Thalassemia Mutation Test | Prima | MedGenome

What is Thalassemia Mutation Testing?

Thalassemia Mutation Testing refers to the analysis of HBA1 and HBA2 genes for alpha-thalassemia and HBB gene for beta-thalassemia to understand the presence of the mutation and inheritance patterns that lead to thalassemia and other related genes.  

Prevalence

  • The average prevalence of beta-thalassemia carriers is 3% to 4%
  • Estimates indicate that there are around 1,00,000 patients with beta-thalassemia syndrome, however, exact numbers are not available due to the absence of a national registry of patients.

Common disorders

  • Beta-thalassemia (β-thalassemia) can be caused by homozygous or compound heterozygous mutations in the HBB gene.
  • Alpha-thalassemia (α-thalassemia) is caused by mutations in the HBA1 and HBA2 genes
  • It has two clinically significant forms:
    • Hemoglobin Bart hydrops fetalis (Hb Bart) syndrome – caused by deletion of all four α-globin genes
    • Hemoglobin H (HbH) disease – most frequently caused by deletion of three α-globin genes.
  •  

Why do you need the test?

  • Identification of pathogenic variants (mutations) in HBA1, HBA2 or HBB gene may be useful for diagnosis in individuals at risk, identified by other non-molecular tests
  • If the pathogenic variants have been identified in an affected family member, molecular genetic testing of at-risk siblings should be offered for an early diagnosis and appropriate treatment.

Who needs to get tested?

  • Individuals suspected of having beta-thalassemia, alpha thalassemia, or hemoglobinopathies
  • Carrier screening for mutation identification
  • Evaluation of a relative of an individual with known thalassemia
  • Prenatal diagnosis of pregnancies at risk of thalassemia

 

Why MedGenome?

MedGenome offers thalassemia tests for carrier screening, diagnosis, mutation detection, identification of deletion/duplication, and small InDels in case of:

  • Beta thalassemia [HBB] gene analysis
  • Comprehensive beta thalassemia [HBB] gene analysis
  • Comprehensive alpha thalassemia gene analysis (HBA1 & HBA2)
  • Comprehensive alpha and beta thalassemia gene panel

Significance of beta-thalassemia test

  • The complete coding region sequencing of HBB gene (can detect all the common point mutations (SNVs) and small indels, large exon spanning Copy Number Variations (CNVs), as well as novel and rare mutations).
  • The most common mutations reported in Indian population are IVS1-5, IVS1-1 G>T, codon 41/42 (-TCTT), Codon 8/9 (+G) and 619-bp deletion accounting for 90% of the thalassemia carriers are covered.
GeneTest MethodThe proportion of pathogenic variants detectable by this method
HBBSequence analysis by NGS (point mutations/small indels in coding regions and splice junctions)~95%
HBBGene-targeted deletion/duplication analysis~05%

 

List of common mutations (SNVs and INDELs) covered in HBB gene (MGM044 and MGM1768)

VariantcDNA PositionCovered by our test
IVS1-5c.92+5G>CNGS
Codon41/42(-TCTT)c.125_128delTCTTNGS
Codon 30 (G>C)c.92G>CNGS
IVS1-1 (G>T/A)c.92+1G>ANGS
619-bp deletionMLPA
Codon 8/9(+G)c.27dupGNGS
codon 15 (G>Ac.47 G>ANGS
Codon 16 (-C)c.51delCNGS
poly-A site (T>C)c.*110T>CNGS
Codon 15 (-T)c.46delTNGS

* This is a list of mutations covered over and above common mutations

List of CNV’s covered in HBB gene (MGM1768):

The assay uses two independent methods in parallel to detect CNVs which are direct detection of 11 CNVs & other CNV’s by Coverage based detection in the HBB gene cluster. This assay could detect following CNV’s in HBB gene cluster

VariantCovered by our test
ChineseDirect & Coverage based
FilipinoDirect & Coverage based
YunnaneseDirect & Coverage based
TaiwaneseDirect & Coverage based
SEA-HPFHDirect & Coverage based
δβ-SiciliaDirect & Coverage based
Hb-Lepore BostonDirect & Coverage based
Hb-Lepore BaltimoreDirect & Coverage based
Hb-Lepore HollandiaDirect & Coverage based
290bp-deletionDirect & Coverage based
HBB 619-deletionDirect & Coverage based
Other deletions in HBB geneCoverage based

Significance of alpha-thalassemia test

  • The complete coding region sequencing of HBA1 and HBA2 gene (can detect all the common point mutations (SNVs) and small indels, large exon spanning Copy Number Variations (CNVs), as well as novel and rare mutations).
  • HBA gene is 100% covered in our assay including promoter, intronic & UTR regions.
GeneTest MethodThe proportion of pathogenic variants detectable by this method
HBA1 and HBA2Targeted deletion analysis~85%
HBA1 and HBA2Sequence analysis~15%

List of common mutations (SNVs and INDELs) covered in HBA1 and HBA2 genes:

VariantCovered by our test
Common two α-globin-gene deletionMLPA
Common single α-globin-gene deletionMLPA
c.2T>CNGS
c.94_95delAGNGS
c.95+2_95+6delTGAGGNGS
c.207C>GNGS
c.207C>ANGS
c.223G>CNGS
c.[339C>G; 340_351delCTCCCCGCCGAG]NGS
c.377T>CNGS
c.*94A>GNGS

* This is a list of mutations covered over and above common mutations

List of CNVs covered in HBA1 and HBA2 genes:

Deletions in Alpha ThalassemiaCNV detection method in our assay
–SEADirect & Coverage based
–FILDirect & Coverage based
–THAIDirect & Coverage based
-(α)20.5Direct & Coverage based
–MEDDirect & Coverage based
-(α)21.9Direct & Coverage based
-(α)27.6Direct & Coverage based
-(α)3.7Coverage based
-(α)4.2Coverage based
HS-40Coverage based
Other deletionsCoverage based

Thalassemia Mutation Testing at MedGenome

Test CodeTest NameMutation TypeGenes CoveredMethodology
MGM044Beta thalassemia [HBB] gene analysisSNVs / Indels / Common Mutations / 619 bp deletionHBBNGS / PCR
MGM1768Comprehensive beta thalassemia [HBB] gene analysisSNVs / Indels / CNVs / Common Mutations / 619 bp deletionHBB and Partial seuqence of HBG1, HBG2 and HBD promotorsNGS
MGM1769Comprehensive alpha thalassemia gene analysis (HBA1 & HBA2)SNVs / Indels / CNVsHBA1 & HBA2NGS
MGM1763Comprehensive alpha and beta thalassemia gene panelSNVs / Indels / CNVsHBB & HBA1 & HBA2 and Partial seuqence of HBG1, HBG2 and HBD
promotors
NGS

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Thalassemia Mutation Testing

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Amit & Akhila (name changed), a non-consanguineous couple with clinical indication of primary infertility consulted a leading gynaecologist in India.

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