Distance Polymerase Chain Reaction Research Articles

Molecular methods for genomic analyses of variantPML-RARAor otherRARA-related chromosomal translocations in acute promyelocytic leukemia

TO THE EDITOR: We read an interesting paper by Palta et al. in a recent issue of the Korean Journal of Hematology titled, variant of acute promyelocytic leukemia with tuberculosis: a case report and review of literature [1]. We would like to add some comments to their article and suggest additional molecular methods to confirm variant translocations in acute promyelocytic leukemia (APL). Apart from its characteristic morphology, APL is strongly correlated with presence of the PML-RARA fusion gene due to a t(15;17) translocation. Patients displaying cryptic PML-RARA gene rearrangements or other translocations involving RARA are very rare. Since RARA generates chimeric fusion genes with various partners such as ZBTB16 at 11q23, NUMA1 at 11q13, NPM1 at 5q35, FIP1L1 at 4q12, and STAT5b at 17q11.2 (Fig. 1), confirmatory molecular methods to detect gene rearrangements are necessary when unique or unusual chromosomal translocations are found in APL cases. Palta et al. reported a case of APL accompanied by tuberculosis where cytogenetic study showed a variant chromosomal translocation, t(11;17)(q23;q21). First, although they describe this case as APL with t(11;17)(q23;q21) through bone marrow (BM), immunophenotyping, and cytogenetic studies, we noted an absence of results based on molecular methods. To demonstrate the existence of the ZBTB16-RARA fusion gene, a single specific reverse transcriptase-polymerase chain reaction (RT-PCR) with a specific primer to detect the gene rearrangement or multiplex RT-PCR (e.g. HemaVision) to detect ZBTB16-RARA could have provided an accurate molecular diagnostic result. Second, the authors' reference to a paper by Kang et al. was puzzling despite the fact that it was cited as a similar case with chromosomal translocations at a similar location, in cases of AML with chromosomal translocation t(11;17) [2]. In the first case, cytogenetic analysis from BM aspirate showed t(11;17)(q23;q21) in 18 out of 20 cells while the MLL probe in fluorescence in situ hybridization (FISH) showed split-out signals in 98.5% of interphase cells. The second case also showed t(11;17)(q23;q25) in the chromosome study while the FISH assay showed split-out signals in 79% of interphase cells. However, normal fluorescence patterns were found in 200 cells in additional FISH assays when a dual-color single-fusion PML-RARA probe was used for both cases, which led to the conclusion that the MLL gene was involved in the 11q23 breakpoint and RARA was not involved in the 17q breakpoint. Hence, the authors' citation of this study to explain the ZBTB16-RARA fusion gene appears inadequate, and a molecular study could unambiguously identify the involvement of ZBTB16 at 11q23 in their case. Fig. 1 Various RARA partner genes in acute promyelocytic leukemias. We suggest the authors conduct RT-PCR analysis of the ZBTB16-RARA fusion gene if any remnant RNA or cDNA samples from their APL patient are available. However, if only genomic DNA is available, analyzing the genomic breakpoints by multiplex long distance-polymerase chain reaction (LD-PCR) would be helpful. LD-PCR or long distance inverse (LDI)-PCR can identify known or unknown partner genes, monitor minimal residual disease (MRD), and identify multi-way chromosomal translocations such as three-way or four-way translocations [3]. We have recently used LD-PCR to confirm APL cases showing unusual karyotypes or discrepant results between conventional cytogenetics and molecular studies. More precisely, we identified a novel PML-ADAMTS17-RARA rearrangement and confirmed the genomic fusion breakpoints of cryptic PML-RARA rearrangement in 2 APL patients [3-5]. In conclusion, detection of leukemia-associated fusion genes is important due to their direct relevance to diagnosis, MRD assessment, and treatment response. Since APL patients with ZBTB16-RARA are resistant to all-trans-retinoic acid (ATRA), molecular methods with higher resolution than chromosome studies must be conducted to detect fusion genes and facilitate selection of the most appropriate treatment. We believe that molecular techniques such as FISH, RT-PCR, and LD-PCR should be used in addition to morphology and cytogenetic studies in APL diagnosis and evaluation so that atypical PML-RARA or RARA variant gene rearrangements are not missed.

Prenatal diagnosis strategy of hemophilia A with different clinical backgrounds

Objective To prenatally diagnose HA fetus with different clinical backgrounds. Methods Genetic tests were performed on 15 gravidas subjected for prenatal diagnosis of HA and different methods were employed for diagnosis according to the gestational weeks and clinical data. Amniotic fluid were taken from pregnant women within 23 gestational weeks for direct genotyping and indirect linkage analysis, since these women had probands with clear-cut mutations. Cordocentesis was performed for linkage analysis in pregnant women over 23 gestational weeks with probands whose types of mutation were unknown, while the FⅧ activity tests were carried out simultaneously. For the pregnant women over 23 gestational weeks without proband, cordocentesis was operated for measurement of FⅧ activity and karyotyping, but carriers of hemophilia A could not be detected in these cases. The introns 22 and 1 inversion of F8 gene were identified by long distance-polymerase chain reaction. Nucleotide sequencing was employed if the gene inversion could not be found and linkage analysis of 7 polymorphic markers, including DXS1108, F8Civs13, INTRON22,DXS1073,DXS9901, DXS15, DXS8069 and sex site (Amelo) were applied eventually. Identification of maternal blood contamination must be done before the tests. Results Fifteen samples were identified without maternal blood contamination. Five fetuses were diagnosed with hemophilia A. Meanwhile there were three pregnant women whose cord blood FⅧ activities were less than 1%. One of them was accompanied by trisomy 21; another had inversion mutation in introns 22 of F8 gene; the remaining one was identified with missense mutation in exon 23 (p. Arg2182Cys) of F8 gene. Conclusions Diverse methods should be applied in prenatal diagnosis of hemophilia A with different clinical backgrounds, for the sake of birth defects prevention. Key words: Hemophilia A; Factor Ⅷ; Prenatal diagnosis

Prenatal diagnosis for fetus with hemophilia A

To study the prenatal genetic diagnostic methods for hemophilia A fetus. From 2002 to 2006, 19 hemophilia A families were diagnosed either by long distance-polymerase chain reaction (LD-PCR) for factor VIII intron 22 inversion or by the DNA polymorphism genetic linkage analysis of factor VIII in the Beijing Chaoyang Hospital. (1) Totally 19 women, with 22 pregnancies received the prenatal diagnosis of fetal hemophilia A. The average week at diagnosis was 23 (17-34 ) weeks. All the direct fetal blood sampling (DFBS) were successful. There was no fetal-loss caused by the procedures. (2) Of the 19 hemophilia A families, 14 appeared to be factor VIII intron 22 inversion, in which 16 prenatal diagnoses were done, 10 fetuses were diagnosed as genetical hemophilia A patients, and 6 fetuses were normal. (3) Using combined polymorphism genetic linkage analysis 6 prenatal diagnoses were done, including one woman's two pregnancies, in which both her fetuses were diagnosed as genetical hemophilia A patients. (4) Factor VIII levels of 16 fetuses were measured, and 6 fetuses were unmeasured either because the pregnancy weeks were lower than 20 weeks or the parents refused. Factor VIII level ranged from 0 to 198%. There were 11 fetuses whose factor VIII levels were lower than 10%. Ten of them were diagnosed to be genetical hemophilia A patients, and in only one boy the factor VIII level was 2%, but the genetic diagnosis was normal and for one year's follow up he was doing normal. LD-PCR combined with polymorphism genetic linkage analysis enables a quick and correct detection of hemophilia A carrier. For a carrier pregnancy, prenatal diagnosis could be done for the male fetus. Factor VIII deficiency of the fetus could help make the diagnosis but the final diagnosis should be based on genetic evidence.

A long distance RT-PCR able to amplify the Pestivirus genome

A method to amplify long genomic regions (up to ∼12.3 kb) from pestiviruses in one RT-PCR is described. The difficulty in designing conserved Pestivirus primers for the amplification of genomes from highly divergent isolates simply by means of overlapping segments is demonstrated using new bioinformatic tools. An alternative procedure consisting of optimizing the length of the genomic cDNA fragments and their subsequent amplification by polymerase chain reaction (PCR) using a limited set of specific primers is described. The amplification of long DNA fragments from a variety of sources, including genomic, mitochondrial, and viral DNAs as well as cDNA produced by reverse transcription (RT) has been achieved using this methodology, known as long distance PCR. In the case of viruses, it is necessary to obtain viral particles from infected cells prior to RT procedures. This work provides improvements in four steps of long distance RT-PCR (L-RT-PCR): (i) preparation of a viral stock, (ii) preparation of template RNA, (iii) reverse transcription and (iv) amplification of the cDNA by LD-PCR. The usefulness of L-RT-PCR is discussed in the light of current knowledge on pestivirus diversity. The genomic sequence of Singer_ Arg reference strain obtained using this method is presented and characterized.

A simple and affordable method for high‐throughput DNA extraction from animal tissues for polymerase chain reaction

We have developed a very simple and inexpensive method for high-throughput DNA extraction from animal tissues. The procedure contains three steps (digestion, heating, and centrifugation) and it is compatible with the 96-well plate format commonly used in polymerase chain reaction (PCR) amplifications. The duration for processing a plate is about 1.5 h; therefore, one researcher can isolate DNA from up to 1000 samples during a single workday. A small piece of tissue (ca. 10-20 mg) yields enough template for at least 50-70 PCR amplifications, as demonstrated by using the processed samples as templates successfully for long distance PCR, multiplex PCR, and randomly amplified polymorphic DNA (RAPD) assay. The application of our method is expected to facilitate studies that require high-throughput DNA isolation for PCR amplification, such as genotyping by microsatellites for mapping and genetic diversity studies, as well as mutant screening in zebrafish.

Long distance polymerase chain reaction of ascites lymphoma cells aids diagnosis establishment of abdominal Burkitt's lymphoma and Burkitt-like lymphoma

Burkitt's lymphoma (BL) and its variants, including Burkitt-like lymphoma (BLL), can be difficult to distinguish morphologically and immunophenotypically from diffuse large B-cell lymphoma (DLBCL). Because the treatment of BL differs markedly from that of other types of non-Hodgkin's lymphoma (NHL), exact pathological diagnosis is crucial. We report 2 cases of patients with BL initially diagnosed as DLBCL. Due to clinical features typical of BL, long distance polymerase chain reaction (PCR) for detecting the t(8;14) translocation involving the c-myc proto-oncogene was performed on ascites lymphoma cells. Re-evaluation by a reference hematopathologist, together with long distance PCR in both patients revealing the t(8;14) translocation, resulted in diagnosis modification to BL and BLL. Consequently, the patients were treated with intense high-dose chemotherapy regimens including central nervous system (CNS) prophylaxis, and complete remission was initially achieved in both patients. Both BL and BLL should be considered in the differential diagnosis of DLBCL if abdominal spread with ascites and metabolic disorders are present. Long distance PCR analysis of ascites lymphoma cells for the detection of the BL-typical c-myc rearrangement offers a convenient and rapid possibility of diagnosis verification in atypical or borderline cases of BL.

The CpG island in intron 22 of the factor VIII gene is predominantly methylated on the X chromosome of human males.

The inactivation of one of the two X chromosomes in females is a random process associated with methylation principally in CpG islands. The methylation status of a CpG island in intron 22 of the human factor VIII (FVIII) gene was investigated using a novel practical approach. Genomic DNA from men and women was digested with various methylation-sensitive (MS) restriction enzymes, the recognition sequences of which occurred at least once in the FVIII CpG island. Long distance-polymerase chain reaction (LD-PCR) was then used to amplify the island. Successful amplification indicated that the island was methylated and the absence of a PCR product indicated that at least one restriction site was unmethylated. To analyze the relative methylation status of the extragenic and intragenic copies of the island, we used Southern blot with MS restriction enzymes. The MS LD-PCR patterns obtained from male and female DNA samples indicated that at least some copies of the intragenic CG island were fully methylated at all sites investigated. Additionally, the island showed consistent differences among individuals. Southern blot studies using female DNA showed partial resistance to MS digestion for the intragenic and extragenic CpG island homologs. Our observations indicate that this CpG island is predominantly methylated on the X chromosome of males and suggest that its methylation pattern does not correlate with X inactivation of females. This prevents the use of this island coupled with DNA polymorphisms for investigation of X-chromosome inactivation.