DRB3 and DRB5

Question

DRB3 and DRB5

bsb2014 opened this issue 10 months ago · 15 comments

bsb2014 commented 10 months ago

Hi, can SpecHLA type DRB3 and DRB5 as kourami? Thanks

Answer 1 · 2023-11-08T16:15:41.000Z

Hello, now SpecHLA does not support DRB3 and DRB5.

Answer 2 · 2023-11-08T16:18:29.000Z

Do you have any plans to make SpecHLA support additional HLAs?

Answer 3 · 2023-11-08T16:33:39.000Z

How does the SpecHLA phase the variants when only short reads are used? Thanks

Answer 4 · 2023-11-08T16:33:42.000Z

Yes. Our group is developing another package to support additional HLA genes. I will let you know once it is finished.

Answer 5 · 2023-11-08T16:38:08.000Z

If the short reads cannot afford enough phase information, SpecHLA will use HLA database, genotype frequency, and pedigree information to phase the variants.

Answer 6 · 2023-11-08T18:05:31.000Z

It would be great if the next release could type HLA using diploid assembly. Thanks

Answer 7 · 2023-11-09T01:49:11.000Z

Great suggestion. We do have some code to extract the sequence of HLA genes from the diploid assembly. I will update SpecHLA to support typing from diploid assembly as soon as possible.

Answer 8 · 2023-11-09T05:50:41.000Z

Hello,
Thanks for the valuable suggestion. As suggested, we added a module to support HLA typing from diploid assemblies (typing_from_assembly.py). Please see the changes in SpecHLA v1.0.3 or the latest commit.

Answer 9 · 2024-05-17T06:58:21.000Z

Yes. Our group is developing another package to support additional HLA genes. I will let you know once it is finished.

Hello, shuai,
Are there any other tools can work for long read HLA typing ( nanopore sequencing) ?
if we just add DRB3/4/5 imgt sequence into SpecHLA db , SpeckHLA can detect accurately DRB3/4/5 allele ?

Expecting your reply !
thanks .

Answer 10 · 2024-05-17T07:47:39.000Z

Hello,
Sorry for the delayed update. If you add DRB3/4/5 imgt sequence into SpecHLA db, it still needs some revisions in the scripts. I believe it will work well after some adjustments. I wonder do you have any benchmark data (with real data and ground truth)? With real benchmark data, we can add this function quickly.

Also, as I know HLA*LA also can work with nanopore sequencing data. But it might require too many computational resources. You can have a try on it.

Best,
Shuai

Answer 11 · 2024-05-17T08:10:15.000Z

Hello, Sorry for the delayed update. If you add DRB3/4/5 imgt sequence into SpecHLA db, it still needs some revisions in the scripts. I believe it will work well after some adjustments. I wonder do you have any benchmark data (with real data and ground truth)? With real benchmark data, we can add this function quickly.

Also, as I know HLA*LA also can work with nanopore sequencing data. But it might require too many computational resources. You can have a try on it.

Best, Shuai

Yeah, I have got the benchmark data for A,B,C ,DRB1, DQA1,DQB1, DPA1, DPB1, DRB3/4/5 , that's why I hope you nice guy can support DRB3/4/5 as soon as possible .
could you update specHLA to support DRB3/4/5 this week ?
Thank you very much !!!

Answer 12 · 2024-05-17T08:27:55.000Z

So great! We will update it very soon. This week is a little challenging but I believe we can finish it next week. Could you please send us the benchmark data, so that we can start to adjust the parameters.

Answer 13 · 2024-05-17T08:52:28.000Z

So great! We will update it very soon. This week is a little challenging but I believe we can finish it next week. Could you please send us the benchmark data, so that we can start to adjust the parameters.

well, what is your email address ?

Answer 14 · 2024-05-17T08:56:55.000Z

Thanks. My email is swang66-c@my.cityu.edu.hk

Answer 15 · 2024-05-17T09:01:10.000Z

Thanks. My email is swang66-c@my.cityu.edu.hk

have sent my email , please check that ,thanks