ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of β-thalassaemia

Diagnosis of Sickle Cell Disease and HBB Haplotyping in the Era of Personalized Medicine: Role of Next Generation Sequencing

Hemoglobin genotype and HBB haplotype are established genetic factors that modify the clinical phenotype in sickle cell disease (SCD). Current methods of establishing these two factors are cumbersome and/or prone to errors. The throughput capability of next generation sequencing (NGS) makes it ideal for simultaneous interrogation of the many genes of interest in SCD. This study was designed to confirm the diagnosis in patients with HbSS and Sβ-thalassemia, identify any ß-thal mutations and simultaneously determine the ß^S HBB haplotype. Illumina Ampliseq custom DNA panel was used to genotype the DNA samples. Haplotyping was based on the alleles on five haplotype-specific SNPs. The patients studied included 159 HbSS patients and 68 Sβ-thal patients, previously diagnosed using high performance liquid chromatography (HPLC). There was considerable discordance between HPLC and NGS results, giving a false +ve rate of 20.5% with a sensitivity of 79% for the identification of Sβthal. Arab/India haplotype was found in 81.5% of β^S chromosomes, while the two most common, of the 13 β-thal mutations detected, were IVS-1 del25 and IVS-II-1 (G>A). NGS is very versatile and can be deployed to simultaneously screen multiple gene loci for modifying polymorphisms, to afford personalized, evidence-based counselling and early intervention.

The Sickle β-Thalassemia Phenotype

Sβ-thalassemia (Sβ-thal) is common among Gulf Arab patients with sickle cell disease, but the phenotype of this group had not been well-documented. We have studied a group of Kuwaiti patients and compared the phenotype in the homozygotes (SS) and Sβ-thal patients. Complete blood count, hemoglobin quantitation, serum bilirubin, and lactate dehydrogenase were determined with standard techniques. The patients were screened for α-globin genotype. The Sβ-thal patients were also screened for the HBG2 Xmn-1 polymorphism. β-Thal mutations were determined by arrayed primer extension or direct sequencing. There were 70 SS and 32 Sβ-thal patients with mean ages of 14.8±5.9 and 14.2±5.9 years, respectively. The Sβ-thal patients had more frequent, severe pain episodes per year compared with the SS, while the patterns among Sβ-thal and Sβ-thal patients were not significantly different. There were no differences in the frequencies of acute chest syndrome, gallstones, and blood transfusion in the SS and Sβ-thal patients. However, none of the Sβ-thal patients had been transfused. Among the Sβ-thal patients, 25 had β-thal and 7 had β-thal mutations, the most common being cd39 (C→T) and IVS-I-110 (G→A), respectively. Sβ-thal shows a severe phenotype in Kuwait, even among those with Sβ-thal, in whom the IVS-I-110 (G→A) mutation is predominant.

Laboratory hematology in the history of Clinical Chemistry and Laboratory Medicine

Background: For the occasion of the 50th anniversary of the journal Clinical Chemistry and Laboratory Medicine (CCLM), an historic overview of papers that the journal has published in the field of laboratory hematology (LH) is presented.

Methods: All past volumes of CCLM were screened for papers on LH and these were categorized. Bibliographic data of these papers were also analyzed.

Results: CCLM published in total 387 LH papers. The absolute number of LH papers published annually showed a significant increase over the years since 1985. Also the share of LH papers demonstrated a steady increase (overall mean 5%, but mean 8% over the past 4 years). The most frequent category was coagulation and fibrinolysis (23.5%). Authors from Germany contributed the most LH papers to the journal (22.7%), followed by the Netherlands and Italy (16.3 and 13.2%, respectively). Recent citation data indicated that other publications cited LH review papers much more frequently than other types of papers.

Conclusions: The history of the journal reflects the emergence and development of laboratory hematology as a separate discipline of laboratory medicine.

Recent advances in the prenatal interrogation of the human fetal genome

The amount of genetic and genomic information obtainable from the human fetus during pregnancy is accelerating at an unprecedented rate. Two themes have dominated recent technological advances in prenatal diagnosis: interrogation of the fetal genome in increasingly high resolution and the development of non-invasive methods of fetal testing using cell-free DNA in maternal plasma. These two areas of advancement have now converged with several recent reports of non-invasive assessment of the entire fetal genome from maternal blood. However, technological progress is outpacing the ability of the healthcare providers and patients to incorporate these new tests into existing clinical care, and further complicates many of the economic and ethical dilemmas in prenatal diagnosis. This review summarizes recent work in this field and discusses the integration of these new technologies into the clinic and society.

Development of a fibrous DNA chip for cost-effective β-thalassemia genotyping

β-thalassemia is one of the most common genetic disorders worldwide. Concerted efforts are being made to prevent the disease, as the medical and economic burden of thalassemia represents a major public health problem. The molecular diagnosis of the β-globin mutations that cause the disease currently involves a combination of classic methodologies. A microarray-based assay for parallel one-shot detection of mutations has been developed, but the assay remains too expensive for routine application. We developed a cost-effective plastic fiber-based DNA chip for the fast and reliable detection of 25 types of β-thalassemia mutations. Assay conditions were established and genotyping was successfully performed on a genomic sample from a β-thalassemia patient. Our data show that this β-thalassemia genotyping chip is an advantageous platform for mass genotyping because of its low cost, rapid results, and reliability.

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.