search

Illumina / ExpansionHunter

A tool for estimating repeat sizes
Other
174 stars 53 forks source link

Is locus structure really important? #188

Open devrankrg opened 4 months ago

devrankrg commented 4 months ago 
[
    {
        "LocusId": "BEAN1",
        "LocusStructure": "(TAAAA)*",
        "VariantType": "RareRepeat",
        "ReferenceRegion": "16:66490398-66490453",
        "RepeatUnit": "TAAAA",
        "Gene": "BEAN1",
        "Inheritance": "AD",
        "GeneRegion": "intron",
        "GeneId": "ENSG00000166546",
        "DiscoveryMethod": "L",
        "DiscoveryYear": 2009,
        "PathogenicMotif": "TGGAA  (+TAGAA)",
        "Diseases": [
            {
                "Symbol": "SCA31",
                "Name": "Spinocerebellar ataxia 31",
                "Inheritance": "AD",
                "OMIM": "117210",
                "PathogenicMin": 500
            }
        ],
        "OfftargetRegions": [
            "10:94531487-94532013",
            "13:71654237-71654677",
            "17:46999846-47000288",
            "20:17081089-17081531",
            "21:23710971-23711386",
            "22:21395520-21395928",
            "2:44013201-44013638",
            "4:21714633-21715248",
            "5:116726213-116726658",
            "5:55105820-55106484",
            "7:151316374-151316835",
            "7:75175257-75175679",
            "9:110701505-110702081",
            "9:25543141-25543554",
            "X:6802782-6803290"
        ],
        "MainReferenceRegion": "16:66490398-66490453"
    }
]

I am doing research on the BEAN1 repeat. This repeat may have different repeat sequences in the same region, such as "TAGAA, TGGAA, TAAAA". The repeat sequence also affects the pathogenicity of the repeat. When I want to investigate pathogenic repeat, changing the locus structure with pathogenic repeat unit (TGGAA) has almost no effect on the result. Even when I write something of the same length but meaningless, like "HASAN", the result is still the same. What does regex used to find repeats do and how does it work?

Repeat's gnomad link = https://gnomad.broadinstitute.org/short-tandem-repeat/BEAN1?dataset=gnomad_r4

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  HG002.GRCh38.2x250
chr16   66490398    .   A   <STR8>,<STR17>  .   PASS    END=66490453;REF=11;RL=55;RU=TGGAA;VARID=BEAN1;REPID=BEAN1  GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:19/18:20/24:0/0:61.009132
chr16   66490398    .   A   <STR8>,<STR17>  .   PASS    END=66490453;REF=11;RL=55;RU=TAAAA;VARID=BEAN1;REPID=BEAN1  GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:20/16:19/25:0/0:60.867580
chr16   66490398    .   A   <STR8>,<STR17>  .   PASS    END=66490453;REF=11;RL=55;RU=TRRRA;VARID=BEAN1;REPID=BEAN1  GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:20/16:19/25:0/0:60.867580
chr16   66490398    .   A   <STR8>,<STR17>  .   PASS    END=66490453;REF=11;RL=55;RU=HASAN,VARID=BEAN1;REPID=BEAN1  GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 1/2:SPANNING/SPANNING:8/17:8-8/17-17:19/16:19/24:0/0:60.726027

Although the RU field changed, the result remained almost unchanged I tried; "LocusStructure": "(TAAAA)" "LocusStructure": "(TGGAA)" "LocusStructure": "(TRRRA)" "LocusStructure": "(HASAN)"