Sample_1006_1007_alleles.csv and Sample_1050_1051_alleles.csv

[liangyanabcd]

Hi，I am a user of scHLApers, thank you for developing such an excellent tool. Could you please explain how the files Sample_1006_1007_alleles.csv and Sample_1050_1051_alleles.csv on the GitHub website were obtained? For example, where did the 'count' column come from? Also, why is the first column different in the two files, Sample_1006_1007_alleles.csv and Sample_1050_1051_alleles.csv? Are they detecting different genes in different samples?" Thank you！

[joycekang]

Hello! The alleles.csv files contain the HLA alleles (defined by IMGT) for each classical HLA gene (HLA-A, -B, -C, -DRB1, -DQA1, -DQB1, -DPA1, -DPB1) for that individual. We obtained these by imputing the HLA alleles from genotype array data using SNP2HLA. You can see the notebook that generated the alleles.csv files for our project here: https://github.com/immunogenomics/hla2023/blob/main/scripts/1_genotype_and_QC/2_HLA_imp_newPanel_SNP2HLA.ipynb

The columns are different for each individual because individuals have different alleles.

For example, in Sample_1006_1007_alleles.csv:

HLA_DQB1*03:01 | HLA_DQB1 | 1
HLA_DQB1*06:03 | HLA_DQB1 | 1
HLA_DPA1*01:03 | HLA_DPA1 | 2
HLA_DPB1*04:01 | HLA_DPB1 | 2

This is saying that the individual is heterozygous for HLA-DQB1 and their alleles are HLA-DQB1*03:01 and 06:03, and they have one copy of each (the "count"). Then, the individual is homozygous for HLA-DPA1 (01:03) with 2 copies of that allele (hence the "2"). They are homozygous for HLA-DPB1 (04:01) with 2 copies of that allele. Does this make sense?

The HLA allele calls can be obtained via HLA imputation, or direct sequence based typing, depending on what data you have available.

[liangyanabcd]

Thanks~

[joycekang]

Hi Yan Liang, Yes, we used the SNP2HLA.py script, as well as version 2 of the multi-ethnic HLA imputation reference panel (Sakaue et al., Nat Protocols, 2023). Is this the same imputation reference that you used? The results should have a column that looks like “0|0, 0|1, 1|0, or 1|1” which denotes the imputed genotype for each allele. In your output, I bet “A” and “P” refer to absent/present, but it doesn’t look like te output I would expect from the multi-ethnic HLA imputation reference so I’m not 100% sure how to interpret it. I’m attaching the imputed data (output from SNP2HLA.py) for the Randolph dataset. You can test it using the code in the notebook, starting at the “New Panel | SNP2HLA | Randolph” section. Let me know if you have any questions! Joyce From: liangyanabcd ***@***.***> Date: Saturday, February 3, 2024 at 10:08 PM To: immunogenomics/scHLApers ***@***.***> Cc: Kang, Joyce ***@***.***>, Comment ***@***.***> Subject: Re: [immunogenomics/scHLApers] Sample_1006_1007_alleles.csv and Sample_1050_1051_alleles.csv (Issue #1) Thank you for your help, so you used the SNP2HLA.py program （https://github.com/immunogenomics/HLA_analyses_tutorial/blob/main/tutorial_HLAQCImputation.ipynb）to<https://github.com/immunogenomics/HLA_analyses_tutorial/blob/main/tutorial_HLAQCImputation.ipynb%EF%BC%89to> perform imputation on HLA? I use SNP2HLA_package_v1.0.3/SNP2HLA/SNP2HLA.csh, and the results are as follows, P A or A P or 0 A makes me confused. In addition, can you give me the data you used in the script https://github.com/immunogenomics/hla2023/blob/main/scripts/1_genotype_and_QC/2_HLA_imp_newPanel_SNP2HLA.ipynb for testing? My email: ***@***.******@***.***>. sg. Thank you! 6 HLA_A_01 0 30019970 P A 6 HLA_A_0101 0 30019970 P A 6 HLA_A_02 0 30019970 P A 6 HLA_A_0201 0 30019970 P A 6 HLA_A_0203 0 30019970 P A 6 HLA_A_0206 0 30019970 P A 6 HLA_A_0207 0 30019970 P A 6 HLA_A_0211 0 30019970 P A 6 HLA_A_0216 0 30019970 P A 6 HLA_A_03 0 30019970 P A 6 HLA_A_0301 0 30019970 P A 6 HLA_A_0302 0 30019970 P A 6 HLA_A_11 0 30019970 P A 6 HLA_A_1101 0 30019970 P A 6 HLA_A_1102 0 30019970 P A 6 HLA_A_24 0 30019970 P A 6 HLA_A_2402 0 30019970 P A 6 HLA_A_2403 0 30019970 0 A 6 HLA_A_2407 0 30019970 P A 6 HLA_A_2410 0 30019970 P A 6 HLA_A_26 0 30019970 P A 6 HLA_A_2601 0 30019970 P A 6 HLA_A_2603 0 30019970 P A 6 HLA_A_29 0 30019970 P A 6 HLA_A_2901 0 30019970 P A 6 HLA_A_2902 0 30019970 0 A 6 HLA_A_30 0 30019970 P A 6 HLA_A_3001 0 30019970 P A 6 HLA_A_31 0 30019970 P A 6 HLA_A_3101 0 30019970 P A 6 HLA_A_32 0 30019970 P A 6 HLA_A_3201 0 30019970 P A 6 HLA_A_33 0 30019970 P A 6 HLA_A_3303 0 30019970 P A 6 HLA_A_34 0 30019970 P A 6 HLA_A_3401 0 30019970 P A 6 HLA_A_68 0 30019970 P A 6 HLA_A_6801 0 30019970 P A 6 HLA_A_74 0 30019970 0 A 6 HLA_A_7401 0 30019970 0 A 6 HLA_C_01 0 31346171 P A 6 HLA_C_0102 0 31346171 P A 6 HLA_C_0103 0 31346171 P A 6 HLA_C_02 0 31346171 0 A 6 HLA_C_0202 0 31346171 0 A 6 HLA_C_03 0 31346171 P A 6 HLA_C_0302 0 31346171 P A 6 HLA_C_0303 0 31346171 P A 6 HLA_C_0304 0 31346171 P A 6 HLA_C_04 0 31346171 P A 6 HLA_C_0401 0 31346171 P A 6 HLA_C_0403 0 31346171 P A 6 HLA_C_0406 0 31346171 0 A 6 HLA_C_06 0 31346171 P A 6 HLA_C_0602 0 31346171 P A 6 HLA_C_07 0 31346171 P A 6 HLA_C_0701 0 31346171 P A 6 HLA_C_0702 0 31346171 P A 6 HLA_C_0704 0 31346171 P A 6 HLA_C_0726 0 31346171 P A 6 HLA_C_08 0 31346171 P A 6 HLA_C_0801 0 31346171 P A 6 HLA_C_12 0 31346171 P A 6 HLA_C_1202 0 31346171 P A 6 HLA_C_1203 0 31346171 P A 6 HLA_C_1204 0 31346171 0 A 6 HLA_C_14 0 31346171 P A 6 HLA_C_1402 0 31346171 P A 6 HLA_C_1403 0 31346171 P A 6 HLA_C_15 0 31346171 P A 6 HLA_C_1502 0 31346171 P A 6 HLA_C_1505 0 31346171 P A 6 HLA_C_1507 0 31346171 0 A 6 HLA_C_16 0 31346171 P A 6 HLA_C_1602 0 31346171 P A 6 HLA_B_07 0 31431272 P A 6 HLA_B_0702 0 31431272 P A 6 HLA_B_0705 0 31431272 P A 6 HLA_B_08 0 31431272 P A 6 HLA_B_0801 0 31431272 P A 6 HLA_B_13 0 31431272 P A 6 HLA_B_1301 0 31431272 P A 6 HLA_B_1302 0 31431272 P A 6 HLA_B_15 0 31431272 P A 6 HLA_B_1501 0 31431272 P A 6 HLA_B_1502 0 31431272 P A 6 HLA_B_1505 0 31431272 P A 6 HLA_B_1507 0 31431272 P A 6 HLA_B_1508 0 31431272 0 A 6 HLA_B_1511 0 31431272 0 A 6 HLA_B_1512 0 31431272 0 A 6 HLA_B_1513 0 31431272 P A 6 HLA_B_1518 0 31431272 P A 6 HLA_B_1521 0 31431272 P A 6 HLA_B_1525 0 31431272 P A 6 HLA_B_18 0 31431272 P A 6 HLA_B_1801 0 31431272 P A 6 HLA_B_1802 0 31431272 0 A 6 HLA_B_27 0 31431272 P A 6 HLA_B_2704 0 31431272 P A 6 HLA_B_2706 0 31431272 P A 6 HLA_B_35 0 31431272 P A 6 HLA_B_3501 0 31431272 P A 6 HLA_B_3503 0 31431272 P A 6 HLA_B_3505 0 31431272 P A 6 HLA_B_3530 0 31431272 0 A 6 HLA_B_37 0 31431272 P A 6 HLA_B_3701 0 31431272 P A 6 HLA_B_38 0 31431272 P A 6 HLA_B_3801 0 31431272 P A 6 HLA_B_3802 0 31431272 P A 6 HLA_B_39 0 31431272 P A 6 HLA_B_3901 0 31431272 P A 6 HLA_B_40 0 31431272 P A 6 HLA_B_4001 0 31431272 P A 6 HLA_B_4002 0 31431272 P A 6 HLA_B_4006 0 31431272 P A 6 HLA_B_44 0 31431272 P A 6 HLA_B_4403 0 31431272 P A 6 HLA_B_46 0 31431272 P A 6 HLA_B_4601 0 31431272 P A 6 HLA_B_48 0 31431272 P A 6 HLA_B_4801 0 31431272 P A 6 HLA_B_49 0 31431272 0 A 6 HLA_B_4901 0 31431272 0 A 6 HLA_B_50 0 31431272 0 A 6 HLA_B_5001 0 31431272 0 A 6 HLA_B_51 0 31431272 P A 6 HLA_B_5101 0 31431272 P A 6 HLA_B_5102 0 31431272 P A 6 HLA_B_5107 0 31431272 0 A 6 HLA_B_52 0 31431272 P A 6 HLA_B_5201 0 31431272 P A 6 HLA_B_54 0 31431272 P A 6 HLA_B_5401 0 31431272 P A 6 HLA_B_55 0 31431272 P A 6 HLA_B_5501 0 31431272 0 A 6 HLA_B_5502 0 31431272 P A 6 HLA_B_56 0 31431272 P A 6 HLA_B_5601 0 31431272 P A 6 HLA_B_57 0 31431272 P A 6 HLA_B_5701 0 31431272 P A 6 HLA_B_58 0 31431272 P A 6 HLA_B_5801 0 31431272 P A 6 HLA_B_59 0 31431272 0 A 6 HLA_B_5901 0 31431272 P A 6 HLA_B_67 0 31431272 P A 6 HLA_B_6701 0 31431272 P A 6 HLA_DRB1_01 0 32660042 P A 6 HLA_DRB1_0101 0 32660042 P A 6 HLA_DRB1_03 0 32660042 P A 6 HLA_DRB1_0301 0 32660042 P A 6 HLA_DRB1_04 0 32660042 P A 6 HLA_DRB1_0401 0 32660042 P A 6 HLA_DRB1_0403 0 32660042 P A 6 HLA_DRB1_0404 0 32660042 P A 6 HLA_DRB1_0405 0 32660042 P A 6 HLA_DRB1_0406 0 32660042 P A 6 HLA_DRB1_0410 0 32660042 0 A 6 HLA_DRB1_07 0 32660042 P A 6 HLA_DRB1_0701 0 32660042 P A 6 HLA_DRB1_08 0 32660042 P A 6 HLA_DRB1_0801 0 32660042 0 A 6 HLA_DRB1_0802 0 32660042 P A 6 HLA_DRB1_0803 0 32660042 P A 6 HLA_DRB1_0809 0 32660042 0 A 6 HLA_DRB1_09 0 32660042 P A 6 HLA_DRB1_0901 0 32660042 P A 6 HLA_DRB1_10 0 32660042 P A 6 HLA_DRB1_1001 0 32660042 P A 6 HLA_DRB1_11 0 32660042 P A 6 HLA_DRB1_1101 0 32660042 P A 6 HLA_DRB1_1105 0 32660042 P A 6 HLA_DRB1_12 0 32660042 P A 6 HLA_DRB1_1201 0 32660042 P A 6 HLA_DRB1_1202 0 32660042 P A 6 HLA_DRB1_1203 0 32660042 P A 6 HLA_DRB1_13 0 32660042 P A 6 HLA_DRB1_1301 0 32660042 P A 6 HLA_DRB1_1302 0 32660042 P A 6 HLA_DRB1_1312 0 32660042 P A 6 HLA_DRB1_14 0 32660042 P A 6 HLA_DRB1_1401 0 32660042 P A 6 HLA_DRB1_1403 0 32660042 0 A 6 HLA_DRB1_1404 0 32660042 P A 6 HLA_DRB1_1405 0 32660042 P A 6 HLA_DRB1_1407 0 32660042 0 A 6 HLA_DRB1_15 0 32660042 P A 6 HLA_DRB1_1501 0 32660042 P A 6 HLA_DRB1_1502 0 32660042 P A 6 HLA_DRB1_1504 0 32660042 P A 6 HLA_DRB1_16 0 32660042 P A 6 HLA_DRB1_1602 0 32660042 P A 6 HLA_DQA1_01 0 32716284 P A 6 HLA_DQA1_0101 0 32716284 P A 6 HLA_DQA1_0102 0 32716284 P A 6 HLA_DQA1_0103 0 32716284 P A 6 HLA_DQA1_02 0 32716284 P A 6 HLA_DQA1_0201 0 32716284 P A 6 HLA_DQA1_03 0 32716284 P A 6 HLA_DQA1_0301 0 32716284 P A 6 HLA_DQA1_04 0 32716284 P A 6 HLA_DQA1_0401 0 32716284 P A 6 HLA_DQA1_05 0 32716284 P A 6 HLA_DQA1_0501 0 32716284 P A 6 HLA_DQA1_06 0 32716284 P A 6 HLA_DQA1_0601 0 32716284 P A 6 HLA_DQB1_02 0 32739039 P A 6 HLA_DQB1_0201 0 32739039 P A 6 HLA_DQB1_03 0 32739039 P A 6 HLA_DQB1_0301 0 32739039 P A 6 HLA_DQB1_0302 0 32739039 P A 6 HLA_DQB1_0303 0 32739039 P A 6 HLA_DQB1_04 0 32739039 P A 6 HLA_DQB1_0401 0 32739039 P A 6 HLA_DQB1_0402 0 32739039 P A 6 HLA_DQB1_05 0 32739039 P A 6 HLA_DQB1_0501 0 32739039 P A 6 HLA_DQB1_0502 0 32739039 P A 6 HLA_DQB1_0503 0 32739039 P A 6 HLA_DQB1_06 0 32739039 P A 6 HLA_DQB1_0601 0 32739039 P A 6 HLA_DQB1_0602 0 32739039 P A 6 HLA_DQB1_0603 0 32739039 P A 6 HLA_DQB1_0604 0 32739039 P A 6 HLA_DQB1_0609 0 32739039 P A 6 HLA_DQB1_0610 0 32739039 0 A 6 HLA_DPA1_01 0 33145064 P A 6 HLA_DPA1_0103 0 33145064 P A 6 HLA_DPA1_0104 0 33145064 0 A 6 HLA_DPA1_02 0 33145064 A P 6 HLA_DPA1_0201 0 33145064 P A 6 HLA_DPA1_0202 0 33145064 A P 6 HLA_DPA1_04 0 33145064 P A 6 HLA_DPA1_0401 0 33145064 P A 6 HLA_DPB1_01 0 33157346 P A 6 HLA_DPB1_0101 0 33157346 P A 6 HLA_DPB1_02 0 33157346 P A 6 HLA_DPB1_0201 0 33157346 P A 6 HLA_DPB1_0202 0 33157346 P A 6 HLA_DPB1_03 0 33157346 P A 6 HLA_DPB1_0301 0 33157346 P A 6 HLA_DPB1_04 0 33157346 P A 6 HLA_DPB1_0401 0 33157346 P A 6 HLA_DPB1_0402 0 33157346 P A 6 HLA_DPB1_05 0 33157346 P A 6 HLA_DPB1_0501 0 33157346 P A 6 HLA_DPB1_09 0 33157346 P A 6 HLA_DPB1_0901 0 33157346 P A 6 HLA_DPB1_10 0 33157346 P A 6 HLA_DPB1_100 0 33157346 0 A 6 HLA_DPB1_10001 0 33157346 P A 6 HLA_DPB1_1001 0 33157346 P A 6 HLA_DPB1_13 0 33157346 P A 6 HLA_DPB1_1301 0 33157346 P A 6 HLA_DPB1_14 0 33157346 P A 6 HLA_DPB1_1401 0 33157346 P A 6 HLA_DPB1_15 0 33157346 P A 6 HLA_DPB1_1501 0 33157346 0 A 6 HLA_DPB1_16 0 33157346 P A 6 HLA_DPB1_1601 0 33157346 P A 6 HLA_DPB1_17 0 33157346 P A 6 HLA_DPB1_1701 0 33157346 P A 6 HLA_DPB1_19 0 33157346 P A 6 HLA_DPB1_1901 0 33157346 P A 6 HLA_DPB1_21 0 33157346 P A 6 HLA_DPB1_2101 0 33157346 P A 6 HLA_DPB1_26 0 33157346 P A 6 HLA_DPB1_2601 0 33157346 P A 6 HLA_DPB1_28 0 33157346 P A 6 HLA_DPB1_2801 0 33157346 P A 6 HLA_DPB1_31 0 33157346 P A 6 HLA_DPB1_3101 0 33157346 P A — Reply to this email directly, view it on GitHub<#1 (comment)>, or 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[liangyanabcd]

Thanks， I need some time to test. I will give you feedback as soon as possible!