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Identical sequences with different feature annotations - 174 alleles #150

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mhalagan opened this issue Jul 12, 2018 · 2 comments
Closed

Identical sequences with different feature annotations - 174 alleles #150

mhalagan opened this issue Jul 12, 2018 · 2 comments

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@mhalagan
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mhalagan commented Jul 12, 2018 •
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Feature annotations should not differ between database releases if the sequence is the same. If an annotation is changed in a later database release, then it should also be updated in all previous database releases that contain that sequence. The feature annotations for 174 alleles change between database releases even though the sequences do not. These differences mainly impact intron-4, exon-5, and intron-5 for HLA-DQB1. Below is a table of all the observed instances of this issue.

DB Allele # Features Removed # Features Added # Features Differ Features Removed Features Added Features that Differ
3160 HLA-B*15:302N 0 0 3 exon_5 exon_2 exon_3
3160 HLA-C*08:89N 0 0 1 exon_2
3170 HLA-B*15:302N 0 0 1 exon_5
3180 HLA-B*39:97N 0 0 1 exon_3
3180 HLA-C*08:89N 0 0 1 exon_2
3190 HLA-C*08:89N 0 0 1 exon_2
3220 HLA-B*07:251N 0 0 1 exon_3
3280 HLA-B*15:149N 0 0 1 exon_4
3280 HLA-B*15:246N 0 0 1 exon_4
3280 HLA-C*08:89N 0 0 1 exon_2
3290 HLA-B*15:149N 0 0 1 exon_4
3290 HLA-B*15:246N 0 0 1 exon_4
3300 HLA-A*24:155N 1 0 0 exon_5
3300 HLA-A*26:01:01:03N 0 0 2 intron_4 exon_4
3300 HLA-B*07:44N 0 0 2 intron_4 exon_4
3300 HLA-B*15:01:01:02N 0 1 1 exon_1 intron_1
3300 HLA-B*15:149N 0 0 1 exon_4
3300 HLA-B*15:246N 0 0 2 exon_5 exon_4
3300 HLA-B*44:02:01:02S 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:02:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:02:04 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:53Q 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:62 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:79 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:80 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:81 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:82 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:83 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:84 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*02:96N 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:04 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:05 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:06 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:07 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:08 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:09 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:10 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:11 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:12 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:14 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:15 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:16 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:17 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:01:18 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:17 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:22 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:35 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:36 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:01:37 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:01:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:09 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:12 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:21 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:22 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:23 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:02:24 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:03:02:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:03:02:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:03:02:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:03:04 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:04:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:04:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:05:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:150 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:191 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:195 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:196 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:197Q 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:19:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:211 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:239 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:243 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:245 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:246 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:247 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:248 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:249 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:250 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:251 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:252 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:253 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:254 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*03:263 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*04:01:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*04:02:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*04:02:11 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*04:02:12 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*04:11 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*04:32 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:01:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:01:04 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:01:05 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:23 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:01:24 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:02:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:02:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:02:01:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:02:07 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:02:11 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:102 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:103 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:104 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:106 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:108 0 1 1 exon_5 exon_6
3300 HLA-DQB1*05:133 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:134 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:135 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:136 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:137 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:148 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:149 1 1 0 exon_6 exon_5
3300 HLA-DQB1*05:31 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:43:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:52 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:57 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*05:96 0 1 1 exon_5 exon_6
3300 HLA-DQB1*05:97 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:01:08 0 1 1 exon_5 exon_6
3300 HLA-DQB1*06:01:10 0 1 1 exon_5 exon_6
3300 HLA-DQB1*06:01:11 0 1 1 exon_5 exon_6
3300 HLA-DQB1*06:02:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:01:03 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:17 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:22 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:23 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:25 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:26 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:27 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:02:28 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:12 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:14 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:20 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:21 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:23 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:24 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:25 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:03:26 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:04:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:09:01:01 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:09:01:02 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:103 0 1 1 exon_5 exon_6
3300 HLA-DQB1*06:111 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:117 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:125 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:187 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:188 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:217 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:218 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:219 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:221 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:222 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:223 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:224 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:225 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:226 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:227 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:228 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:37 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:44 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:84 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:90 0 2 1 exon_5 intron_5 intron_4
3300 HLA-DQB1*06:99:02 0 1 1 exon_5 exon_6
3320 HLA-C*07:02:01:17N 0 0 2 intron_3 exon_3
@mhalagan mhalagan changed the title Same sequence different feature annotations - *167 alleles* Identical sequences with different feature annotations - *167 alleles* Jul 12, 2018
@mhalagan mhalagan changed the title Identical sequences with different feature annotations - *167 alleles* Identical sequences with different feature annotations - 167 alleles Jul 12, 2018
@mhalagan mhalagan changed the title Identical sequences with different feature annotations - 167 alleles Identical sequences with different feature annotations - 174 alleles Jul 12, 2018
@jrob119
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jrob119 commented Jul 31, 2018

Thanks for reporting these inconsistencies, we are reviewing the output and will be checking the latest release first for any corrections, and then will look at the feasibility of updating previous releases.

@jrob119
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jrob119 commented Oct 4, 2019

The descriptions of null alleles and in particular those with indels, can be subject to change as the we look at implementing new feature qualifiers. The example given includes HLA-DQB1 where the non-expressed exon 5 sequence is now marked up rather than be included in intron. This is an example of where changing the description adds information but does cause a discrepancy between versions.

@jrob119 jrob119 closed this as completed Oct 15, 2019
This issue was closed.
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@mhalagan @jrob119