Prenatal diagnosis of ?-thalassaemia and other haemoglobinopathies in India

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

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.

The Changing Trends in Prenatal Diagnosis of Hemoglobinopathies in India: The Quest of a Single Center to Reduce the Burden of Disease over Three Decades

The β-thalassemias and sickle cell disorders pose a considerable health burden in India. Of the more than 10,000 annual births of children with a severe hemoglobinopathy, only around 10.0% are managed optimally. Thus, genetic counseling and prenatal diagnosis (PND) is a valid option for a large and diverse country. Our center was one of the first to initiate PND and we present our experience over 30 years to evaluate the impact of awareness in changing the trends of PND of hemoglobinopathies. Both second and first-trimester diagnoses were undertaken by fetoscopy/cordocentesis and globin biosynthesis/high-performance liquid chromatography (HPLC) analysis of fetal blood and chorionic villus sampling (CVS) and DNA analysis. Over 30 years, 3478 couples (first trimester: 2475; second trimester: 1003) from all over India were offered PND. The number of couples coming in the first trimester increased significantly over each decade and couples coming prospectively increased from 2.5 to 18.4%. A cost-effective stepwise approach was used for molecular analysis. Eight hundred and one fetuses (23.0%) were affected and all except three couples opted for termination of these pregnancies. Genetic counseling and PND is the only way to reduce the burden of disease. With awareness, there was a shift from second trimester to first trimester PND over each decade, with an increasing number of couples coming during the first pregnancy. There are only 15 to 20 centers in India offering PND. We have compared our study with other reports on PND from different regions in India.

A multiplex ARMS PCR approach to detection of common β-globin gene mutations

BACKGROUND

β-thalassaemia is a group of inherited single-gene disorders worldwide. Each ethnic population has its own common mutations. Heterogeneity of β-thalassaemia mutations in multi-ethnic population of Surat, makes molecular diagnosis expensive and time consuming.

METHODS

Specific primers were used to differentiate four common mutations, IVS I-5 (G→C), Codon 41/42 (- TCTT), 619-bp deletion and FS 8/9 (+G), by a simple PCR involving a multiplex amplification refractory mutation system.

RESULTS

Several high prevalence β-Thalassemia trait groups constituted by Muslims, Patels, Sindhis, ModhBanias, and Mahayavanshi. Four most common mutations detected in them are IVS I-5 (G→C), Codon 41/42 (- TCTT), 619-bp deletion and FS 8/9 (+G). We identified each of these β-thalassemia mutations in multiplexed ARMS from positive control samples. Our multiplex-ARMS-PCR system was first standardized on positive DNA samples with above known four most common β-thalassemia mutations, and these positive samples had been diagnosed with β-thalassemia and also all these samples belonged to Surat ethnic groups. The system was subsequently tested on 110 blood samples from different ethnic backgrounds with unknown β-thalassemia mutations which were in all specimens.

CONCLUSION

The ARMS multiplex system was found reliable, cost effective, fast and most applicable for mutation screening of Thalassemia in Surat populations.

Establishment of prenatal diagnosis for β-thalassaemia: A step towards its control in a developing country

Beta-thalassaemia constitutes a major health burden on the limited health resources of India and prenatal diagnosis is seen as an important preventive measure to reduce the burden of the disease. Prenatal diagnosis has been offered to 99 women in 112 pregnancies by fetal DNA analysis, using a PCR-based Amplification Refractory Mutation System (ARMS) for the common and uncommon Indian mutations. Restriction fragment length polymorphism (RFLP) for the beta-globin gene was used when the mutation remained unidentified in one of the parents or to complement the ARMS result. In 53 cases the fetus tested had beta-thalassaemia trait (betaTT) (47.3%), 22 were normal (19.6%) and 31 had thalassaemia major (27.6%). In five cases (4.5%), a definitive report could not be given due to maternal contamination. In one case (0.9%), there was a misdiagnosis. Pitfalls encountered in the diagnosis were maternal contamination and occasional non-amplification of the primers. Having established a regional centre for the prenatal diagnosis for thalassaemia, the screening programmes will be enlarged both to identify carriers and prevent the birth of further homozygous children, even during the first pregnancy.

Beta-thalassemia mutations in western India

OBJECTIVE

To study occurrence of common mutations in the population of Gujarat and the most prevalent mutation in certain high-risk communities.

METHODS

The mutation screening was carried out using ARMS-PCR in children with beta thalassemia.

RESULTS

Population screening has identified certain communities like Sindhis, Lohana, Rajputs, and SC/ST/OBC to be at higher risk as compared to others. The most common mutation was IVS 1-5 (G-->C) followed by 619 bp deletions of the total cases coming to Gujarat.

CONCLUSION

Molecular evaluation for Thalassemia should be considered for families whose ethnicity indicates origin from high-risk community.

Prenatal diagnosis of sickle cell anemia in twin pregnancies and identification by VNTRs

BACKGROUND

Sickle cell anemia (SCA) is an inherited disorder of hemoglobin synthesis that is characterized by life-long severe hemolytic anemia, attacks of pain crisis, and chronic organ system damage. In this study, prenatal diagnosis was performed to three couples (families A, B, and C) with twin pregnancies who were at risk for SCA.

METHODS

The SCA carrier state of the couples were confirmed at molecular level. Chorionic villus samples (CVS) of twins were obtained at 10-12 weeks of gestation. Amplification refractory mutation system (ARMS) and restriction fragment length polymorphism (RFLP) techniques were applied to determine and confirm the presence of the sickle cell anemia of the fetuses. Identification of each twin, confirmation of parentage and elimination of maternal contamination of chorionic villus samples were ruled out by variable number of tandem repeats (VNTR) analysis of four different loci [D1S80 (pMCT118), ApoB, IgJH, D4S95].

RESULTS

We found that one of the fetuses was heterozygous for SCA and the other was normal in family A; in family B both fetuses were heterozygous and in family C both fetuses were normal.

CONCLUSION

Prenatal diagnosis is the major way of prevention of the genetic disorders including sickle cell anemia. Prenatal diagnosis of twins contains additional risks such as confusion in differentiation leading to false molecular diagnosis. VNTR loci analysis is a useful tool and can be safely used for the elimination of all problems mentioned above.

Prenatal diagnosis of sickle syndromes in India: dilemmas in counselling

OBJECTIVES

The sickle gene is prevalent in the scheduled caste and tribal populations in India. The clinical presentation of sickle cell disease is extremely variable, and there are no neonatal screening programmes. This is the first report on prenatal diagnosis of sickle syndromes in 85 couples at risk (sickle cell anemia-69; sickle thalassemia-16) from different regions in India. Most of the couples were from a low socioeconomic group and their decisions were entirely dependent on the local counselling given. We have evaluated the acceptability of prenatal diagnosis and the dilemmas faced in counselling these families.

METHODS

Chorion villus sampling was done in the first trimester and DNA analysis using reverse dot blot hybridization or restriction enzyme digestion with Dde1 in 65 cases. Cordocentesis was done in the second trimester and fetal blood analyses by automated HPLC in 20 cases who came late.

RESULTS

32.9% of couples came prospectively for diagnosis. 23.5% of fetuses were affected (sickle cell anemia-18, sickle thalassemia-2). The beta-thalassemia mutation in both cases was IVS 1-5(G->C). All the couples with an unfavourable diagnosis opted for termination of pregnancy.

CONCLUSION

Sickle cell anemia has a relatively benign clinical course in some tribal groups in India. This raises a dilemma whether we are justified in advising prenatal diagnosis in all such cases.

Genetic counseling and prenatal diagnosis in India--experience at Sir Ganga Ram Hospital

The experiences in genetic counseling and prenatal diagnosis at a tertiary genetic center in India are described. Of 3500 subjects provided genetic counseling 28.7% were for prenatal diagnosis, 13.7% for mental retardation +/- malformations, 11.5% for thalassemia, hemophilia and leukemia, 8.5% for neural tube defects and other malformations, and 8% for muscle dystrophy and spinal muscle atrophy. Chromosomal studies in blood (n = 5459) were for recurrent abortions (57.8%), delayed milestones (14.7%), malformations (11%), and infertility and amenorrhea (10.2%). Indications for amniotic fluid studies (n = 835) were advanced maternal age (35.7%), high risk result on triple test (21.3%), previous child with trisomy 21 (21.3%) and abnormalities seen on ultrasound (11.1%). Molecular studies were mostly for thalassemia (843, 24.3%), Duchenne muscular dystrophy (443, 12.5%), fragile X syndrome (367, 10.3%), spinal muscular atrophy (315, 8.9%), thrombophilia profile (233, 6.6%), triplet repeat disorders-spinocerebellar ataxias, Huntington disease and Friedreich ataxia-162 (4.6%), cystic fibrosis 140 (3.9%) and mitochondrial disorders 101 (2.9%). Other disorders for which molecular diagnosis was done were intrauterine infections by PCR on the amniotic fluid, Prader Willi/Angelman syndromes, hemophilia, achondroplasia, congenital adrenal hyperplasia, and Apert syndrome etc. In biochemical studies triple marker tests were the most common (3239), followed by aminoacid chromatography (774). Among neurolipidosis metachromatic leukodystrophy was the commonest, followed by Krabbe's disease, Tay Sach disease and Gaucher disease. Of the mucopolysacharidoses Hurler syndrome was the commonest, followed by Hunter syndrome. These data are compared with previous studies and a change towards increased prenatal diagnostic tests is observed. The commonest indication for amniocentesis has changed to advanced maternal age.

CONCLUSION

Advanced molecular, cytogenetic and biochemical techniques have been a useful addition for genetic counseling and prenatal diagnosis in India.

Prenatal diagnosis

With the leaping advances in knowledge of genetics, its applications in patient management are also increasing. Prenatal diagnosis is the most useful application as it offers prospective parents the assurance of having an unaffected child in situations of high recurrence risks. Pretest and post test counseling is an integral part of prenatal diagnosis. All Pediatricians and Obstetricians should be familiar with the basic prerequisites of prenatal screening/testing. Timely referral, preferably pre-pregnancy is important. There is more or less a consensus regarding offering prenatal diagnosis for lethal/chronic disabling or difficult/expensive to treat conditions. Ethical issues are already around regarding prenatal testing for disabilities like deafness and late onset disorders. The present communication is an effort to present the clinician's perspective of prenatal diagnosis.

Recommendations for introducing genetics services in developing countries

Many concerned scientists believe that developments in the medical application of genomics will widen the gap between the developed and the developing world. We argue that most developing countries now urgently need to incorporate genetic approaches (including DNA diagnosis) into their health services, and that many are able to do so. DNA diagnosis is relatively inexpensive, helps to develop skills in molecular biology and provides a basis for developing national expertise in genomics.

Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human beta-globin locus control region (LCR) in Indian population

LCR, a genetic regulatory element, was examined in beta-thalassemia patients who do not show any mutation in the beta-globin genes. We sequenced LCR-HS2, HS3, and HS4 in samples from 16 such patients from the Indian population and found only one SNP A-G in the inverted repeat in HS4. A significant association was observed between the G allele and occurrence of beta-thalassemia by Fisher's exact test. The AG and GG genotypes showed higher relative risk as compared to the AA genotype. We also observed linkage disequilibrium between the A/G polymorphism and the AT-rich motif of the LCR HS2 region, suggesting that the G allele could be an evolutionarily new mutation in the study population.

Use of real-time gene-specific polymerase chain reaction to measure RNA expression of three family members of rat cytochrome P450 4A

Exposure of rats to peroxisome proliferators induces members of the cytochrome P450 4A (CYP4A) family. In rats, the CYP4A family consists of four related genes, CYP4A1, CYP4A2, CYP4A3, and CYP4A8. We are specifically interested in examining CYP4A1, CYP4A2, and CYP4A3, each of which is expressed in a tissue-dependent and sex-dependent manner. While CYP4A1 is sufficiently different from the other two members to enable relatively easy specific quantitation, the close similarity between CYP4A2 and CYP4A3 makes quantitative discrimination difficult. We have combined a fluorescent real-time PCR assay (TaqMan) with the sequence-specific mismatch amplification mutation assay (MAMA) to allow us to carry out specific quantitation of all three members of this family. The assay is designed such that a single fluorescent TaqMan(R) probe binds to all three gene products, while specificity is conferred by sequence-specific primers. This specific MAMA technique takes advantage of the ability of Taq polymerase to distinguish between the two cDNAs based on mismatches at the 3' end of a PCR primer. In the 84-base PCR product used for this assay, there is only a single-base difference between CYP4A2 and CYP4A3. Despite this similarity, there is at least a 1000-fold discrimination between the two sequences, using CYP4A2 or CYP4A3 specific standards. Analysis of rat liver RNA from both sexes demonstrates that this discrimination is also achieved in complex RNA mixtures. This technique should be broadly applicable to other areas of research such as allelic discrimination, detecting mutational hotspots in tumors, and discrimination among closely related members of other gene families.