Denaturing High-pressure Liquid Chromatography Research Articles

Novel plasminogen gene mutations in Turkish patients with type I plasminogen deficiency.

The plasminogen (Plg) protein is the inactive proenzyme form of plasmin that dissolves fibrin thrombi by a process called fibrinolysis. It has been shown that homozygous or compound-heterozygous deficiency of this protein is a major cause of a rare inflammatory disease affecting mainly mucous membranes found in different body sites. In this study, five individual Turkish patients and nine Turkish families with type 1 Plg deficiency were investigated for PLG gene mutations. All of the coding regions of the PLG gene mutations were screened for mutations using denaturing high-pressure liquid chromatography (DHPLC). Samples showing a different DHPLC profile were subjected to DNA sequencing analysis. Here, we described five novel mutations namely, Cys49Ter, +1 IVS6 G>A, Gly218Val, Tyr283Cys, and Gly703Asp. Previously identified five nonsynonymous (Lys38Glu, Glu180Lys, Gly420Asp, Asp453Asn, Pro763Ser), five synonymous (330 C>T, 582 C>T, 771 T>C, 1083 A>G, 2286 T>G), and a 3' untranslated region (3' UTR) mutation (c.*45 A>G) were also reported in this present study. In this study, we have identified a total of eight mutations, five of which are novel. The mutations/polymorphisms identified in eight of the patients do not explain the disease phenotype. These cases probably carry other pathological mutations (homozygous or compound heterozygous) that cannot be detected by DHPLC.

Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing

Unfiltered vinegar samples collected from three oxidation cycles of the submerged industrial production of each, red wine and organic apple cider vinegars, were sampled in a Slovene vinegar producing company. The samples were systematically collected from the beginning to the end of an oxidation cycle and used for culture-independent microbial analyses carried out by denaturing high pressure liquid chromatography (DHPLC) and Illumina MiSeq sequencing of 16S rRNA gene variable regions. Both approaches showed a very homogeneous bacterial structure during wine vinegar production but more heterogeneous during organic apple cider vinegar production. In all wine vinegar samples Komagataeibacter oboediens (formerly Gluconacetobacter oboediens) was a predominating species. In apple cider vinegar the acetic acid and lactic acid bacteria were two major groups of bacteria. The acetic acid bacterial consortium was composed of Acetobacter and Komagataeibacter with the Komagataeibacter genus outcompeting the Acetobacter in all apple cider vinegar samples at the end of oxidation cycle. Among the lactic acid bacterial consortium two dominating genera were identified, Lactobacillus and Oenococcus, with Oenococcus prevailing with increasing concentration of acetic acid in vinegars. Unexpectedly, a minor genus of the acetic acid bacterial consortium in organic apple cider vinegar was Gluconobacter, suggesting a possible development of the Gluconobacter population with a tolerance against ethanol and acetic acid. Among the accompanying bacteria of the wine vinegar, the genus Rhodococcus was detected, but it decreased substantially by the end of oxidation cycles.

126 novel mutations in Italian patients with neurofibromatosis type 1.

Genetic analysis of Neurofibromatosis type 1 (NF1) may facilitate the identification of patients in early phases of the disease. Here, we present an overview of our diagnostic research spanning the last 11years, with a focus on the description of 225 NF1 mutations, 126 of which are novel, found in a series of 607 patients (513 unrelated) in Italy. Between 2003 and 2013, 443 unrelated patients were profiled by denaturing high pressure liquid chromatography (DHPLC) analysis of 60 amplicons derived from genomic NF1 DNA and subsequent sequencing of heterozygotic PCR products. In addition, a subset of patients was studied by multiplex ligation-dependent probe amplification (MLPA) to identify any duplications, large deletions or microdeletions present at the locus. Over the last year, 70 unrelated patients were investigated by MLPA and sequencing of 22 amplicons spanning the entire NF1 cDNA. Mutations were found in 70% of the 293 patients studied by DHPLC, thereby fulfilling the NIH criterion for the clinical diagnosis of NF1 (detection rate: 70%); furthermore, 87% of the patients studied by RNA sequencing were genetically characterized. Mutations were also found in 36 of the 159 patients not fulfilling the NIH clinical criteria. We confirmed a higher incidence of intellectual disability in patients harboring microdeletion type 1 and observed a correlation between a mild phenotype and the small deletion c.2970_2972delAAT or the missense alteration in amino acid residue 1809 (p.Arg1809Cys). These data support the use of RNA-based methods for genetic analysis and provide novel information for improving the management of symptoms in oligosymptomatic patients.

Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis.

Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)–based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.

P14.01 * INTEGRATED GENETIC STUDIES OF NEUROFIBROMATOSIS TYPE 1. A TEN YEAR, ITALIAN EXPERIENCE

BACKGROUND: Neurofibromatosis type 1 (NF1) is a human autosomal dominant disorders that affects approximately 1 in 3,500 individuals worldwide. The most common features of NF1 are pigmentary abnormalities, such as cafe-au-lait macules, skinfold freckling, Lisch nodules and cutaneous and plexiform neurofibromas (PNs). These signs are age-dependent and present high variability in penetrance and expressivity even between affected members of a family. NF1 is the most common cancer predisposing syndrome affecting the nervous system. Glioma is the most common central nervous system neoplasia in NF1 patients: 15-20% NF1 children develop low grade optic gliomas. PNs occur in 30% of NF1 patients in peripheral nervous system. Patients with PNs have a 20-fold higher risk of developing malignant peripheral nerve sheath tumours (MPNSTs) than other NF1 patients. NF1 is caused by mutations in the neurofibromin gene encoding a negative regulator of Ras guanosine triphosphate (GTP)ase proteins: for this reason is considered a tumor suppressor gene. Mutation detection in the NF1 gene is complex, due to the large size of the gene (>350 kb), the presence of pseudogenes, the lack of hot spots, and the great variety of possible mutations. Hence, the clinical and molecular diagnosis of NF1 may be challenging and its fine-tuning is desirable. METHODS: During 2003-2013 NF1 mutation analysis of genomic DNA was performed in 458 patients using the multiplex ligation-dependent probe amplification (MLPA) to look for deletions or insertions located inside the NF1 gene. Subjects who tested negative for MLPA were investigated using denaturing high pressure liquid chromatography (DHPLC) and sequencing DNA. RNA-based cDNA-PCR sequencing was used in a limited group of patients. RESULTS: 299 of 458 patients were diagnosed according to NIH criteria. 54% were children and about 53% of all NF1 patients were found to have sporadic mutations. We identified 197 single mutations and more than 57% were novel. This genetic protocol permitted us to find mutations in 210 of 299 of clinically diagnosed patients (detection rate: 70%). To improve such detection rate we have recently developed a sensitive, integrated genetic protocol using MLPA and RNA-based cDNA-PCR sequencing. This protocol was validated in a cohort of 33 blood samples from NF1 patients with complete NF1 features, identifying the mutations in 30 cases (91% detection rate). CONCLUSIONS: These data suggest that integrated DNA/RNA-based protocols can improve detection rate in patients suspected to have NF1.

Gut Microbiota Patterns Associated with Colonization of Different Clostridium difficile Ribotypes

C. difficile infection is associated with disturbed gut microbiota and changes in relative frequencies and abundance of individual bacterial taxons have been described. In this study we have analysed bacterial, fungal and archaeal microbiota by denaturing high pressure liquid chromatography (DHPLC) and with machine learning methods in 208 faecal samples from healthy volunteers and in routine samples with requested C. difficile testing. The latter were further divided according to stool consistency, C. difficile presence or absence and C. difficile ribotype (027 or non-027). Lower microbiota diversity was a common trait of all routine samples and not necessarily connected only to C. difficile colonisation. Differences between the healthy donors and C. difficile positive routine samples were detected in bacterial, fungal and archaeal components. Bifidobacterium longum was the single most important species associated with C. difficile negative samples. However, by machine learning approaches we have identified patterns of microbiota composition predictive for C. difficile colonization. Those patterns also differed between samples with C. difficile ribotype 027 and other C. difficile ribotypes. The results indicate that not only the presence of a single species/group is important but that certain combinations of gut microbes are associated with C. difficile carriage and that some ribotypes (027) might be associated with more disturbed microbiota than the others.

Predictive value of KIT immunohistochemical staining for KIT mutations in patients with gastrointestinal stromal tumors (GIST): A systematic review.

30 Background: Immunohistochemical staining for KIT (CD117) is used as part of diagnostic tool for GIST. Approximately 95% of GIST are known to be positive for CD117. Studies have shown that not all CD117-positive GIST carry KIT mutations nor does CD117 negativity rule out KIT or PDGFRA mutations. We performed a systematic review to investigate the positive and negative predictive values of KIT immunostaining for KIT mutations in GIST. Methods: A Medline search of the MeSH terms “KIT mutation” and “GIST” and “prevalence” yielded 54 articles from year 1999 to 2011. English language studies on GIST with data available for KIT immunostaining as well as KIT gene mutations were included. Studies lacking data on either CD117 positivity or KIT mutations were excluded. Immunostaining was done using Dako polyclonal rabbit antibody or PKCh monoclonal mouse antibody in eligible studies. Denaturing high-pressure liquid chromatography (DHPLC) was used to screen mutations in majority of eligible studies, and ABI Prism Genetic Analyzer to sequence DNA. Results: 6 studies including 708 CD117-positive GIST patients were eligible for analysis of positive predictive value of KIT immunostaining for KIT mutations and 5 studies including 47 CD117-negative GIST patients for negative predictive value. Many studies were excluded due to insufficient data on CD117 positivity or KIT mutational analysis. 72.8% of CD117-positive GIST tumors carried KIT mutations (exon 11 62.2%, exon 9 10.2%, exon 13 1.8% and exon 17 1%), and 4.1% harbored PDGFRA mutations. In contrast, 74.5% of CD117-negative GIST tumors did not have KIT mutations. 25.5% of CD117-negative GIST harbored KIT exon 11 mutations (no mutations in exon 9, 13 or 17 were observed). In addition, 30% of CD117-negative GIST were found to have PDGFRA mutations. Conclusions: PDGFRA mutations were found to be 7 times more common in CD117-negative than in CD117-positive GIST (30% vs. 4.1%). Over half (55.5%) of CD117-negative GIST carried KIT exon 11 or PDGFRA mutations. We recommend mutational analysis in all tumors clinically suspected of GIST and that are CD117-negative for two reasons: 1. in order to make a diagnosis, and 2. to help tailor therapy.

Course of Visual Decline in Relation to the Best1 Genotype in Vitelliform Macular Dystrophy

To describe the disease course in patients with vitelliform macular dystrophy (VMD) with a Best1 mutation and to determine the association between Best1 genotype and visual prognosis. Consecutive case series. Fifty-three patients with VMD with Best1 mutations from 27 Dutch families, aged 11 to 87 years. Best-corrected visual acuity (VA), fundus appearance, and Arden ratio on the electro-oculogram (EOG) during clinical follow-up were assessed from medical records. Mutation analysis of the Best1 gene was performed on DNA samples using denaturing high-pressure liquid chromatography and direct sequencing. Cumulative lifetime risk of visual decline below 0.5, 0.3, and 0.1 for the entire group and stratified for genotype. Median age of onset of visual symptoms was 33 years (range: 2-78). The cumulative risk of VA below 0.5 (20/40) was 50% at 55 years and 75% at 66 years. The cumulative risk of decline less than 0.3 (20/63) was 50% by age 66 years and 75% by age 74 years. Two patients progressed to VA less than 0.1 (20/200). Fourteen different mutations were found. Most patients (96%) had missense mutations; the Thr6Pro, Ala10Val, and Tyr227Asn mutations were most common. Visual decline was significantly faster in patients with an Ala10Val mutation than either the Thr6Pro or the Tyr227Asn mutation (P=0.001). Age of onset of visual symptoms varies greatly among patients with VMD. All patients show a gradual decrease in VA, and most progress to visual impairment at a relatively late age. Our data suggest a phenotype-genotype correlation, because the Ala10Val mutation has a more rapid disease progression than other common mutations. The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Detection of c-KITandPDGFRAGene Mutations in Gastrointestinal Stromal Tumors

Mutational analysis of c-KIT or PDGFRA has become an important laboratory assay for patients with gastrointestinal stromal tumors (GISTs) because the results are useful in predicting the responsiveness to imatinib. To assess the diagnostic usefulness of denaturing high-pressure liquid chromatography (DHPLC) in this setting, we performed DHPLC and DNA sequencing to study exons 9, 11, 13, and 17 of c-KIT and exons 12 and 18 of PDGFRA in 54 consecutive cases of GIST collected from a single population. Most (40/54 [74%]) carried c-KIT mutations, and 7 (13%) carried PDGFRA mutations. These results were similar to those described in the literature. It is important to note that DHPLC was found to be highly sensitive, detecting all of the mutations in these 6 exons that were identified by DNA sequencing. Our data suggest that DHPLC is a cost-effective, rapid, and sensitive test for screening for mutations of c-KIT and PDGFRA in GISTs.

Novel technique for rapid detection of α-globin gene mutations and deletions

Populations in Southeast Asia and South China have high frequencies of alpha-thalassemia caused by alpha-globin gene mutations and/or deletions. This study was designed to find an efficient and simple diagnostic test for the mutations and deletions. A duplex polymerase chain reaction (PCR)/denaturing high-pressure liquid chromatography (DHPLC) was used to detect the mutations and deletions. A blinded study of 110 samples, which included 92 alpha-thalassemia samples with various genotypes and 18 normal DNA samples, was carried out by the methods. The duplex PCR products of the sample with known Constand spring mutation (CS)/alphaalpha, Quonsze mutation (QS)/alphaalpha, and Weastmead mutation (WS)/alphaalpha DNA showed significantly different profiles, which suggests that DHPLC analysis at 63.8 degrees C can detect potential mutations directly. The DHPLC at 50 degrees C analysis can distinguish the --SEA and nondeletional alleles. The new assay is 100% concordant with the original genotype. In conclusion, the technique including the duplex PCR assay followed by DHPLC analysis can be used to diagnose alpha-thalassemia; this methodology is simple, rapid, accurate, semiautomatic, and high output, and thus, it is suitable for large-scale screening.

Mechanisms of Resistance in Nontyphoidal Salmonella enterica Strains Exhibiting a Nonclassical Quinolone Resistance Phenotype

Nontyphoidal Salmonella enterica strains with a nonclassical quinolone resistance phenotype were isolated from patients returning from Thailand or Malaysia to Finland. A total of 10 isolates of seven serovars were studied in detail, all of which had reduced susceptibility (MIC > or = 0.125 microg/ml) to ciprofloxacin but were either susceptible or showed only low-level resistance (MIC < or = 32 microg/ml) to nalidixic acid. Phenotypic characterization included susceptibility testing by the agar dilution method and investigation of efflux activity. Genotypic characterization included the screening of mutations in the quinolone resistance-determining regions (QRDR) of gyrA, gyrB, parC, and parE by PCR and denaturing high-pressure liquid chromatography and the amplification of plasmid-mediated quinolone resistance (PMQR) genes qnrA, qnrB, qnrS, qnrD, aac(6')-Ib-cr, and qepA by PCR. PMQR was confirmed by plasmid analysis, Southern hybridization, and plasmid transfer. No mutations in the QRDRs of gyrA, gyrB, parC, or parE were detected with the exception of a Thr57-Ser substitution within ParC seen in all but the S. enterica serovar Typhimurium strains. The qnrA and qnrS genes were the only PMQR determinants detected. Plasmids carrying qnr alleles were transferable in vitro, and the resistance phenotype was reproducible in Escherichia coli DH5alpha transformants. These data demonstrate the emergence of a highly mobile qnr genotype that, in the absence of mutation within topoisomerase genes, confers the nontypical quinolone resistance phenotype in S. enterica isolates. The qnr resistance mechanism enables bacteria to survive elevated quinolone concentrations, and therefore, strains carrying qnr alleles may be able to expand during fluoroquinolone treatment. This is of concern since nonclassical quinolone resistance is plasmid mediated and therefore mobilizable.

Universal multiplex PCR and CE for quantification of SMN1/SMN2 genes in spinal muscular atrophy

We established a universal multiplex PCR and CE to calculate the copy number of survival motor neuron (SMN1 and SMN2) genes for clinical screening of spinal muscular atrophy (SMA). In this study, one universal fluorescent primer was designed and applied for multiplex PCR of SMN1, SMN2 and two internal standards (CYBB and KRIT1). These amplicons were separated by conformation sensitive CE. Mixture of hydroxyethyl cellulose and hydroxypropyl cellulose were used in this CE system. Our method provided the potential to separate two 390-bp PCR products that differ in a single nucleotide. Differentiation and quantification of SMN1 and SMN2 are essential for clinical screening of SMA patients and carriers. The DNA samples included 22 SMA patients, 45 parents of SMA patients (obligatory carriers) and 217 controls. For evaluating accuracy, those 284 samples were blind-analyzed by this method and denaturing high pressure liquid chromatography (DHPLC). Eight of the total samples showed different results. Among them, two samples were diagnosed as having only SMN2 gene by DHPLC, however, they contained both SMN1 and SMN2 by our method. They were further confirmed by DNA sequencing. Our method showed good agreement with the DNA sequencing. The multiplex ligation-dependent probe amplification (MLPA) was used for confirming the other five samples, and showed the same results with our CE method. For only one sample, our CE showed different results with MLPA and DNA sequencing. One out of 284 samples (0.35%) belonged to mismatching. Our method provided a better accurate method and convenient method for clinical genotyping of SMA disease.

263 PATERNAL ISODISOMY FOR CHROMOSOME 2 AS CAUSE OF BILE SALT EXPORT PUMP (BSEP) DEFICIENCY

Background: Bile salt export pump (BSEP) deficiency, a defect in a canalicular bile acid excretion, falls into the progressive familial intrahepatic cholestasis. It is an autosomal recessive disorder with several mutations being reported in the ABCB11 gene on chromosome 2q24−31. We describe a case of BSEP deficiency with a new mutation, where the patient received both mutated alleles from the father, through the rare phenomenon of uniparental disomy (UPD). Methods: A 4-year-old infant, underwent to orthotopic liver transplantation (OLT) at the age of 9 months because of persistent cholestasis and liver failure. Immunohistochemistry was performed with BSEP antibody. Genomic DNA was extracted from the baby and his parents. Molecular studies of ABCB11 were performed using denaturing high-pressure liquid chromatography (DHPLC) and direct sequencing. Gene copy number determination, segregation of the mutation and reconstruction of the flanking haplotype employed quantitative real time PCR (qPCR), single nucleotide polymorphisms (SNPs) genotyping, and polymorphic microsatellites. Results: Liver histology showed cirrhosis. Immunohistochemistal stain using anti-BSEP antibodies revealed wholly absent marking at canalicular margin of hepatocytes, consistent with the diagnosis of BSEP deficiency. DHPLC and sequencing analysis showed a novel, homozygous c.2620C>T transition in exon 20 of the ABCB11 gene. The mutation replaces arginine for cysteine at residue 833 (p. R833C). This change was absent in a large panel of normal chromosomes, and it was heterozygous in peripheral blood from the father, but not in several tissues obtained from the child’s mother. qPCR analyses did not disclose abnormal gene copy number in both the patient and his mother ruling out a microdeletion of ABCB11. Segregation analysis of seven intragenic SNPs and six flanking microsatellite markers showed data suggestive of UID of the region on chromosome 2q24−31 inherited from the father. Conclusion: In severe forms, infants with BSEP deficiency developed cholestasis and fibrosis, and end-stage liver disease requires OLT. Molecular studies are needed to offer measures as to avoid recurrence of the disease. The present case highlights the importance of full gene analyses to offer a more accurate genetic counselling.

Genetic Testing for Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

AbstractHereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominant cancer syndrome that confers an elevated risk of early‐onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. HNPCC accounts for up to 5% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl‐directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA. HNPCC is most often associated with mutations in the MLH1 gene on 3p21, the MSH2 gene on 2p21, and to a lesser extent MSH6 on 2p16. This unit presents a comprehensive molecular and genetic screening strategy for HNPCC mutations in the MLH1, MSH2, and MSH6 genes, including analysis of MSI, mutation scanning by denaturing high‐pressure liquid chromatography (DHPLC), and DNA sequencing analysis. Curr. Protoc. Hum. Genet. 61:10.12.1‐10.12.28. © 2009 by John Wiley &amp; Sons, Inc.

Application of PCR derived technology for diagnosis of hematological disease

Polymerase chain reaction (PCR) technique for the diagnosis of hematological disease brought about revolutionary progress. It has become indispensable and basic technology for genotyping of acute and chronic leukemia and diagnosis of myeloproliferative disorders, thalassemia, hemophilia and other genetic diseases. Based on the PCR technology, multiple nested-PCR, real-time fluorescence quantitative PCR (Q-PCR), denaturing high pressure liquid chromatography (DHPLC), capillary electrophoresis, the molecular hybridization and directly sequencing technique have been developed. The multip]e nested-PCR can be used to examine a variety of leukemia genes and confirm the type of leukemia. The application of Q-PCR has effectively solved the problem of pollution of the PCR and it can be used to monitor minimal residual disease of leukemia. Capillary electrophoresis is more suitable for gene fragment length change. DHPLC can be applied for high-throughput screening of gene mutation. Sequencing is a reliable method and it has been used for routine diagnosis. Key words: Hematologic diseases; Polymerase chain reaction

Characteristics of participants with self-reported hemochromatosis or iron overload at HEIRS study initial screening.

There are few descriptions of young adults with self-reported hemochromatosis or iron overload (H/IO). We analyzed initial screening data in 7,343 HEmochromatosis and IRon Overload Screening (HEIRS) Study participants ages 25-29 years, including race/ethnicity and health information; transferrin saturation (TS) and ferritin (SF) measurements; and HFE C282Y and H63D genotypes. We used denaturing high-pressure liquid chromatography and sequencing to detect mutations in HJV, TFR2, HAMP, SLC40A1, and FTL. Fifty-one participants reported previous H/IO; 23 (45%) reported medical conditions associated with H/IO. Prevalences of reports of arthritis, diabetes, liver disease or liver cancer, heart failure, fertility problems or impotence, and blood relatives with H/IO were significantly greater in participants with previous H/IO reports than in those without. Only 7.8% of the 51 participants with previous H/IO reports had elevated TS; 13.7% had elevated SF. Only one participant had C282Y homozygosity. Three participants aged 25-29 years were heterozygous for potentially deleterious mutations in HFE2, TFR2, and HAMP promoter, respectively. Prevalences of self-reported conditions, screening iron phenotypes, and C282Y homozygosity were similar in 1,165 participants aged 30 years or greater who reported previous H/IO. We conclude that persons who report previous H/IO diagnoses in screening programs are unlikely to have H/IO phenotypes or genotypes. Previous H/IO reports in some participants could be explained by treatment that induced iron depletion before initial screening, misdiagnosis, or participant misunderstanding of their physician or the initial screening questionnaire.

Microfluidic Deletion/Insertion Analysis for Rapid Screening of KIT and PDGFRA Mutations in CD117-Positive Gastrointestinal Stromal Tumors : Diagnostic Applications and Report of a New KIT Mutation

Gastrointestinal stromal tumors (GISTs) frequently harbor mutations in the KIT and PDGFRA genes, the presence and type of which correlate with the response to the kinase inhibitor imatinib mesylate. Because most GIST mutations are deletions/insertions, we used a microfluidic apparatus to detect these size variations in polymerase chain reaction-amplified DNA. This approach, termed microfluidic deletion/insertion analysis (MIDIA), identified mutations in 30 of 50 DNA samples from paraffin-embedded CD117-positive GISTs (60%), comprising 25 deletions and five insertions. Sequencing of 14 MIDIA-positive samples confirmed the deletions/insertions, including two 3-bp alterations. Sequencing of all 20 MIDIA-negative samples also showed highly consistent results with MIDIA because 10 cases were wild type and eight displayed a single base substitution in which detection by MIDIA was not expected. Sequencing also revealed a 3-bp deletion undetected by MIDIA, thus establishing the resolution limit of MIDIA at deletions/insertions >or=3 bp. Denaturing high-pressure liquid chromatography analysis confirmed all mutations detected by MIDIA and sequencing. We pro-pose MIDIA as the first step in mutational screening of GIST because it allowed the detection of 75% of mutated cases (94% of deletions/insertions) in less than 30 minutes after polymerase chain reaction amplification and at a lower cost compared with denaturing high-pressure liquid chromatography and sequencing, which might then be used only for MIDIA-negative cases.

Analysis of GATA-1 Mutations in Chronic Myeloid Leukaemia.

Despite extensive characterisation of the molecular pathogeneisis of chronic myeloid leukaemia (CML), little is known about the events underlying progression to accelerated phase and blast crisis. The haematopoietic transcription factor GATA1 plays an essential role in the commitment to, and differentiation within, erythroid, megakaryocyte, eosinophil and mast cell lineages. The observation of frequent eosinophilia and thrombocytosis alongside granulocytic hyperplasia suggests that GATA1 is actively expressed in CML chronic phase. GATA1 is mutated in the acute megakaryoblastic leukaemia of Down syndrome and in its preleukaemic form, transient abnormal myelopoiesis. The latter can morphologically resemble CML with basophilia and eosinophilia in addition to circulating blast cells.Examination of the expressed sequence tag (EST) database for GATA1 shows 4 variant sequences. 3 of these are derived from CML patient bone marrow.Given the plausible association between perturbations in GATA1 function and progression of CML, along with suggestive EST evidence, we hypothesized that mutations in GATA1 could be involved in the transition from chronic phase to blast crisis in CML.Materials and methods: Following appropriate informed consent and ethical approval genomic DNA was extracted from blast cells from 24 patients with CML in accelerated phase (n=1), myeloid blast crisis (n=15) or lymphoid blast crisis (n=8). Polymerase chain reaction (PCR) products were generated encompassing each coding exon of GATA1 and about 50 base pairs of flanking sequence. Exons 3 and 6 were divided into 2 fragments each for analysis. Gel purified PCR products were screened for mutations in GATA1 using DHPLC (denaturing high pressure liquid chromatography, WAVE, Transgenomics, USA). Samples with abnormal migration profiles were directly sequenced by bi-directional sequencing using an ABI 3100 Capillary Array sequencer (Perkin Elmer, UK). Mutations detected by this method were confirmed by a repeat PCR reaction, Topo cloning into pCR4TOPO vector (Invitrogen) and commercial sequencing (Agowa, Germany)Results and discussion 2/24 samples showed abnormal migration patterns by WAVE analysis. Sequencing confirmed 2 different single nucleotide changes in the intronic sequence flanking exon 5. These do not correspond to any known single nucleotide polymorphisms. Since these 2 mutations do not arise in coding or known regulatory regions of the gene it seems unlikely that they are of functional significance. Abnormal regulation of GATA1 activity either at the transcriptional or post-translational level may still play an important part in the pathogenesis of the disease. The mitogen-activated protein kinase (MAPK) pathway has recently been shown to be important in controlling the oncogenic potential of bcr-abl. MAPK mediated phosphorylation of GATA1 at critical serine residues promotes cell survival via increased Bcl-XL expression. In addition study of the upregulation of inducible heat shock protein 70 (Hsp70) in CML has shown the major p210 bcr-abl responsive element upstream of the Hsp70 promoter to be a GATA binding motif.Conclusion These findings suggest that GATA1 mutations are not frequent occurrences in the evolution of blast crisis from CML chronic phase. However, this study does not rule out an important role for dysregulated GATA1 activity in the molecular pathogenesis of chronic myeloid leukaemia.

Glucocorticoid resistance in two key models of acute lymphoblastic leukemia occurs at the level of the glucocorticoid receptor

Glucocorticoids (GCs) specifically induce apoptosis in malignant lymphoblasts and are thus pivotal in the treatment of acute lymphoblastic leukemia (ALL). However, GC-resistance is a therapeutic problem with an unclear molecular mechanism. We generated approximately 70 GC-resistant sublines from a GC-sensitive B- and a T-ALL cell line and investigated their mechanisms of resistance. In response to GCs, all GC-resistant subclones analyzed by real-time polymerase chain reaction (PCR) showed a deficient up-regulation of the GC-receptor (GR) and its downstream target, GC-induced leucine zipper. This deficiency in GR up-regulation was confirmed by Western blotting and on retroviral overexpression of GR in resistant subclones GC-sensitivity was restored. All GC-resistant subclones were screened for GR mutations using denaturing high-pressure liquid chromatography (DHPLC), DNA-fingerprinting, and fluorescence in situ hybridization (FISH). Among the identified mutations were some previously not associated with GC resistance: A484D, P515H, L756N, Y663H, L680P, and R714W. This approach revealed three genotypes, complete loss of functional GR in the mismatch repair deficient T-ALL model, apparently normal GR genes in B-ALLs, and heterozygosity in both. In the first genotype, deficiency in GR up-regulation was fully explained by mutational events, in the second by a putative regulatory defect, and in the third by a combination thereof. In all instances, GC-resistance occurred at the level of the GR in both models.

Emergence of Ofloxacin Resistance in Mycobacterium tuberculosis Clinical Isolates from China as Determined by gyrA Mutation Analysis Using Denaturing High-Pressure Liquid Chromatography and DNA Sequencing

A high rate of double point mutations in gyrA (56% of 87 ofloxacin-resistant Mycobacterium tuberculosis clinical isolates) indicates the emergence of fluoroquinolone resistance. This is the first report to describe denaturing high-pressure liquid chromatography analysis of mutations in gyrA of M. tuberculosis in a large number of clinical isolates.