Can Base Pair Positions Change Between Patches Of Builds? (Say Between Grch37.P5 And Grch37.P10)

Question

[Abdel]

Can base pair positions change between patches of builds? Are there for example SNPs or genes that can have different base pair positions between GRCh37.p5 and GRCh37.p10?

[Pierre Lindenbaum]

related : What's the difference between two versions of the same assembly ?

Answer 1

[deanna.church]

I'm not sure where you are getting your data- but here are some things to think about. 1. Assembly: The only difference between the patch releases (GRCh37.p*) and GRCh37 are the actual patch sequences. There are a few examples of patches that have updated between patch releases, but this is relatively rare- and the data was released as part of GRCh37 never changes. Here is some more information about the assembly model: http://www.ncbi.nlm.nih.gov/assembly/model/. For more information about the GRC you can check here: http://genomereference.org

1. Annotation runs: Annotation runs tend to be independent of assembly builds. Ensembl re-annotates on a regular basis, as does NCBI. Because the patch releases happen quarterly, it is typical that they will have different patch versions of the assembly in any given release. So- annotation locations can change between patch releases- but this can be due to annotation run issues (new evidence, algorithms, etc). Also including different sequences in the assembly can affect the annotation - for example, if a gene isn't well represent in the Primary assembly (say GRCh37) it may align to a related location and get annotated there. If the GRC releases a fix patch containing the real location for this gene, the the annotation at the location in the Primary assembly would likely (hopefully!) change.

Does that help?

Deanna

Answer 2

[DavidStreid]

No (I believe), assuming that gene/snp still maps to the primary assembly.

Patches "add information to the assembly without disrupting the chromosome coordinates" and like Deanna said, these patches, i.e. >patch_id ... in the reference FASTA file, are the only differences. So assuming that dbsnp entry, sequencing read, etc. of that snp/gene still maps to the primary assembly in both GRCh37.p5 and GRCh37.p10, and not a patched scaffold unique to GRCh37.p10, the position is the same.

For instance, take an example SNP mapping to the primary assembly, chromosome 8 - it says it's mapped to chromosome 8 (>chr8 ... in the reference file) and that position will stay constant, as long as anything w/ that SNP still maps there.

However, take another SNP mapping to a patched scaffold, NT_187515.1 - if a read w/ this SNP were mapped to a reference w/o this patch/scaffold, then it would map to a different scaffold, and position.