a few reasons to are seeing this liftOver behavior. Could you share the SNP that lifted to the difference coordinate so we can take a look?

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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[Benthal, Joseph T]

Hi Lou,

 

Thanks for the quick response. The SNP is chr3:72523023 on the mm6 build, which is being lifted over to chr5:89687694.

 

Thanks,

 

Joe

 

From: Luis Nassar <lrna...@ucsc.edu>
Sent: Monday, September 19, 2022 5:13 PM
To: Benthal, Joseph T <joseph.t...@vanderbilt.edu>
Cc: gen...@soe.ucsc.edu; Southard-smith, Michelle Michelle (University) <michelle.so...@vanderbilt.edu>
Subject: Re: [genome] SNP/Variant "Changing" chromosomes with LiftOver from mm6 to mm10 for Linux Command Line

 

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[Benthal, Joseph T]

Hi Lou,

 

I did a little investigating on my own using sequence alignment tools in R: I took sequences that are each 243 base pairs long (with the middle base being the locus of the SNP of interest) from the original mm6 chromosome 3 sequence and the lifted over mm10 chromosome 5 sequence, and they align perfectly. See the image below, which I’m not sure will show up on the Google group. Could this be that mm6’s chromosome 3 has a chunk of chromosome 5 in it, which was corrected in the mm10 genome build (or an earlier subsequent build)?

 

Thanks,

 

Joe

 

[Luis Nassar]

Hello, Joe.

Thank you for your interest in the Genome Browser.

That specific SNP you mentioned in chr3 of mm6 (chr3:72523023) falls into the following sequence clone for that assembly (https://www.ncbi.nlm.nih.gov/nuccore/AC102056.16#comment_AC102056.16). In mm6, that clone was placed in chr3.

If you take a look at the comment, AC102056.16 was replaced by AC102056.17 (https://www.ncbi.nlm.nih.gov/nucleotide/AC102056.17#comment_AC102056.17) in 2005 which was placed in chr5. So that updated clone (I believe the two just have a few base pairs difference) went from being in chr3 in assemblies before the change to chr5 afterwards.

With that in mind, liftOver is correctly placing the variant in chr5 in mm10.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute