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Maskoen AM, Rahayu NS, Laksono B, Fibriani A, Soewondo W, Mose JC, Sahiratmadja E, Panigoro R. 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; 10:902879. [PMID: 35990000 PMCID: PMC9386223 DOI: 10.3389/fped.2022.902879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Ani Melani Maskoen
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia.,Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Nurul Setia Rahayu
- Laboratory of Molecular Genetics, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Bremmy Laksono
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia.,Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Azzania Fibriani
- Department of Biology, School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Willyanti Soewondo
- Department of Pediatric Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
| | - Johanes C Mose
- Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Edhyana Sahiratmadja
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ramdan Panigoro
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
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Barker MK, Henderson AM, Naguib K, Vercauteren SM, Devlin AM, Albert AY, Bahizire E, Tugirimana PL, Akilimali PZ, Boy E, Green TJ, Karakochuk CD. Serum Soluble Transferrin Receptor Concentrations Are Elevated in Congolese Children with Glucose-6-Phosphate Dehydrogenase Variants, but Not Sickle Cell Variants or α-Thalassemia. J Nutr 2017; 147:1785-1794. [PMID: 28768839 DOI: 10.3945/jn.117.252635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/02/2017] [Accepted: 06/23/2017] [Indexed: 11/14/2022] Open
Abstract
Background: Anemia is common in Congolese children, and inherited blood disorders may be a contributing cause. The presence of sickle cell variants, X-linked glucose-6-phosphate dehydrogenase (G6PD) deficiency and α-thalassemia, has been previously reported. G6PD A- deficiency is characterized by the co-inheritance of G6PD 376 and 202 variants and is common in sub-Saharan Africa.Objective: We aimed to measure the associations between inherited blood disorders and hemoglobin, ferritin, and soluble transferrin receptor (sTfR) concentrations in Congolese children.Methods: Venous blood was collected from 744 children aged 6-59 mo from 2 provinces. We measured biomarkers of nutritional and inflammation status and malaria. Pyrosequencing was used to detect sickle cell variants. Polymerase chain reaction was used to detect G6PD variants and α-thalassemia deletions.Results: Overall, 11% of children had a sickle cell variant, 19% of boys were G6PD A- hemizygotes, 12% and 10% of girls were G6PD A- hetero- or homozygotes, respectively, and 12% of children had α-thalassemia. Multivariable linear regression models (adjusted for age, province, altitude, malaria, and biomarkers of nutritional and inflammation status) showed that G6PD A- hemizygous boys and G6PD 376 homozygous girls had higher sTfR concentrations [geometric mean ratios (95% CIs): 1.20 (1.03, 1.39) and 1.25 (1.02, 1.53), respectively] than children with no G6PD variants. Hemoglobin and ferritin concentrations were not independently associated with any of the inherited blood disorder genotypes.Conclusions: We found that 2 G6PD variant genotypes were associated with elevated sTfR concentrations, which limits the accuracy of sTfR as a biomarker of iron status in this population.
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Affiliation(s)
- Mikaela K Barker
- Food, Nutrition, and Health and.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Amanda M Henderson
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Karimah Naguib
- Food, Nutrition, and Health and.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Suzanne M Vercauteren
- British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada.,Hematopathology, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Angela M Devlin
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Arianne Y Albert
- Women's Health Research Institute, British Columbia Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Esto Bahizire
- Faculty of Medicine, Catholic University of Bukavu, Bukavu, Democratic Republic of Congo.,Center of Research in Epidemiology, Biostatistics and Clinical Research, Free University of Brussels, Brussels, Belgium
| | | | - Pierre Z Akilimali
- Department of Nutrition, Kinshasa School of Public Health, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Erick Boy
- HarvestPlus, International Food Policy Research Institute, Washington, DC
| | - Tim J Green
- Healthy Mothers, Babies, and Children, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; and.,Discipline of Paediatrics, University of Adelaide, Adelaide, South Australia, Australia
| | - Crystal D Karakochuk
- Food, Nutrition, and Health and .,British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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Traeger-Synodinos J, Harteveld CL. Preconception carrier screening and prenatal diagnosis in thalassemia and hemoglobinopathies: challenges and future perspectives. Expert Rev Mol Diagn 2017; 17:281-291. [DOI: 10.1080/14737159.2017.1285701] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Joanne Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, Athens, Greece
| | - Cornelis L. Harteveld
- Department of Clinical Genetics, Laboratory for Diagnostic Genome Analysis (LDGA), Leiden, The Netherlands
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Traeger-Synodinos J, Harteveld CL. Advances in technologies for screening and diagnosis of hemoglobinopathies. Biomark Med 2014; 8:119-31. [PMID: 24325233 DOI: 10.2217/bmm.13.103] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hemoglobinopathies constitute the most common monogenic disorders worldwide, caused by mutations in the globin genes that synthesize the globin chains of hemoglobin. Synthesis may be reduced (thalassemia) or underlie abnormal hemoglobins. Mutation interactions produce a wide range of disorders. For neonatal and antenatal screening, identification of affected newborns or carriers is achieved by hematological tests. DNA analysis supports definitive diagnosis, and additionally facilitates prenatal diagnosis procedures. Most methods used today have been developed over several decades, with few recent advances in hematology methods. However, DNA methods evolve continuously. With global migration and multiethnic societies the trend is from targeted, population-specific methods towards generic methods, such as Sanger sequencing (point mutations) and multiplex ligation probe amplification (deletions). DNA microarrays constitute an advanced DNA method for some mutation categories. The newest DNA technology is next-generation sequencing. Although not completely ready for routine use currently, next-generation sequencing may soon become a reality for some hemoglobin diagnostic laboratories.
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Affiliation(s)
- Jan Traeger-Synodinos
- Medical Genetics, University of Athens, St Sophia's Children's Hospital, Athens 11527, Greece.
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De Battisti C, Marciano S, Magnabosco C, Busato S, Arcangeli G, Cattoli G. Pyrosequencing as a tool for rapid fish species identification and commercial fraud detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:198-205. [PMID: 24350776 DOI: 10.1021/jf403545m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The increased consumption of fish products, as well as the occurrence of exotic fish species in the Mediterranean Sea and in the fish market, has increased the risk of commercial fraud. Furthermore, the great amount of processed seafood products has greatly limited the application of classic identification systems. DNA-based identification allows a clear and unambiguous detection of polymorphisms between species, permitting differentiation and identification of both commercial fraud and introduction of species with potential toxic effects on humans. In this study, a novel DNA-based approach for differentiation of fish species based on pyrosequencing technology has been developed. Raw and processed fish products were tested, and up to 25 species of fish belonging to Clupeiformes and Pleuronectiformes groups were uniquely and rapidly identified. The proper identification based on short and unique genetic sequence signatures demonstrates that this approach is promising and cost-effective for large-scale surveys.
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Affiliation(s)
- Cristian De Battisti
- Research & Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie , Viale dell'Università 10, 35020 Legnaro, Padova, Italy
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Ho SSY, Huan PT, Leow GH, Ching LK, Chiu L, Law HY, Koay ESC. Rapid prenatal diagnosis of common beta-thalassemia mutations in Southeast Asia using pyrosequencing. Prenat Diagn 2013; 33:1017-22. [PMID: 23794144 DOI: 10.1002/pd.4183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 04/28/2013] [Accepted: 06/18/2013] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Current methods of prenatal diagnosis to detect beta-thalassemia are Sanger sequencing and reverse dot blot. These methods are time-consuming and can prolong assay turnaround time. We aim to develop a sensitive and rapid method to detect 27 beta-thalassemia mutations using pyrosequencing. METHOD Pyrosequencing primer pairs and sequencing primers were designed to detect 27 most common beta-thalassemia mutations found in Singapore. Pyrosequencing was performed on 191 DNA samples with known beta-thalassemia mutations isolated from 143 peripheral blood and 48 prenatal samples (seven chorionic villus biopsies, 26 cultured amniocytes, 15 uncultured amniocytes). All mutations were validated with Sanger sequencing. RESULTS Pyrosequencing identified 210 alleles with beta-thalassemia mutations and 82 alleles without mutations with 100% sensitivity (lower 95% confidence interval [CI], 97.8%) and 100% specificity (lower 95% CI, 94.4%). All pyrosequences were concordant with Sanger-based sequences. Pyrosequencing was able to detect DNA concentrations as low as 2 ng, obviating the need for cell culture in volume-restricted samples. Sample receipt-to-report assay turnaround times were 16 to 18 h (Sanger sequencing) and 4 to 6 h (pyrosequencing). CONCLUSION Pyrosequencing is a rapid and sensitive method to detect common beta-thalassemia mutations without the need for cell culture, thus reducing the assay turnaround time.
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Affiliation(s)
- Sherry Sze Yee Ho
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, Singapore, Singapore
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