Mutation in Thalassemia: Testing for Alpha & Beta Thalassemia

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

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.

Gene	Test Method	The proportion of pathogenic variants detectable by this method
HBB	Sequence analysis by NGS (point mutations/small indels in coding regions and splice junctions)	~95%
HBB	Gene-targeted deletion/duplication analysis	~05%

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

Variant	cDNA Position	Covered by our test
IVS1-5	c.92+5G>C	NGS
Codon41/42(-TCTT)	c.125_128delTCTT	NGS
Codon 30 (G>C)	c.92G>C	NGS
IVS1-1 (G>T/A)	c.92+1G>A	NGS
619-bp deletion	–	MLPA
Codon 8/9(+G)	c.27dupG	NGS
codon 15 (G>A	c.47 G>A	NGS
Codon 16 (-C)	c.51delC	NGS
poly-A site (T>C)	c.*110T>C	NGS
Codon 15 (-T)	c.46delT	NGS

* 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

Variant	Covered by our test
Chinese	Direct & Coverage based
Filipino	Direct & Coverage based
Yunnanese	Direct & Coverage based
Taiwanese	Direct & Coverage based
SEA-HPFH	Direct & Coverage based
δβ-Sicilia	Direct & Coverage based
Hb-Lepore Boston	Direct & Coverage based
Hb-Lepore Baltimore	Direct & Coverage based
Hb-Lepore Hollandia	Direct & Coverage based
290bp-deletion	Direct & Coverage based
HBB 619-deletion	Direct & Coverage based
Other deletions in HBB gene	Coverage 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.

Gene	Test Method	The proportion of pathogenic variants detectable by this method
HBA1 and HBA2	Targeted deletion analysis	~85%
HBA1 and HBA2	Sequence analysis	~15%

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

Variant	Covered by our test
Common two α-globin-gene deletion	MLPA
Common single α-globin-gene deletion	MLPA
c.2T>C	NGS
c.94_95delAG	NGS
c.95+2_95+6delTGAGG	NGS
c.207C>G	NGS
c.207C>A	NGS
c.223G>C	NGS
c.[339C>G; 340_351delCTCCCCGCCGAG]	NGS
c.377T>C	NGS
c.*94A>G	NGS

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

List of CNVs covered in HBA1 and HBA2 genes:

Deletions in Alpha Thalassemia	CNV detection method in our assay
–SEA	Direct & Coverage based
–FIL	Direct & Coverage based
–THAI	Direct & Coverage based
-(α)20.5	Direct & Coverage based
–MED	Direct & Coverage based
-(α)21.9	Direct & Coverage based
-(α)27.6	Direct & Coverage based
-(α)3.7	Coverage based
-(α)4.2	Coverage based
HS-40	Coverage based
Other deletions	Coverage based

Thalassemia Mutation Testing at MedGenome

Test Code	Test Name	Mutation Type	Genes Covered	Methodology
MGM044	Beta thalassemia [HBB] gene analysis	SNVs / Indels / Common Mutations / 619 bp deletion	HBB	NGS / PCR
MGM1768	Comprehensive beta thalassemia [HBB] gene analysis	SNVs / Indels / CNVs / Common Mutations / 619 bp deletion	HBB and Partial seuqence of HBG1, HBG2 and HBD promotors	NGS
MGM1769	Comprehensive alpha thalassemia gene analysis (HBA1 & HBA2)	SNVs / Indels / CNVs	HBA1 & HBA2	NGS
MGM1763	Comprehensive alpha and beta thalassemia gene panel	SNVs / Indels / CNVs	HBB & HBA1 & HBA2 and Partial seuqence of HBG1, HBG2 and HBD promotors	NGS