ABSTRACT
We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings.
Subject(s)
DNA Mutational Analysis/instrumentation , DNA Probes/genetics , DNA, Viral/genetics , Genetic Variation/genetics , Human papillomavirus 18/genetics , Oligonucleotide Array Sequence Analysis/instrumentation , Polymorphism, Single Nucleotide/genetics , Equipment Design , Equipment Failure Analysis , Human papillomavirus 18/isolation & purification , Reproducibility of Results , Sensitivity and SpecificityABSTRACT
OBJECTIVE: To investigate the role of KAL1 abnormalities in Brazilian patients with Kallmann syndrome. DESIGN: In vitro experiments. SETTING: Academic medical center. PATIENT(S): One hundred fifteen Brazilian patients (98 men) with Kallmann syndrome. INTERVENTION(S): Peripheral blood leukocytes were used to obtain DNA. MAIN OUTCOME MEASURE(S): Direct sequencing and multiplex ligation-dependent probe amplification were used to identify KAL1 abnormalities. RESULT(S): We identified four KAL1 mutations (p.Met1?, p.Ala33Glyfs, p.Arg257*, and p.Trp462*) and two multiple exon deletions (exons 1-2 and 3-14) in six new male patients. Overall, 17 KAL1 defects (14.8%) were identified in the entire cohort of patients with Kallmann syndrome, including previously studied cases. KAL1-mutated patients presented with a more severe reproductive and nonreproductive phenotype (synkinesia, renal malformations, cryptorchidism, and anatomic olfactory abnormalities) in comparison with patients without KAL1 mutations. Intragenic deletions were one of the most often encountered defects (29.4%). These deletions can be missed by polymerase chain reaction (PCR) due to Yq11.2 KAL1 pseudogene (KALP) spurious amplification. CONCLUSION(S): These results indicate that intragenic multiexon deletions are one of the most frequent KAL1 abnormalities, which can be more accurately detected by multiplex ligation-dependent probe amplification. In addition, KAL1 sequencing results should be interpreted with caution, and stringency conditions of the PCR reaction should be adjusted to avoid pseudogene amplification.
Subject(s)
DNA Mutational Analysis/methods , Extracellular Matrix Proteins/genetics , High-Throughput Nucleotide Sequencing/methods , Kallmann Syndrome/genetics , Multiplex Polymerase Chain Reaction , Nerve Tissue Proteins/genetics , Adult , Automation , Base Sequence , DNA Mutational Analysis/instrumentation , Female , Gene Frequency , High-Throughput Nucleotide Sequencing/instrumentation , Humans , Kallmann Syndrome/diagnosis , Kallmann Syndrome/epidemiology , Male , Mutation/genetics , Mutation/physiology , Prevalence , Pseudogenes/geneticsABSTRACT
A extração de DNA de leucócitos periféricos é o meio de obtenção de DNA mais amplamente utilizado. Entretanto, a coleta de células a partir de swab oral, geralmente utilizada em medicina forense, é útil para obtenção de amostras de DNA de recém-nascidos, crianças e de pacientes que vivem em locais onde a coleta e o envio da amostra de sangue não é factível. Nosso objetivo foi padronizar a técnica de extração de DNA a partir de swab de células de mucosa oral utilizando NaCl, comparando-a com a extração pelo kit comercial. Para testar a qualidade do DNA, amplificamos os 3 éxons do gene PROP1 de 12 pacientes com hipopituitarismo hipofisário em DNA extraído simultaneamente de células da mucosa oral e de sangue periférico. A amplificação de fragmentos maiores foi testada em DNA de mucosa oral de indivíduos normais utilizando-se primers do éxon 10 do gene do FSHR (1000pb) e do gene CYP21A2 (1200pb). Ambos os métodos resultaram em DNA de boa qualidade, permitindo o estudo molecular. O método por NaCl mostrou-se mais rápido e barato, resultando em maior quantidade de DNA quando comparado ao kit comercial. Nos pacientes com hipopituitarismo, identificamos a mutação delAG301-302 em 6 pacientes, 4 em homozigose (33 por cento) e 2 em heterozigose (16 por cento), e a mutação G51A em heterozigose em uma paciente. Em conclusão, padronizamos a técnica de extração de DNA de células de swab oral com NaCl que, quando comparada à extração com kit comercial, apresentou menor custo e maior rapidez, indicando ser esta uma forma confiável de obtenção de DNA para estudos genéticos.
Subject(s)
Humans , Infant, Newborn , Child , DNA Mutational Analysis/standards , Sodium Chloride , DNA , Hypopituitarism/genetics , Homeodomain Proteins/genetics , DNA Mutational Analysis/instrumentation , DNA Mutational Analysis/methods , Case-Control Studies , Gene Amplification , Leukocytes/chemistry , Mouth Mucosa/cytology , Polymerase Chain Reaction , Reproducibility of Results , Sensitivity and SpecificityABSTRACT
DNA extraction of peripheral leukocytes is the most broadly used technique to obtain DNA. However, cell collection from an oral swab, frequently used in forensics, is useful to obtain DNA samples, mainly in newborns, children and patients who live far from the collection sites, where blood sample collection and sending is not feasible. Our objective was to standardize DNA extraction from an oral swab, using the NaCl method, comparing it with a commercial kit. To test DNA quality, we amplified the 3 exons of PROP1 gene of 12 patients with hypopituitarism in DNA obtained from oral cells and peripheral blood cells. Amplification of larger fragments was tested in oral DNA of normal subjects using primers of exon 10 of FSHR gene (1000 bp) and of CYP21A2 gene (1200 bp). Both methods yielded good quality DNA, allowing the amplification of 3 exons of PROP1 gene. The NaCl method showed to be faster and less expensive, resulting in a larger amount of DNA when compared to the commercial kit. We identified the delAG301-302 mutation in 6 patients, 4 in homozygous (33%) and 2 in heterozygous (16%) state and G51A mutation in heterozygous state in a single patient. In conclusion, we standardized the DNA extraction of oral cells with NaCl, which presented lower costs and faster results, when compared with the extraction by a commercial kit indicating that DNA from oral swabs are a reliable source for genetic studies.