Frequency of Gc-globin promoter 158 [C>T] XmnI polymorphism in patients with homozygous/compound heterozygous beta thalassaemia

BACKGROUND: Response to hydroxyurea therapy in homozygous or compound heterozygous beta thalassaemia [BT] has been reported as more favourable in the presence of XmnI polymorphism. The prevalence of XmnI polymorphism may vary with BT phenotypes and genotypes, and differs geographically in distribution. Prevalence of XmnI polymorphism is not known in northern Pakistan. Objective: To determine the frequency of Gc-globin promoter 158 [C>T] XmnI polymorphism [XmnI polymorphism] in patients with homozygous or compound heterozygous beta thalassaemia. MATERIALS: Polymerase chain reaction [PCR] for common beta thalassaemia mutations and Gc-globin promoter 158 [C>T] XmnI polymorphism was performed on 107 blood samples of transfusion dependent beta thalassaemia [BT] patients in Pakistan. One hundred samples of unrelated BT traits and 94 samples of healthy subjects as controls were also analysed for BT mutations and XmnI polymorphism. Results: Out of 301 DNA samples, XmnI polymorphism was detected in 71[24%]; in normal controls, XmnI polymorphism was detected in 34/94 [36%] subjects; while in homozygous/compound heterozygous BT, it was detected in 14/107[13%] patients [Fisher's exact test, p =. 0002]. In heterozygous BT group, XmnI polymorphism was detected in 23/100 subjects [Fisher's exact test, p =. 03 with normal controls, and p =. 049 with homozygous/compound heterozygous BT]. The most common BT genotype was Frame Shift [Fr] 8–9/Fr 8–9, and none of the patients with this genotype had XmnI polymorphism. The second most common genotype was IVSI-5/IVSI-5; 4/26 [15%]. Cases with this genotype had XmnI polymorphism. Conclusion: XmnI polymorphism in homozygous/compound heterozygous BT group is 13%. The most common genotype associated with XmnI polymorphism was IVSI-5/IVSI-5

Real time polymerase chain reaction in diagnosis of chronic myeloid leukemia

To compare the sensitivity and specificity of Real Time Polymerase Chain Reaction [RT-PCR] with conventional cytogenetics in diagnosis of chronic myeloid leukemia. A cross-sectional, analytical study. The Armed Forces Institute of Pathology [AFIP], Rawalpindi, from December 2010 to January 2012. A total number of 40 patients were studied, in which all were diagnosed as CML on peripheral blood and bone marrow aspiration. The subjects were tested for the presence of Philadelphia [Ph] chromosome by cytogenetics and BCR-ABL fusion gene by RT-PCR. 2-3 ml of venous blood was collected, half in sodium heparin [anti-coagulant] for cytogenetics and half in EDTA for PCR. For cytogenetics, cells were cultured for 72 hours in RPMI 1640 medium and examined by arresting in metaphase using Colchicine to identify Philadelphia chromosome. For PCR, RNA extraction was done by Tri Reagent LS [MRC, USA] and cDNA was synthesized using reverse transcriptase and gene specific primer. RT- PCR was done on ABI-7500. The positive samples were identified when fluorescence exceeded threshold limit. Results of cytogenetics and RT PCR were compared. Out of the 40 patients, PCR showed 37 [92.5%] were positive and 3 [7.5%] were negative for BCR-ABL fusion gene, whereas in cytogenetics 28 [70%] were positive for Ph chromosome and 12 [30%] were negative for Ph chromosome. Sensitivity and specificity of cytogenetics was 75.6% and 100% respectively. Real time PCR as compared to cytogenetics is less tedious, gives quick results, does not require multiple sampling due to culture failure and can be done on peripheral blood