Emedgene
Illumina Connected Software
  • Get Started with Emedgene
    • Get started with Emedgene
    • How can Emedgene help you solve a case?
  • Emedgene analyze manual
    • Getting around the platform
      • Top navigation panel
      • Emedgene Applications menu
      • Dashboard
      • Settings
      • User roles
      • Help
      • Okta identity management
    • Managing data storage
      • Manage data storages
      • Manage Azure Blob data storage
      • Manage S3 credentials
      • Manage BaseSpace storage
      • Manage GCS storage (V37.0+)
      • Bring Your Own Bucket
      • Bring Your Own Key
    • Cases tab
      • Cases tab
      • Cases table
      • Case status
      • Browse and select cases
      • Case details
    • Creating a single case
      • Add a new case
      • Select sample type
      • Create a family tree
      • Family tree legend
      • Add a sample
      • Supported Variant callers
      • Adding patient info for the proband
      • Adding patient info for the non-proband samples
      • Secondary findings
      • Labeling a case
      • Gene list
      • Supported parental ethnicities
    • Creating multiple cases
      • Batch case upload from platform
      • CSV format requirements
      • Batch case upload via CLI
    • Reviewing a case
      • Individual case page
      • Individual case page: Top bar
      • Individual case page: Top bar
      • Candidates tab
      • Most Likely Candidates and Candidates
      • Genome Overview
      • Analysis tools tab
      • Variant table columns
      • Variant table
      • Variant search
      • Multiselection of variants and bulk actions (34.0+)
      • Download variants
      • Manually add variants to a delivered case
      • Filters/Presets panel
      • Filters
      • Presets
      • Preset groups
      • Variant Type Filters
      • Variant Effect Filters
      • Quality Filters
      • Polymorphism Filters
      • Gene Filters
      • Phenomatch Filters
      • Inheritance Filters
      • Zygosity Filters
      • User Filters
      • Evidence page
      • Phenotypic match strength
      • Lab tab
      • Versions tab
      • Editing an existing case
      • Finalizing a case
      • Clinical Report
      • Reflex genetic testing
      • Variant zygosity notations
      • STR calling and interpretation
    • Variant page
      • Variant page
      • Variant page top bar
      • Variant tagging widget
      • Variant activity panel
      • Desktop apps panel
      • Clinical Significance section
      • Summary section
      • Quality section
      • Visualization section
      • Population Statistics section
      • Related Cases section
      • CNV overlap percentage
      • Evidence section
      • ACMG SNV Classification wizard
      • Logic behind ACMG classification of SNVs
      • ACMG CNV Classification wizard
      • Variant page sidebar (2.29+)
    • Variant visualization setup
      • Enabling visualization for a VCF case
      • Integration between emedgene and desktop IGV
      • Loading alignment files to your desktop IGV (32.0+)
    • Analyze Network
      • Analyze Network Setup
      • Network sharing configuration
      • Case subject consent for extended sharing
      • Public vs Private network
      • Create a network
      • Set network data sharing policy
      • Leave a network
      • Delete a network
    • Settings
      • My settings
      • Management
      • User Management
      • Network
      • Organization Settings (33.0+)
    • Integrations
      • API Beginner Guide
      • Advanced API Implementations
      • API Key Generation
      • BSSH Integration
      • ICA Integration
      • Webhook Integration
  • Emedgene Curate Manual
    • Curate overview
      • Curate overview
      • Emedgene Applications menu
      • Curate navigation panel
      • Genome assemblies supported by Curate
    • Curate Variants
      • Curate Variants overview
      • Curate Variant table
      • Curate Variant page
      • How to add a variant to Curate
      • Curate Variant annotations in the case
    • Curate Genes (2.28+)
      • Curate Genes overview
      • Curate Gene table
      • Curate Gene page
      • How to add a gene to Curate
    • Import Curate annotations to the case (30.0+)
      • Import Curate Variant annotations to the case (30.0+)
      • Import Curate Gene annotations to the case (30.0+)
  • Frequently Asked Questions
    • All FAQ
      • Which browser should I use with Emedgene?
      • Emedgene annotations and update frequency
      • How do I use developer tools to collect logs?
      • Can I analyze Illumina Complete Long Reads in Emedgene?
      • How do I prepare VCF files generated by DRAGEN MANTA to be used as input for Emedgene?
      • Source of gnomAD data for small variants on GRCh38
      • How are MNVs handled on the platform?
      • Support for gene lists with up to 10,000 genes
      • Genomic Regions by Case Type
      • How do I analyze mtDNA variants?
      • Can I use exome data for CNV detection?
      • How does joint calling work on Emedgene?
      • What is the required format for a BED file defining a kit?
      • Which reference genomes can I use?
      • How do I move between organizations?
      • How do I check the version of my environment?
      • "Failed to generate report". What should I do?
      • How do I prepare VCF files generated by Dragen STR (ExpansionHunter) to be used as input?
      • How does Emedgene Analyze prioritize transcripts?
      • How does Emedgene Analyze merge variants from different sources?
      • Performance issue troubleshooting
      • How does Emedgene calculate variant effect and severity ?
      • How to I prepare metrics files generated by DRAGEN to be used as input for Emedgene
      • How are timekeeping and log timestamps kept accurate and consistent?
  • Release Notes
    • Workbench & Pipeline Updates
      • New in Emedgene V37.0 (February 20, 2025)
        • V37 Patches
      • New in Emedgene V36.0 (October 8 2024)
        • V36 Patches
      • New in Emedgene V35.0 (May 22nd 2024)
        • V35 Patches
      • New in Emedgene V34.0 (January 28th 2024)
        • V34 Patches
      • New in Emedgene V33.0 (September 6th 2023)
        • V33 Patches
      • New in Emedgene V32.0 (June 8th 2023)
        • New pipeline 32 (June 8th 2023)
        • V32 Patches
      • More release notes
        • New in emedgene 31 (March 1st 2023)
        • New in emedgene 30 (January 8th 2023)
        • New in emedgene 2.29 (August 25 2022)
        • New pipeline 5.29 (May 1st 2022)
        • New in emedgene 2.28 (May 1 2022)
        • New in emedgene 2.27 (March 7, 2022)
        • New in emedgene 2.26 (Dec 14, 2021)
        • New in emedgene 2.24-2.25 (Aug 11, 2021)
        • New in emedgene 2.23 (Jun 15, 2021)
        • New in emedgene 2.19-2.22 (Apr 8, 2021)
        • New in emedgene 2.16-2.19 (Dec 7, 2020)
        • New in emedgene 2.12-2.16 (Oct 18, 2020)
    • Knowledgebase Updates
      • 2025
        • Variant Databases (March 30th 2025)
        • Zoidberg 77 (March 17th 2025)
        • Zoidberg 76 (February 3rd 2025)
        • Zoidberg 75 (January 6th 2025)
      • 2024
        • Variant Databases (December 8th 2024)
        • Zoidberg 74 (December 2nd 2024)
        • Zoidberg 73 (October 21th 2024)
        • Variant Databases (September 22nd 2024)
        • Zoidberg 72 (September 10th 2024)
        • Variant Databases (July 21st 2024)
        • Zoidberg 71 (July 24th 2024)
        • Zoidberg 70 (June 3rd 2024)
        • Zoidberg 69 (April 19th 2024)
        • Variant Databases (April 9th 2024)
        • Zoidberg 68 (March 18th 2024)
        • Variant Databases (February 5th 2024)
        • Zoidberg 67 (January 28th 2024)
        • Variant Databases (January 5th 2024)
      • 2023
        • Zoidberg 66 (December 24th 2023)
        • Variant Databases (December 3rd 2023)
        • Zoidberg 65 (November 21th 2023)
        • Variant Databases (November 5th 2023)
        • Zoidberg 64 (October 24th 2023)
        • Variant Databases (October 8th 2023)
        • Zoidberg 63 (September 18th 2023)
        • Variant Databases (September 5th 2023)
        • Zoidberg 62 (August 23th 2023)
        • Zoidberg 61 (August 16th 2023)
        • Variant Databases (August 6th 2023)
        • Zoidberg 60 (July 30th 2023)
        • Variant Databases (July 2nd 2023)
        • Zoidberg 59 (June 18th 2023)
        • Variant Databases (June 4th 2023)
          • Variant Databases (May 7th 2023)
        • Zoidberg 58 (May 21th 2023)
        • Zoidberg 57 (April 16th 2023)
        • Variant Databases (April 2nd 2023)
        • Zoidberg 56 (March 19th 2023)
        • Variant Databases (March 11th 2023)
        • Zoidberg 55 (February 19th 2023)
        • Zoidberg 54 (January 16th 2023)
    • Change log
      • Change log pipeline v34
      • Change log pipeline 31
      • Change log workbench 31
      • Change log pipeline 30
      • Change log workbench 30
      • Change log workbench 2.29
      • Change log pipeline 5.29
      • Change log workbench 2.28
  • Legal
    • Privacy, Security & Compliance
    • Release Policy
Powered by GitBook
On this page
  • Calling methodology
  • STR calling with ExpansionHunter
  • Spanning reads
  • Flanking reads
  • In-repeat reads (IRRs)
  • Recommendation for interpretation

Was this helpful?

Export as PDF
  1. Emedgene analyze manual
  2. Reviewing a case

STR calling and interpretation

PreviousVariant zygosity notationsNextVariant page

Last updated 5 months ago

Was this helpful?

Calling methodology

Emedgene uses ExpansionHunter by DRAGEN to call short tandem repeats (STR), also known as repeats expansions.

Thirty clinical genes associated with diseases caused by repeat expansion are called in and presented in the platform. Those genes are: AFF2, AR, ATN1, ATXN1, ATXN10, ATXN2, ATXN3, ATXN7, ATXN8OS, C9ORF72, CACNA1A, CBL, CNBP, CSTB, DIP2B, DMPK, FMR1, FXN, GIPC1, GLS, HTT, JPH3, NIPA1, NOP56, PABPN1, PHOX2B, PPP2R2B, RFC1, TBP, TCF4.

STR calling with ExpansionHunter

Spanning reads

Exact sizes of short repeats are identified from spanning reads that completely contain the repeat sequence.

Flanking reads

When the repeat length is close to the read length, the size of the repeat is approximated from the flanking reads that partially overlap the repeat and one of the repeat flanks.

In-repeat reads (IRRs)

If the repeat is longer than the read length, its size is estimated from reads completely contained inside the repeat (in-repeat reads). In-repeat reads anchored by their mate to the repeat region are used to estimate the size of the repeat up to the fragment length. When there is no evidence of long repeats with the same repeat motif elsewhere in the genome, pairs of in-repeat reads can also be used to estimate the size of long (greater-than-fragment-length) repeats.

Note: ExpansionHunter for STR calling is designed for use in PCR-free WGS only. While STR variants might be called in exome cases, the limitations are currently unknown and it is therefore not recommended for use.

Recommendation for interpretation

In light of our recent experience and an internal investigation by the Illumina’s scientific team, we believe it is appropriate to enable prioritization for a subset of STR loci, but not all loci typed by DRAGEN. This is due to technical genotyping challenges and/or lack of scientific evidence of pathogenicity for the remaining loci. Current list of genes where STR may be tagged when appropriate is provided below:

Gene
Associated Condition
Mode of Inheritance
Repeat Unit

ATXN10

Spinocerebellar ataxia 10 (SCA10)

Autosomal Dominant

ATTCT

ATXN8OS

Spinocerebellar ataxia 8 (SCA8)

Autosomal Dominant

CTG

ATN1

Dentatorubral-pallidoluysian atrophy (DRPLA)

Autosomal Dominant

CAG

ATXN1

Spinocerebellar ataxia 1 (SCA1)

Autosomal Dominant

CAG

ATXN2

Spinocerebellar ataxia 2 (SCA2)

Semi-dominant

CAG

ATXN3

Spinocerebellar ataxia 3 (SCA3)

Autosomal Dominant

CAG

ATXN7

Spinocerebellar ataxia 7 (SCA7)

Autosomal Dominant

CAG

CACNA1A

Spinocerebellar ataxia 6 (SCA6)

Autosomal Dominant

CAG

DMPK

Myotonic dystrophy 1 (DM1)

Autosomal Dominant

CTG

DMPK

Myotonic dystrophy 1, mild

Autosomal Dominant

CTG

FMR1

Fragile X tremor/ataxia syndrome (FXTAS) or Premature Ovarian Failure (POF)

X-linked

CGG

FMR1

Fragile X Syndrome (FXS)

X-linked

CGG

HTT

Huntington's disease (HD)

Autosomal Dominant

CAG

PPP2R2B

Spinocerebellar ataxia 12 (SCA12)

Autosomal Dominant

CAG

TBP

Spinocerebellar ataxia 17 (SCA17)

Autosomal Dominant

CAG

C9orf72

Amyotrophic lateral sclerosis and/or frontotemporal dementia (FTDALS1)

Autosomal Dominant

GGGGCC

AR

Spinal and bulbar muscular atrophy (SBMA)

X-linked

CAG

FXN

Friedreich ataxia (FRDA)

Autosomal Recessive

GAA

CNBP

Myotonic dystrophy 2 (DM2)

Autosomal Dominant

CCTG

JPH3

Huntington disease-like 2 (HDL2)

Autosomal Dominant

CTG

NOP56

Spinocerebellar ataxia 36 (SCA36)

Autosomal Dominant

GGCCTG

DRAGEN version 3.9