Amino acid mutations/alignments with reference genes about mixcr HOT 4 CLOSED

Complex issue. For example how to report two consequent substitutions, which are only non-synonymous when present together. Either report them as synonymous or allow to aggregate mutations (milib)

from mixcr.

I'm thinking about simplest algorithm:

• Translate mutated sequence
• Enumerate substitutions between mutated and germline sequences

ATTAAGACACAGATA
||||  |||| ||||
ATTATAACACCGATA

->

ATTAAGACACAGATA
 I  K  T  Q  I
 |     |     |
 I  I  T  P  I
ATTATAACACCGATA

->

SK1I, SQ3P

Exceptional cases:

• If sequence contain long (~ >15 nt) region with shifted frame, don't output mutations, just print something like (frameshift)
• But if region is not too long (like the following), still print mutations for it.

ATTAAGACACA-GATA
ATTA-GACACATGATA

->

ATTAAGACACAGATA
 I  K  T  Q  I
 |           |
 I  R  H  M  I
ATTAGACACATGATA

->

SK1R, ST2H, SQ3M

• For deletions of 3,6,9... nucleotides there is also possible to output amino acid deletions... But it is not so simple in general case

from mixcr.

Basic feature for this is already implemented in com.milaboratory.core.mutations.MutationsUtil.nt2aa()...

from mixcr.

"it is now the case a mixture of SHM and NGS-related"

NGS error should be negligible compared with shm, since 'the mutation occur at a rate of about one muation per V-region sequence per cell division" ?

I am trying to calculated SHM using mixcr.

I use the command

mixcr exportClones -vHit -jHit -dHit -count -aaFeature CDR3 -vAlignment -jAlignment

to export the clone with v j alignment, and calculate the mutation based on alignment. but the shm result is very different from what I get using igblast. (we are switching from igblast to mixcr)

Am I in the right direction? Thanks.

of course, if the shm can be exported directly, it will be great.

from mixcr.