mutation notation

[DesitnationMD]

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Can anyone tell me if there is a typical or standard notation you use to identify a specific mutation type?

For example if given the following information:

the mutation is known as CKR-5Δ32

and I am shown the original and mutated gene

how am I supposed to know what type of mutation this is?

the correct answer is deletion, but what's to say its not an insertion since both sequences have the exact same # of bases?

I know its not missense or nonsense cause it not a point mutation. any help?

 

[aldol16]

If it's an insertion, you wouldn't have shifted the sequence to the left. Notice that at the site of mutation (ATT AAA GAT AGT...), the sequence replicates the WT sequence later on near the end (TTA AAG ATA...). If it were an insertion, it should be shifted to the right instead of the left.

 

[Wolfpack93]

If it's an insertion, you wouldn't have shifted the sequence to the left. Notice that at the site of mutation (ATT AAA GAT AGT...), the sequence replicates the WT sequence later on near the end (TTA AAG ATA...). If it were an insertion, it should be shifted to the right instead of the left.

I'm pretty sure this would be a deletion. You're comparing the wild type to the delta 32 (which I'm pretty sure means deletion of 32 bases but I'm too lazy to count them all). Your wild type is the normal gene, so since that huge area between ttaaagata.... Is gone it must be a deletion

 

[Wolfpack93]

If it's an insertion, you wouldn't have shifted the sequence to the left. Notice that at the site of mutation (ATT AAA GAT AGT...), the sequence replicates the WT sequence later on near the end (TTA AAG ATA...). If it were an insertion, it should be shifted to the right instead of the left.

Just realized I pretty much repeated what you said haha

 

[aldol16]

I'm pretty sure this would be a deletion. You're comparing the wild type to the delta 32 (which I'm pretty sure means deletion of 32 bases but I'm too lazy to count them all). Your wild type is the normal gene, so since that huge area between ttaaagata.... Is gone it must be a deletion

I know. I'm saying that it's a deletion. I'm explaining why it's not an insertion.

 

[DesitnationMD]

If it's an insertion, you wouldn't have shifted the sequence to the left. Notice that at the site of mutation (ATT AAA GAT AGT...), the sequence replicates the WT sequence later on near the end (TTA AAG ATA...). If it were an insertion, it should be shifted to the right instead of the left.

I'm pretty sure this would be a deletion. You're comparing the wild type to the delta 32 (which I'm pretty sure means deletion of 32 bases but I'm too lazy to count them all). Your wild type is the normal gene, so since that huge area between ttaaagata.... Is gone it must be a deletion

Sorry, i'm still confused. My physics background makes this stuff particularly aggrivating for me.

I get that in the 57 base sequence, it looks like a whole chunk is missing or replaced

WILD TYPE: TCT CAT TTT CCA TAC AGT CAG TAT CAA TTC TGG AAG AAT TTC CAG ACA TTA AAG ATA
MUTANT: TCT CAT TTT CCA TAC ATT AAA GAT AGT CAT CTT GGG ATG ACG CAC TGC TGC ATC AAC

@aldol16 you seem to be referring to the sequence in green to indicate the bold stuff from the wild type has been deleted, correct? How can I know that is not just randon coincedence, and that another chunk has been inserted that is longer, and includes the green and red bases in the mutant strain?

@Wolfpack93 are you saying that when I see a delta seign in a notation like that I can just infer deletion? if @aldol16 is correct then it was 32 bases (all bold black) that was deleted.

I get that deletion seems correct. I guess my problem would be how can I rule out or exclude insertion definitively?

INSERTION VERSION:

WILD TYPE: TCT CAT TTT CCA TAC AGT CAG TAT CAA TTC TGG AAG AAT TTC CAG ACA TTA AAG ATA

MUTANT: TCT CAT TTT CCA TAC ATT AAA GAT AGT CAT CTT GGG ATG ACG CAC TGC TGC ATC AAC

the blue bases would be the inserted mutation and to me the answer looks the same (although it would be a 41 base insert). Anyone able to elaborate or is it just i need to know delta = deletion and the # indicated. Does the sequence not matter at all once i see that delta sign?

Thanks!

 

[Wolfpack93]

Sorry, i'm still confused. My physics background makes this stuff particularly aggrivating for me.

I get that in the 57 base sequence, it looks like a whole chunk is missing or replaced

WILD TYPE: TCT CAT TTT CCA TAC AGT CAG TAT CAA TTC TGG AAG AAT TTC CAG ACA TTA AAG ATA
MUTANT: TCT CAT TTT CCA TAC ATT AAA GAT AGT CAT CTT GGG ATG ACG CAC TGC TGC ATC AAC

@aldol16 you seem to be referring to the sequence in green to indicate the bold stuff has been deleted, correct? How can I know that is not just randon coincedence, and that another chunk has been inserted that is longer, and includes the green and red bases in the mutant strain?

@Wolfpack93 are you saying that when I see a delta seign in a notation like that I can just infer deletion? if @aldol16 is correct then it was 32 bases (all bold black) that was deleted.

I get that deletion seems/is correct. I guess my problem would be how can I rule out or exclude insertion definitively, if at all?

INSERTION VERSION:

WILD TYPE: TCT CAT TTT CCA TAC AGT CAG TAT CAA TTC TGG AAG AAT TTC CAG ACA TTA AAG ATA

MUTANT: TCT CAT TTT CCA TAC ATT AAA GAT AGT CAT CTT GGG ATG ACG CAC TGC TGC ATC AAC

the blue bases would be the inserted mutation and to me the answer looks the same. Anyone able to elaborate?

Thanks!

No there's no insertion going on here. Yes the bolder black is the 32 bp deleted from the wt. I think what you're thinking is an insertion is just the downstream DNA that you can't see in the wild type because it still has the original sequence present. The only thing going on between the two is the deletion of 32 bp. and idk if you can say all delta followed by a number mutations mean a deletion of that many bases but i believe the delta signifies a mutation (any kind) has occurred.

 

[aldol16]

@aldol16 you seem to be referring to the sequence in green to indicate the bold stuff from the wild type has been deleted, correct? How can I know that is not just randon coincedence, and that another chunk has been inserted that is longer, and includes the green and red bases in the mutant strain?

Because the MCAT focuses on "most likely." It's entirely possible that you could have replicated the sequence in green completely by chance in your "insertion." But think of what must occur for that to happen. Each spot in the sequence has a 1/4 chance of being a particular nucleotide base. There are nine bases in the green sequence that occurs both in the mutation and in the WT. For an insertion to do all that by chance only, well, you're the physicist. You should know the probably if that occurring is close to nil. (1/4)^9, precisely.

 

[DesitnationMD]

Because the MCAT focuses on "most likely." It's entirely possible that you could have replicated the sequence in green completely by chance in your "insertion." But think of what must occur for that to happen. Each spot in the sequence has a 1/4 chance of being a particular nucleotide base. There are nine bases in the green sequence that occurs both in the mutation and in the WT. For an insertion to do all that by chance only, well, you're the physicist. You should know the probably if that occurring is close to nil. (1/4)^9, precisely.

Thaanks @aldol16 and @Wolfpack93 this whole "most likely" thing is what threw me. i expected the correct answer to be correct, not just more likely and a wrong answer to be entirely incorrect. damn medicine and its lack of definitive answers sometimes!