Cell-free fetal DNA as a non-invasive method using pyrosequencing in detecting beta-globin gene mutation: A pilot study from area with limited facilities in Indonesia

Ani Melani Maskoen; Nurul Setia Rahayu; Bremmy Laksono; Azzania Fibriani; Willyanti Soewondo; Johanes C Mose; Edhyana Sahiratmadja; Ramdan Panigoro

doi:10.3389/fped.2022.902879

Cell-free fetal DNA as a non-invasive method using pyrosequencing in detecting beta-globin gene mutation: A pilot study from area with limited facilities in Indonesia

Front Pediatr. 2022 Aug 4:10:902879. doi: 10.3389/fped.2022.902879. eCollection 2022.

Authors

Ani Melani Maskoen^{1

2}, Nurul Setia Rahayu³, Bremmy Laksono^{1

2}, Azzania Fibriani⁴, Willyanti Soewondo⁵, Johanes C Mose⁶, Edhyana Sahiratmadja², Ramdan Panigoro²

Affiliations

¹ Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia.
² Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
³ Laboratory of Molecular Genetics, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
⁴ Department of Biology, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia.
⁵ Department of Pediatric Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia.
⁶ Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.

Abstract

Background: Thalassemia is a monogenic, autosomal recessive, inherited disorder of the red blood cells caused by mutations or deletions in the globin gene. Approximately 6-10% of the Indonesian population carries the β-globin gene mutation; however, premarital screening is rarely conducted, and antenatal screening is optional. We explored the use of cell-free fetal DNA (cffDNA) as a potential non-invasive method of detecting the fetal β-globin gene mutation prenatally in pregnant women.

Materials and methods: Pregnant mothers (n = 10), who were known carriers of thalassemia and who had a history of having borne a baby with thalassemia major, and their carrier husbands (n = 4) were recruited after providing consent. EDTA blood was drawn, and maternal DNA, including cffDNA, and paternal DNA were isolated. Maternal contamination tests were conducted using the variable number tandem repeat test for ApoB and D1S80 loci. Allele quantification was performed by pyrosequencing. Known mutations from the bio-archived DNA of patients with thalassemia major (n = 16) were run alongside as a control.

Results: In total, 7 out of 10 cffDNA successfully passed the maternal contamination test. The results of the allele quantification showed that six fetuses were predictive carriers of IVS1nt5 and one was predictive normal, in line with the allele quantification for the bio-archived DNA from patients with thalassemia major. The minimum threshold percentage for mutant A allele at cd26 was 32%, mutant T allele at IVS1nt1 was 23%, and mutant C allele at IVS1nt5 was 39%.

Conclusion: Taking cffDNA from the mother's blood proved useful as a non-invasive means of detecting the β-globin gene mutation using pyrosequencing allele quantification. This non-invasive method is of great interest for prenatal diagnosis in settings with limited facilities, as it minimizes the risk of abortion. Further study of other mutations of the β-globin gene is needed.

Keywords: beta-thalassemia; cell-free fetal DNA; non-invasive; prenatal screening; pyrosequencing.