This results in the following genotypes being assigned:
locus
subject_1
subject_2
subject_3
subject_4
subject_5
A
A*01:01:140,A*11:303
A*24:608N,A*24:608N
A*01:01:143,A*03:01:103
A*29:01:01,A*29:01:01
A*03:01:119,A*24:608N
B
B*07:386N,B*07:386N
B*07:386N,B*40:01:02
B*07:386N,B*57:01:01
B*07:386N,B*07:386N
B*07:386N,B*07:386N
C
C*07:01:106,C*07:02:104
C*03:392N,C*07:02:101
C*07:02:128,C*07:02:128
C*15:05:02,C*15:05:02
C*07:02:101,C*07:02:101
DQA1
DQA1*03:01:11,DQA1*03:03:01
DQA1*01:02:01,DQA1*01:02:01
DQA1*01:03:01,DQA1*01:05:01
DQA1*01:01:01,DQA1*01:05:01
DQA1*05:05:01,DQA1*01:02:01
DQB1
DQB1*03:02:01,DQB1*03:01:01
DQB1*06:304N,DQB1*06:02:01
DQB1*06:352,DQB1*05:01:01
DQB1*05:01:01,DQB1*05:01:01
DQB1*03:01:46,DQB1*06:02:01
DRB1
DRB1*04:01:01,DRB1*04:01:01
DRB1*08:01:01,DRB1*08:01:01
DRB1*10:01:01,DRB1*13:01:01
DRB1*10:01:01,DRB1*01:02:01
DRB1*11:04:01,DRB1*15:01:01
Since the subjects were selected because they share a CD8+ T cell response to a certain antigen I'm not surprised that they share class B alleles. However, I don't think it's plausible that they all share B*07:386N, since it's a null allele. In case of subjects 1, 4 & 5 the result even implies that B*07:386N makes up both alleles.
Do you have an explanation for this?
Is there a way to exclude null alleles from the reference?
Thanks for creating arcasHLA!
Since 10X references that arcasHLA does a good job at genotyping I tried to use it with scRNA data.
I extracted reads using the following command:
And then genotyped:
This results in the following genotypes being assigned:
Since the subjects were selected because they share a CD8+ T cell response to a certain antigen I'm not surprised that they share class B alleles. However, I don't think it's plausible that they all share B*07:386N, since it's a null allele. In case of subjects 1, 4 & 5 the result even implies that B*07:386N makes up both alleles.
Do you have an explanation for this? Is there a way to exclude null alleles from the reference?