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Results for “clinical sequencing”

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PubMed1990

Direct sequencing of the HA gene of influenza (H3N2) virus in original clinical samples reveals sequence identity with mammalian cell-grown virus.

When influenza (H3N2) viruses from infected individuals are grown in embryonated chicken eggs, viruses are isolated which differ antigenically and structurally from viruses grown in mammalian Madin-Darby canine kidney (MDCK) cell culture [G.C. Schild, J.S. Oxford, J.C. de Jong, and R.G. Webster, Nature (London) 303:706-709, 1983]. To determine which of these viruses is most representative of virus replicating in the infected individual, a region of the HA gene of virus present in original clinical samples was amplified by using the polymerase chain reaction and sequenced directly. Comparison of 170 amino acid residues of HA1 flanking and containing the receptor-binding site and antigenic sites indicated that over this region, the HA of virus replicating in the infected individual was identical to that of virus after growth in MDCK cells and was distinct from the HA of viruses grown in eggs. Therefore, cultivation of human influenza H3N2 virus in mammalian MDCK cells results in a virus similar to the predominant population of virus found in the infected individual.

Amino Acid Sequence↗

PubMed2005

Routine clinical brain MRI sequences for use at 3.0 Tesla.

PURPOSE: To establish image parameters for some routine clinical brain MRI pulse sequences at 3.0 T with the goal of maintaining, as much as possible, the well-characterized 1.5-T image contrast characteristics for daily clinical diagnosis, while benefiting from the increased signal to noise at higher field. MATERIALS AND METHODS: A total of 10 healthy subjects were scanned on 1.5-T and 3.0-T systems for T(1) and T(2) relaxation time measurements of major gray and white matter structures. The relaxation times were subsequently used to determine 3.0-T acquisition parameters for spin-echo (SE), T(1)-weighted, fast spin echo (FSE) or turbo spin echo (TSE), T(2)-weighted, and fluid-attenuated inversion recovery (FLAIR) pulse sequences that give image characteristics comparable to 1.5 T, to facilitate routine clinical diagnostics. Application of the routine clinical sequences was performed in 10 subjects, five normal subjects and five patients with various pathologies. RESULTS: T(1) and T(2) relaxation times were, respectively, 14% to 30% longer and 12% to 19% shorter at 3.0 T when compared to the values at 1.5 T, depending on the region evaluated. When using appropriate parameters, routine clinical images acquired at 3.0 T showed similar image characteristics to those obtained at 1.5 T, but with higher signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), which can be used to reduce the number of averages and scan times. Recommended imaging parameters for these sequences are provided. CONCLUSION: When parameters are adjusted for changes in relaxation rates, routine clinical scans at 3.0 T can provide similar image appearance as 1.5 T, but with superior image quality and/or increased speed.

Brain↗

PubMed2026

First nationwide full-genome characterisation of human-derived Andes virus in Chile: a retrospective genomic epidemiology study.

BACKGROUND: Andes virus (ANDV) is the only hantavirus known to transmit between humans and causes hantavirus cardiopulmonary syndrome in Chile and Argentina. In Chile, ANDV genomic diversity remains incompletely characterised. This study aimed to characterise the genetic diversity, geographical structure, and molecular signatures of ANDV using human clinical samples collected over a 13-year period (2011-24). METHODS: We conducted a retrospective genomic epidemiology study of ANDV infections in Chile. Clinical samples from patients with confirmed ANDV, collected between March 9, 2011, and June 27, 2024, were analysed and sequenced. Clinical and epidemiological data were obtained from diagnostic laboratories and surveillance programmes. Consensus sequences for the S, M, and L segments were generated, and genetic clustering and divergence were assessed using phylogenetic inference and variant calling. FINDINGS: We analysed clinical samples from 58 infected individuals and identified two major genomic variants of ANDV with distinct geographical distributions, defined by regionally structured patterns of nucleotide and amino acid substitutions across the S, M, and L segments: ANDV Chi-North (central Chile) and ANDV-South (southern Chile). No consistent clustering by clinical severity was observed, and no recurrent non-synonymous substitutions were uniquely associated with severe disease. Substitutions previously associated with person-to-person transmission in outbreaks in Argentina were not consistently observed in Chilean sequences, including in four person-to-person transmission cases. Although some substitutions described in ANDV-like viruses were present in the Chi-North lineage, this lineage remained phylogenetically distinct and geographically restricted to central Chile. INTERPRETATION: To our knowledge, this study provides the first nationwide genomic characterisation of human-derived ANDV in Chile. The identification of geographically structured variants indicates that ANDV diversity in Chile is driven by regional diversification rather than clinical outcome. The absence of consistent amino acid signatures associated with disease severity or person-to-person transmission suggests that these phenotypes are unlikely to be explained by viral genetic variation alone. These findings refine current understanding of ANDV evolution and highlight the need for continued integrated genomic surveillance in endemic regions. FUNDING: Agencia Nacional de Investigación y Desarrollo de Chile and National Institutes of Health.

Humans↗

PubMed1990

Electroencephalographic (EEG) video monitoring.

Electroencephalographic (EEG) video monitoring is the simultaneous documentation of the clinical and electroencephalographic manifestations of seizures. The video recording permits repeated viewing of the clinical sequence and enables comparisons with recordings of known seizures. Epilepsy is a clinical diagnosis in which most cases can be characterized with the standard clinical history, examination, and EEG. Studies of the treatment of intractable seizures (unsatisfactory control of seizure) indicate that more complex cases may require the data obtained with EEG video monitoring. For patients with intractable seizures, EEG video monitoring may help to confirm or support a diagnosis of epilepsy or confirm or support a differential diagnosis of physiologic or psychogenic seizures (nonepileptic attacks) from epilepsy. Monitoring also may provide a more accurate classification of the epileptic seizures and, for patients evaluated for surgical treatment, establish clinical focality. Estimates of the percentage of epilepsy patients requiring EEG video monitoring range from 5 to 30 percent. The average length of monitoring is approximately 10 to 16 days. In some cases outpatient monitoring in conjunction with activation procedures provides patient evaluation in only 6 to 8 hours.

Attitude of Health Personnel↗

PubMed2006

Identification of Mycobacterium species by comparative analysis of the dnaA gene.

For the establishment of a diagnostic tool for mycobacterial species, a part of the dnaA gene was amplified and sequenced from clinically relevant 27 mycobacterial species as well as 49 clinical isolates. Sequence variability in the amplified segment of the dnaA gene allowed the differentiation of all species except for Mycobacterium tuberculosis, Mycobacterium africanum and Mycobacterium microti, which had identical sequences. Partial sequences of dnaA from clinical isolates belonging to three frequently isolated species revealed a very high intraspecies similarity, with a range of 96.0-100%. Based on the dnaA sequences, a species-specific primer set for Mycobacterium kansasii and Mycobacterium gastri was successfully designed for a simple loop-mediated isothermal amplification method. These results demonstrate that the variable sequences in the dnaA gene were species specific and were sufficient for the development of an accurate and rapid diagnosis of Mycobacterium species.

Animals↗

PubMed2000

The predictive value of BRCA1 and BRCA2 mutation testing.

Genetic testing for mutations in BRCA1 and BRCA2, two genes predisposing to breast and ovarian cancers, is available to women with a relevant family history. The aim of this study was to estimate the positive and negative predictive value of clinical sequence analysis of these genes. A reference graph showing positive and negative predictive values over a range of pre-test risk was derived, taking into account the sensitivity and specificity of a full-sequence analysis test. High positive and negative predictive values were found for women with pre-test risk between 4% and 40%, a range of risk commonly seen in clinical testing. The predictive value of full sequence and single-site analysis of BRCA1 and BRCA2, therefore, compares favorably with other diagnostic medical tests. Our results provide a numerical estimate of the predictive value of BRCA testing, and as such, provide a valuable tool to healthcare providers and families as they interpret BRCA1 and BRCA2 test results.

BRCA1 Protein↗

PubMed2005

Serial diffusion-weighted magnetic resonance imaging in cases of glioma: distinguishing tumor recurrence from postresection injury.

OBJECT: Diffusion-weighted magnetic resonance (MR) imaging is an invaluable tool in the diagnosis of acute stroke and other types of brain injury. Abnormalities in and around the resection cavity on diffusion-weighted imaging have been observed following surgery for infiltrating glioma. The purpose of this study was to investigate prospectively the incidence, time course, and ultimate outcome of these abnormalities. METHODS: Forty-four consecutive patients with newly diagnosed gliomas were prospectively observed using serial MR imaging including diffusion-weighted sequences. Clinical and surgical data were also collected. Immediately postoperatively neuroimaging identified 28 patients (64%) in whom areas of reduced diffusion appeared in or around the resection cavity (mean volume 8.2 +/- 1.5 cm3). Complete resolution of this reduced diffusion was demonstrated within 90 days in 24 patients (86%). On subsequent neuroimages these areas demonstrated Gd enhancement as early as postoperative Day 15 and as late as Day 198 and ultimately took on the appearance of encephalomalacia in 26 (93%) of 28 cases. Postoperative reduced diffusion was not predicted by the clinical or surgical parameters that were assessed. No clinical deficits were attributable to the reduced diffusion. CONCLUSIONS: An abnormality related to diffusion-weighted sequences on postoperative MR imaging can occur after resection of newly diagnosed gliomas. In this study the abnormality typically resolved and was replaced by contrast enhancement on follow-up imaging, ultimately demonstrating encephalomalacia on long-term follow up. Findings on neuroimaging during the period of enhancement could be confused with recurrent tumor and interpreted as early treatment failure. Based on the findings of this study the authors strongly suggest that the inclusion of diffusion-weighted sequences in postoperative MR imaging is essential, as is MR imaging immediately before radiation therapy to monitor disease progression. A new enhancement observed after glioma surgery should be interpreted in the context of the diffusion-weighted image obtained immediately postoperatively.

Adult↗

PubMed1999

Spectral analysis of periodic fluctuations in electrocardiographic repolarization.

Repolarization alternans (RPA) indicates alternate-beat fluctuations in the temporal or spatial characteristics of the echocardiogram (ECG) STU segment which may represent dispersion in repolarization. Spectral decomposition has revealed microvolt-level RPA which has been found to correlate with ventricular tachycardia (VT) and fibrillation, and is increasingly being used for clinical risk stratification. However, while interruptions in periodicity are known to affect spectral decomposition, their quantitative impact on RPA and its clinical utility have been poorly described. We therefore studied the effect of variable alignment, extrasystoles, dissimilar beats and beat exclusion on RPA magnitude in simulations and on the sensitivity and specificity of RPA for VT in a pilot clinical study. RPA magnitude was exquisitely sensitive to QRS alignment such that +/- 1 ms random beat misalignment reduced it by 68% in simulations. Correspondingly, suboptimal QRS alignment in clinical ECG's caused the sensitivity of RPA for inducible VT to fall from 93% to as low as 63%; while JT alignment was also less effective for RPA recovery. As an experiment in minimizing morphometric irregularities in clinical ECG's, we found that RPA magnitude actually fell when replacing either measurably dissimilar or ectopic beats with more representative beats. In addition, inserting or deleting beats also reduced RPA magnitude in clinical sequences and simulations. These statistical analyses suggest that the precision of beat alignment and interruptions to ECG periodicity, which may occur physiologically, may greatly reduce the clinical utility of RPA for VT. Dynamic alterations in RPA in response to sequence irregularities require further study before RPA may be optimally applied to screen for ventricular arrhythmias.

Chi-Square Distribution↗

PubMed1994

Identification of a unique group of human papillomavirus type 16 sequence variants among clinical isolates from Barbados.

The naturally occurring sequence variation of human papillomavirus type 16 (HPV-16) was analysed by direct sequence analysis of the PCR products of the long control region (LCR), the E5 and E7 open reading frames (ORFs), a segment of the L2 ORF overlapping the early viral poly(A) signal and a small segment of the L1 ORF or clinical isolates from Barbados and The Netherlands. Despite the widely different geographical and ethnic origin of the two groups of specimens, sequence analysis revealed relatively few mutational differences. Analysis of the LCR and the E5 ORF appeared to be the minimum requirement for the correct positioning of these variants in the HPV-16 phylogenetic tree. Most of the Barbadian variants appeared to be located at a unique position in the HPV-16 phylogenetic tree, at the internal branch close to the point where the European and Asian branches diverge. In contrast, most of the Dutch samples were located on the European branch.

Asia↗

PubMed2006

Accuracy of seed reconstruction in prostate postplanning studied with a CT- and MRI-compatible phantom.

BACKGROUND AND PURPOSE: Postimplant dosimetry of prostate seed implants is usually performed by seed localisation on transversal CT or MR images. In order to obtain reliable dosimetric evaluation data, it is important that seeds are reconstructed accurately. Currently, there is no comparative data available on seed localisation accuracy of CT-and MRI-based reconstructions, mainly due to the lack of a suitable QA tool. In this study, we developed a CT-and MRI compatible prostate phantom to investigate the intrinsic accuracy of seed detection for both imaging modalities. PATIENTS AND METHODS: A 60 seed geometry was created according to a clinically meaningful plan, including rotated and shifted seeds. After implantation of the seeds in the phantom, CT and MRI scans with 3, 4 and 5mm slice thickness were performed. The seed locations were reconstructed in the treatment planning system and compared with the known reference positions. RESULTS: Due to the comparable density and relaxation times of the phantom material to prostate tissue, the seeds are visualised similarly as on real patient images. The observed mean reconstruction uncertainties were in general smaller for CT (0.9+/-0.6, 0.9+/-0.6, 2.1+/-0.8 mm on 3, 4 and 5mm scans, respectively), than for MRI (Philips 1.5 T: 2.1+/-1.4, 1.6+/-1.2, 1.9+/-0.9 mm on 3, 4 and 5 mm scans, respectively, and Siemens 1.5 T: 2.3+/-0.8, 2.0+/-1.6, 1.6+/-0.8 mm on 3, 4 and 5mm scans, respectively). CONCLUSIONS: For our clinical sequences of both CT and MRI, the mean deviation of the reconstructed seed positions were all within acceptable limits for clinical use (<2.3 mm). The phantom was found to be a suitable quality assurance tool to assess the reliability and accuracy of the seed reconstruction procedure. Moreover, as the phantom material has the same imaging characteristics as real prostate tissue, it is a useful device to define proper MRI sequences.

Brachytherapy↗

PubMed2002

A comprehensive survey of mutations in the OPA1 gene in patients with autosomal dominant optic atrophy.

PURPOSE: To characterize the spectrum of mutations in the OPA1 gene in a large international panel of patients with autosomal dominant optic atrophy (adOA), to improve understanding of the range of functional deficits attributable to sequence variants in this gene, and to assess any genotype-phenotype correlations. METHODS: All 28 coding exons of OPA1, intron-exon splice sites, 273 bp 5' to exon 1, and two intronic regions with putative function were screened in 94 apparently unrelated white patients of European origin with adOA by single-strand conformational polymorphism (SSCP)-heteroduplex analysis and direct sequencing. Clinical data were collated, and putative mutations were tested for segregation in the respective families by SSCP analysis or direct sequencing and in 100 control chromosomes. Further characterization of selected splice site mutations was performed by RT-PCR of patient leukocyte RNA. Staining of mitochondria in leukocytes of patients and control subjects was undertaken to assess gross differences in morphology and cellular distribution. RESULTS: Twenty different mutations were detected, of which 14 were novel disease mutations (missense, nonsense, deletion-frameshift, and splice site alterations) and six were known mutations. Mutations were found in 44 (47%) of the 94 families included in the study. Ten new polymorphisms in the OPA1 gene were also identified. Mutations occur throughout the gene, with three clusters emerging: in the mitochondrial leader, in the highly conserved guanosine triphosphate (GTP)-binding domain, and in the -COOH terminus. Examination of leukocyte mitochondria from two unrelated patients with splice site mutations in OPA1 revealed no abnormalities of morphology or cellular distribution when compared with control individuals. CONCLUSIONS: This study describes 14 novel mutations in the OPA1 gene in patients with adOA, bringing the total number so far reported to 54. It is likely that many cases of adOA are due to mutations outside the coding region of OPA1 or to large-scale rearrangements. Evaluation of the mutation spectrum indicates more than one pathophysiological mechanism for adOA. Preliminary data suggests that phenotype-genotype correlation is complex, implying a role for other genetic modifying or environmental factors. No evidence was found of pathologic changes in leukocyte mitochondria of patients with adOA.

Adolescent↗

PubMed2006

A large GLC1C Greek family with a myocilin T377M mutation: inheritance and phenotypic variability.

PURPOSE: POAG is a complex disease; therefore, families in which a glaucoma gene has been mapped may carry additional POAG genes. The goal of this study was to determine whether mutations in the myocilin (MYOC) gene on chromosome 1 are present in two POAG families, which have previously been mapped to the GLC1C locus on chromosome 3. METHODS: The three exons of MYOC were screened by denaturing (d)HPLC. Samples with heteroduplex peaks were sequenced. Clinical findings were compared with genotype status in all available family members over the age of 20 years. RESULTS: A T377M coding sequence change in MYOC was identified in family members of the Greek GLC1C family but not in the Oregon GLC1C family. Individuals carrying both the MYOC T377M variant and the GLC1C haplotype were more severely affected at an earlier age than individuals with just one of the POAG genes, suggesting that these two genes interact or that both contribute to the POAG phenotype in a cumulative way.

Adult↗

PubMed2006

Virchow-Robin spaces on magnetic resonance images: normative data, their dilatation, and a review of the literature.

INTRODUCTION: Virchow-Robin spaces (VRS) are perivascular spaces in the brain and can be visualized on magnetic resonance images (MRI). We attempt to provide a better understanding of the significance of VRS for pathological and physiological processes by reviewing the literature, presenting normative data for the first time, and proposing a definition for the dilatation of the VRS on MRI that is based on shape rather than size. METHODS: We evaluated the VRS in 125 healthy subjects (age range 1-30 years) using high-resolution 3D images, and in 36 patients (age range 2-16 years) with normal MRI, using routine clinical sequences. RESULTS: VRS were visible in all high-resolution images of the 125 healthy subjects. Two of them revealed dilated VRS, giving a prevalence of 1.6%. VRS could be visualized in 29 (80%) of the 36 paediatric clinical scans; none was dilated. It was demonstrated that the visibility of VRS on MRI is sequence-dependent. CONCLUSION: From the results of this study and the literature on the nature and pathology of VRS, we conclude that VRS on MR images of healthy individuals are normal findings, even if they are dilated. A judgement on whether dilated VRS in an individual patient is a normal variant or part of a disease process can be made by taking into account the appearance of the adjacent tissue on MRI and the clinical context.

Adolescent↗

PubMed1999

Intratype sequence variation among clinical isolates of the human papillomavirus type 6 L1 ORF: clustering of mutations and identification of a frequent amino acid sequence variant.

Human papillomavirus type 6 (HPV-6) is the causative agent of condyloma acuminata, a common sexually transmitted disease. Virus-like particles (VLPs) assembled from the L1 major capsid protein represent promising candidates for prophylactic vaccines. However, any intratype sequence variation among HPV-6 L1 ORFs will influence which sequence is used for a vaccine according to its prevalence in the population and its propensity for VLP production. Therefore, we have analysed the entire L1 nucleotide sequence of 17 clinical isolates of HPV-6 from the London area. We found 28 positions where changes from the prototype HPV-6b L1 occurred, showing that HPV-6 L1 intratype variation is greater than previously reported. The most frequently observed substitutions are clustered into three discrete regions: R1 (nt 5920-6075), R2 (nt 6590-6670) and R3 (nt 7070-7230). Indeed, most of the nucleotide substitutions within the HPV-6 L1 reported worldwide also map to these regions. The R3 region contains predominantly non-silent substitutions, the most common of which is a G-to-C substitution at position 7079. This results in a Glu-to-Gln change at aa 431, although this change had no effect on VLP yield or stability. This substitution defines a new HPV-6 L1 amino acid sequence that is more abundant in the isolates examined than any other reported sequence.

Amino Acid Sequence↗

PubMed2001

Partial-coverage posterior ceramic restorations. Part 2: operative innovations.

UNLABELLED: The application of multisurfaced tooth-colored restorations in the posterior dentition is an exercise in risk tolerance when dentin occupies the bulk of the tooth substrate. Part 1 of this article discussed the capricious nature of dentin bonding and acknowledged the prime tenet that clinical success involves more than esthetic realism in the posterior dentition. Success with indirect ceramic restorations is dependent on interfacial integrity, which is contingently related to operative competence. Innovative clinical techniques are described in this article, along with a discussion of the need for excellence in all phases of this demanding restorative sequence. CLINICAL SIGNIFICANCE: Restorative success in the posterior dentition is profoundly influenced by the variability of operative competence and diligence. Part 2 of this two-part article offers innovative solutions to the unique challenges of partial-coverage ceramic restorations.

Bicuspid↗

PubMed2006

PROP1 gene analysis in Portuguese patients with combined pituitary hormone deficiency.

OBJECTIVE: Mutations of the PROP1 gene lead to combined pituitary hormone deficiency (CPHD), which is characterized by a deficiency of GH, TSH, LH/FSH, PRL and, less frequently, ACTH. This study was undertaken to investigate the molecular defect in a cohort of patients with CPHD. DESIGN, PATIENTS AND MEASUREMENTS: A multicentric study involving 46 cases of CPHD (17 familial cases belonging to seven kindreds and 29 sporadic cases) selected on the basis of clinical and hormonal evidence of GH deficiency, central hypothyroidism and hypogonadotrophic hypogonadism, in the absence of an identified cause of hypopituitarism. Mutations of PROP1 were investigated by DNA sequencing. Clinical, hormonal and neuroradiological data were collected at each centre. RESULTS: PROP1 mutations were identified in all familial cases: five kindreds presented a c. 301-302delAG mutation, one kindred presented a c. 358C --> T (R120C) mutation and one presented a previously unreported initiation codon mutation, c. 2T --> C. Of the 29 sporadic cases, only two (6.9%) presented PROP1 germline mutations (c. 301-302delAG, in both). Phenotypic variability was observed among patients with the same mutations, particularly the presence and age of onset of hypocortisolism, the levels of PRL and the results of pituitary imaging. One patient presented a sellar mass that persisted into adulthood. CONCLUSIONS: This is the first report of a mutation in the initiation codon of the PROP1 gene and this further expands the spectrum of known mutations responsible for CPHD. The low mutation frequency observed in sporadic cases may be due to the involvement of other unidentified acquired or genetic causes.

Adolescent↗

PubMed1998

Homozygotic patient with betaig-h3 gene mutation in granular dystrophy.

PURPOSE: This study investigated patients with granular dystrophy and identified a homozygotic patient and his family with a mutation in the betaig-h3 gene. METHODS: Genomic DNAs were extracted from leukocytes of the peripheral blood of the proband, his parents, and his grandmother. All had granular dystrophy. Genomic DNAs from 50 unrelated normal volunteers were used as controls. Exon 4 of betaig-h3 gene was amplified and analyzed by direct sequence. Clinical data were collected. RESULTS: A single-base-pair transition was detected. This was a substitution of G to A of the second nucleotide position of codon 124 in the betaig-h3 gene that led to a replacement of histidine for arginine (Arg124His, CGC-->CAC). This mutation was the precise one previously reported for Avellino dystrophy. Although the proband was homozygotic for the mutant alleles, his grandmother, and parents were heterozygotic for these alleles. No sequence modification in the codon 124 from 50 nonaffected control individuals was detected. Clinical findings of the proband were severe. Keratectomies were performed for both his eyes 5 times for a 24-year period. His grandmother and parents showed mild clinical symptoms, had a few annular granules in the subepithelial stroma, and maintained good visual acuities. CONCLUSION: Arg124His mutation of the betaig-h3 gene was found in a pedigree with granular dystrophy. This mutation was the precise one previously reported for Avellino dystrophy. This fact shows an existence of Avellino form in Japanese. Homozygotic patient for mutant gene showed severe symptoms and an early onset.

Adolescent↗

PubMed1995

[Lafora's disease: a possible diagnosis of juvenile dementia].

Five patients aged 12 to 16 years old were admitted between 1987 and 1994 at the neurological unit because of uncontrolled epilepsy. They had had a normal development until the adolescence, when a history of poor school performance and memory difficulty started. It is emphasized the clinical sequence of dementia followed by tonic-clonic seizures and myoclonus, the positive family history and the difficult therapeutic management, in spite of multiple anticonvulsant combinations, including sodium valproate and clonazepam. The clinical and laboratory differential diagnosis were discussed to show that similar cases should be submitted to skin biopsy looking for Lafora bodies in apocrine and eccrine glands. However, the liver is considered as the most reliable site for the biopsy, which in our study showed positivity in four out of the five cases.

Adolescent↗