Novel and known microsatellite markers within the β-globin cluster to support robust preimplantation genetic diagnosis of β-thalassemia and sickle cell syndromes

Detection of Transversions and Transitions in HBG2 Cis-Elements Associated with Sickle Cell Allele in Ghanaians

Short tandem repeats located 5' prime to the β-globin gene, have been observed to be in linkage disequilibrium with the HbS allele, and thought to affect the severity of sickle cell disease. Here, we report on new mutants within the HBG2 region that may impact sickle cell disease. To determine the cis-acting elements microsatellites, indels and single nucleotide polymorphisms (SNPs), within the HBG2 region by sequencing, in subjects with sickle cell disease. The case-control study was located at the Center for Clinical Genetics, Sickle cell unit, Korle-Bu Teaching Hospital. A questionnaire was used for demographic data and clinical information. Hematological profile (red blood cell, white blood cell, platelet, hemoglobin and mean corpuscular volume) were assessed in 83 subjects. A set of 45 samples comprising amplified DNA on the HBG2 gene from HbSS (22), HbSC (17) and 6 controls (HbAA) were sequenced. Differences in the microsatellite region between sickle cell disease (SCD) (HbSS and HbSC) genotypes and control subjects were identified by counting and assessed by Chi-square analysis. Red blood cells, hematocrit, platelets, white blood cells and hemoglobin indices differed in genotypic groups. HbSS subjects were affirmed to have severer hemolytic anemia than HbSC subjects. Two indels (T1824 and C905) were seen in both SS and SC genotypes. Two peculiar SNPs: G:T1860 (transition) and A:G1872 transversions were found within the HBG2 gene that were significantly associated with the HbSS genotype (Fisher's exact test, p = 0.006) and HbS allele respectively (Fisher's exact test, p = 0.006). Cis-acting elements in HbSS and HbSC were different and may contribute to the phenotype seen in the disease state.

Hemoglobinopathies and preimplantation diagnostics

Hemoglobinopathies constitute some of the most common inherited disorders worldwide. Manifestations are very severe, patient management is difficult and treatment is not easily accessible. Preimplantation genetic testing for monogenic disorders (PGT-M) is a valuable reproductive option for hemoglobinopathy carrier-couples as it precludes the initiation of an affected pregnancy. PGT-M is performed on embryos generated by assisted reproductive technologies and only those found to be free of the monogenic disorder are transferred to the uterus. PGT-M has been applied for 30 years now and β-thalassemia is one of the most common indications. PGT may also be applied for human leukocyte antigen typing to identify embryos that are unaffected and also compatible with an affected sibling in need of hemopoietic stem cell transplantation. PGT-M protocols have evolved from PCR amplification-based, where a small number of loci were analysed, to whole genome amplification-based, the latter increasing diagnostic accuracy, enabling the development of more generic strategies and facilitating multiple diagnoses in one embryo. Currently, numerous PGT-M cycles are performed for the simultaneous diagnosis of hemoglobinopathies and screening for chromosomal abnormalities in the embryo in an attempt to further improve success rates and increase deliveries of unaffected babies.

Short Tandem Repeats Used in Preimplantation Genetic Testing of Β-Thalassemia: Genetic Polymorphisms For 15 Linked Loci in the Vietnamese Population

BACKGROUND

β-thalassemia is one of the most common monogenic diseases worldwide. Preimplantation genetic testing (PGT) of β-thalassemia is performed to avoid affected pregnancies has become increasingly popular worldwide. In which, the indirect analysis using short tandem repeat (STRs) linking with HBB gene to detect different β-globin (HBB) gene mutation is a simple, accurate, economical and also provides additional control of contamination and allele-drop-out ADO.

AIM

This study established microsatellite markers for PGT of Vietnamese β-thalassemia patient.

METHODS

Fifteen (15) STRs gathered from 5 populations were identified by in silico tools within 1 Mb flanking the HBB gene. The multiplex PCR reaction was optimized and performed on 106 DNA samples from at-risk families.

RESULTS

After estimating, PIC values were ≥ 0.7 for all markers, with expected heterozygosity and observed heterozygosity values ranged from 0.81 to 0.92 and 0.53 to 0.86, respectively. One hundred percent of individuals had at least seven heterozygous markers and were found to be heterozygous for at least two markers on either side of the HBB gene.

CONCLUSION

In general, a pentadecaplex marker (all < 1 Mb from the HBB gene) assay was constituted for β-thalassemia PGT on Vietnamese population.

Validating a rapid, real-time, PCR-based direct mutation detection assay for preimplantation genetic diagnosis

Although co-amplification of polymorphic microsatellite markers is the current gold standard for preimplantation genetic diagnosis (PGD) of single-gene disorders (SGD), this approach can be hampered by the lack of availability of informative markers. We recently (2011) devised a novel in-house assay for PGD of aromatic L-amino acid decarboxylase deficiency, based on an amplification refractory mutation system and quantitative PCR (ARMS-qPCR). The objective of the present study was to verify ARMS-qPCR in a cohort of 20 PGD cycles with a diverse group of SGDs (15 couples at risk for 10 SGDs). Day-3 cleavage-stage embryos were subjected to biopsy and genotyping, followed by fresh embryo transfer (FET). The diagnostic rate was 82.9%; unaffected live births were achieved in 9 of 20 FET cycles (45%), with only one false negative (among 54 transferred embryos). Overall, the ARMS-qPCR had frequent allele-dropout (ADO), rendering it inappropriate as the sole diagnostic method (despite a favorable live-birth rate). Regardless, it has the potential to complement the current gold-standard methodology, especially when trophectoderm biopsy becomes a preferred option and genotyping needs to be timely enough to enable FET.

The prevention of thalassemia

The thalassemias are among the most common inherited diseases worldwide, affecting individuals originating from the Mediterranean area, Middle East, Transcaucasia, Central Asia, Indian subcontinent, and Southeast Asia. As the diseases require long-term care, prevention of the homozygous state constitutes a major armament in the management. This article discusses the major prevention programs that are set up in many countries in Europe, Asia, and Australia, often drawing from the experience in Sardinia. These comprehensive programs involve carrier detections, molecular diagnostics, genetic counseling, and prenatal diagnosis. Variability of clinical severity can be attributable to interactions with α-thalassemia and mutations that increase fetal productions. Special methods that are currently quite expensive and not widely applicable are preimplantation and preconception diagnosis. The recent successful studies of fetal DNA in maternal plasma may allow future prenatal diagnosis that is noninvasive for the fetus.

Preimplantation testing: Transition from genetic to genomic diagnosis

Preimplantation genetic testing refers to the procedure to determine the genetic status of embryos formed by in vitro fertilization (IVF) prior to initiating a pregnancy. Traditional genetic methods for preimplantation genetic diagnosis (PGD) examine distinct parts of an individual genome, require the development of a custom assay for every patient family, and are time consuming and inefficient. In the last decade technologies for whole-genome amplification (WGA) from single cells have led to innovative strategies for preimplantation testing. Applications of WGA technology can lead to a universal approach that uses single-nucleotide polymorphisms (SNPs) and mutations across the entire genome for the analysis. Single-cell WGA by multiple displacement amplification has enabled a linkage approach to PGD known as “preimplantation genetic haplotyping”, as well as microarray-based techniques for preimplantation diagnosis. The use of microarrays in preimplantation diagnosis has provided genome-wide testing for gains or losses of single chromosomes (aneuploidies) or chromosomal segments. Properly designed randomized controlled trials are, however, needed to determine whether these new technologies improve IVF outcomes by increasing implantation rates and decreasing miscarriage rates. In genotype analysis of single cells, allele dropout occurs frequently at heterozygous loci. Preimplantation testing of multiple cells biopsied from blastocysts, however, can reduce allele dropout rates and increase the accuracy of genotyping, but it allows less time for PGD. Future development of fast SNP microarrays will enable a universal preimplantation testing for aneuploidies, single-gene disorders and unbalanced translocations within the time frame of an IVF cycle.

Prenatal, noninvasive and preimplantation genetic diagnosis of inherited disorders: hemoglobinopathies

Disorders of hemoglobin synthesis have been used as a prototype for the development of most approaches for prenatal diagnosis (PND). PND for hemoglobinopathies based on molecular analysis of trophoblast or amniocyte DNA has accumulated approximately 30 years of experience. Disadvantages with conventional PND include 'invasive' fetal sampling and the need to terminate affected ongoing pregnancies. New developments are directed towards improving both the timing and/or safety of procedures. Preimplantation genetic diagnosis, an established procedure with 20 years of clinical application, avoids the need to terminate affected pregnancies through the identification and selective transfer of unaffected in vitro fertilization embryos. Approaches towards 'noninvasive' PND, through analyzing fetal cells or free fetal DNA present in the circulation of pregnant women, are a focus of ongoing research. Overall, PND, preimplantation genetic diagnosis (and potentially 'noninvasive' PND) represent valuable reproductive options for couples at risk of having a child affected with a severe inherited disease.