[Signal loss in magnetic resonance imaging caused by intraoral anchored dental magnetic materials]

PURPOSE

To measure the maximum extent of the signal loss areas in the center of the susceptibility artifacts generated by ferromagnetic dental magnet attachments using three different sequences in the 1.5 and 3.0 Tesla MRI.

MATERIALS AND METHODS

Five different pieces of standard dental magnet attachments with volumes of 6.5 to 31.4 mm(3) were used: a NdFeB magnet with an open magnetic field, a NdFeB magnet with a closed magnetic field, a SmCo magnet with an open magnetic field, a stainless steel keeper (AUM-20) and a PdCo piece. The attachments were placed between two cylindrical phantoms and examined in 1.5 and 3.0 Tesla MRI using gradient echo and T1- and T2-weighted spin echoes. We measured the maximum extent of the generated signal loss areas parallel and perpendicular to the direction of B (O).

RESULTS

In gradient echoes the artifacts were substantially larger and symmetrically adjusted around the object. The areas with total signal loss were mushroom-like with a maximum extent of 7.4 to 9.7 cm parallel to the direction of B (O) and 6.7 to 7.4 cm perpendicular to B (O). In spin echoes the signal loss areas were obviously smaller, but not centered. The maximum values ranged between 4.9 and 7.2 cm (parallel B (O)) and 3.6 and 7.0 cm (perpendicular B (O)). The different ferromagnetic attachments had no clinically relevant influence on the signal loss neither in 1.5 T nor 3.0 T MRI.

CONCLUSIONS

Ferromagnetic materials used in dentistry are not intraorally standardized. To ensure, that the area of interest is not affected by the described artifacts, the maximum extent of the signal loss area should be assumed: a radius of up to 7 cm in 1.5 and 3.0 T MRI by T1 and T2 sequences, and a radius of up to 10 cm in T2* sequences. To decide whether magnet attachments have to be removed before MR imaging, physicians should consider both the intact retention of the keepers and the safety distance between the ferromagnetic objects and the area of interest.

In vitro and in vivo pharmacology of synthetic olivetol- or resorcinol-derived cannabinoid receptor ligands

BACKGROUND AND PURPOSE

We have previously reported the development of CB-25 and CB-52, two ligands of CB1 and CB2 cannabinoid receptors. We assessed here their functional activity.

EXPERIMENTAL APPROACH

The effect of the two compounds on forskolin-induced cAMP formation in intact cells or GTP-gamma-S binding to cell membranes, and their action on nociception in vivo was determined.

KEY RESULTS

CB-25 enhanced forskolin-induced cAMP formation in N18TG2 cells (EC50 approximately 20 nM, max. stimulation = 48%), behaving as an inverse CB1 agonist, but it stimulated GTP-gamma-S binding to mouse brain membranes, behaving as a partial CB1 agonist (EC50 =100 nM, max. stimulation = 48%). At human CB1 receptors, CB-25 inhibited cAMP formation in hCB1-CHO cells (EC50 = 1600 nM, max. inhibition = 68% of CP-55,940 effect). CB-52 inhibited forskolin-induced cAMP formation by N18TG2 cells (IC50 = 450 nM, max. inhibition = 40%) and hCB1-CHO cells (EC50 = 2600 nM, max. inhibition = 62% of CP-55,940 effect), and stimulated GTP-gamma-S binding to mouse brain membranes (EC50 = 11 nM, max. stimulation approximately 16%). Both CB-25 and CB-52 showed no activity in all assays of CB2-coupled functional activity and antagonized CP55940-induced stimulation of GTP-gamma-S binding to hCB2-CHO cell membranes. In vivo, both compounds, administered i.p., produced dose-dependent nociception in the plantar test carried out in healthy rats, and antagonised the anti-nociceptive effect of i.p. WIN55,212-2. In the formalin test in mice, however, the compounds counteracted both phases of formalin-induced nociception.

CONCLUSIONS AND IMPLICATIONS

CB-25 and CB-52 behave in vitro mostly as CB1 partial agonists and CB2 neutral antagonists, whereas their activity in vivo might depend on the tonic activity of cannabinoid receptors.

Non-palpable breast lesions in asymptomatic women: diagnostic value of initial ultrasonography and comparison with mammography

AIM

This prospective double-blind study was designed to assess (i) if primary breast screening by ultrasonography is capable of detecting breast cancer independent of tissue density and (ii) if the rate of unnecessary biopsies remains acceptable when diagnostics are based on ultrasonography.

PATIENTS AND METHODS

Bilateral breast ultrasonography was performed in 448 asymptomatic women as the initial diagnostic method. Sonograms were interpreted using a set of standardized diagnostic criteria. Subsequently, mammograms were obtained. The radiologists reading the mammograms were blinded to the sonographic results.

RESULTS

Overall, 3 non-palpable breast cancers were detected by ultrasound and mammography. All 3 ultrasonographically detected breast cancers were smaller than 1 cm (0.7, 0.7, 0.6 cm). All 3 carcinomas were correctly detected by both methods. For ultrasonography, the false positive rate was 1.1% (n=5) and for mammography 0.6% (n=3). When both methods were combined, the rate of unnecessary open biopsies was 1.6% (n=7). The ratio of benign to malignant lesions was 3.7/1.

CONCLUSION

Without prior mammography, primary high-resolution breast ultrasonography is capable of detecting non-palpable breast carcinomas in asymptomatic women at an early stage. The rate of unnecessary open biopsies is low and the ratio of benign to malignant biopsies acceptable.

Real-time elastography--an advanced method of ultrasound: First results in 108 patients with breast lesions

OBJECTIVES

To evaluate whether real-time elastography, a new, non-invasive method for the diagnosis of breast cancer, improves the differentiation and characterization of benign and malignant breast lesions.

METHODS

Real-time elastography was carried out in 108 potential breast tumor patients with cytologically or histologically confirmed focal breast lesions (59 benign, 49 malignant; median age, 53.9 years; range, 16-84 years). Tumor and healthy tissue were differentiated by measurement of elasticity based on the correlation between tissue properties and elasticity modulus. Evaluation was performed using the three-dimensional (3D) finite element method, in which the information is color-coded and superimposed on the B-mode ultrasound image. A second observer evaluated the elastography images, in order to improve the objectivity of the method. The results of B-mode scan and elastography were compared with those of histology and previous sonographic findings. Sensitivities and specificities were calculated, taking histology as the gold standard.

RESULTS

B-mode ultrasound had a sensitivity of 91.8% and a specificity of 78%, compared with sensitivities of 77.6% and 79.6% and specificities of 91.5% and 84.7%, respectively, for the two observers evaluating elastography. Agreement between B-mode ultrasound and elastography was good, yielding a weighted kappa of 0.67.

CONCLUSIONS

Our initial clinical results suggest that real-time elastography improves the specificity of breast lesion diagnosis and is a promising new approach for the diagnosis of breast cancer. Elastography provides additional information for differentiating malignant BI-RADS (breast imaging reporting and data system) category IV lesions.

Visual hallucinations in Parkinson's disease: clues to separate origins

Our paper discusses two experimental studies suggesting that Visual Hallucinations (VH) in Parkinson's Disease (PD) may have separate origins. The first is a prospective 8years study evaluating the appearance of VH, visual abnormalities assessed by Visual Evoked Potentials (VEPs) and REM sleep Behaviour Disorder (RBD), in 80 PD patients treated with l-Dopa and Dopaminoagonists (DA). In chronically treated, cognitively unimpaired, PD patients VH were statistically related (p=0.001) to RBD occurrence and high DA doses. Visual abnormalities were significantly reduced by l-Dopa or DA intake, and were statistically unrelated to VH. The second study involved PD patients placed in a Virtual Reality Environment, to decontextualize visual input. When motor symptoms worsened and VEP abnormalities developed patients consistently described hallucinatory dysperceptions of the virtual environment. The two studies therefore show that VH can occur in two seemingly distinct conditions, one is related to chronic treatment and to a sleep disorder frequently observed in PD, the other is probably related to a hypodopaminergic state. Our studies support a recently proposed integrative model of VH, and show that the neural circuits purported to explain VH must include the retinal dopaminergic system and the REM sleep regulatory system.

Magnesium restores altered aquaporin-4 immunoreactivity following traumatic brain injury to a pre-injury state

Magnesium reduces edema following traumatic brain injury (TBI), although the associated mechanisms are unknown. Recent studies suggest that edema formation after TBI may be related to alterations in aquaporin-4 (AQP4) channels. In this study, we characterize the effects of magnesium administration on AQP4 immunoreactivity following TBI. Male Sprague-Dawley rats were injured by impact-acceleration diffuse TBI and a subgroup was administered 30 mg/kg magnesium sulphate 30 minutes after injury. Animals were fixed by perfusion 5 hours later, which corresponded to the time of maximum edema formation according to previous studies. One half of the brain was cut using a Vibratome and the other half blocked in paraffin wax. Wax and Vibratome sections were immunostained for detection of AQP4 by light and electron microscopy, respectively. In untreated animals, AQP4 immunoreactivity was increased in the subependymal inner glia limitans and the subpial outer glia limitans, and decreased in perivascular astrocytic processes in the cerebrum and brain stem. In contrast, animals treated with magnesium sulphate had AQP4 profiles similar to normal and sham control animals. We conclude that magnesium decreases brain edema formation after TBI, possibly by restoring the polarized state of astrocytes and by down-regulation of AQP4 channels in astrocytes.

Evaluation of the safety of C-1311 administered in a phase 1 dose-escalation trial as a 1-hour infusion once every 3 weeks in patients with advanced solid tumors

12005

Background: C-1311 (Symadex) is the most active member of a new series of anti-cancer agents, the imidazoacridinones, specially designed compounds developed from research on the structure-activity relationships of existing cancer therapies. This clinical trial was designed to assess the safety profile of ascending doses of C-1311 and to determine the recommended dose when administered every 3 weeks (Q3W). Methods: Patients with advanced solid tumors refractory to conventional therapy were enrolled. The dose escalation scheme was divided into 2 phases with different schedules. Initially, C-1311 was given as a 1-hour daily infusion over 5 consecutive days. Following review of pre-clinical data, coupled with preliminary results of a parallel weekly study, a day 1 only schedule was explored. The maximum tolerated dose (MTD) is defined as the dose at which 2/3 or 2/6 pts experience a dose-limiting toxicity (DLT). The recommended dose (RD) is defined as the dose level below the MTD, confirmed by expansion of the RD cohort to 9 pts. Results: The first 5 patients were treated at doubling doses of 6, 12, 24, 48 and 96 mg/m2 on a schedule of 1-hour daily infusions over 5 consecutive days, repeated every 3 weeks; no DLTs were seen. The 6th pt received the same total dose as the 5th (480 mg/m2) but on day 1 only, following which a modified Fibonacci design with cohorts of 3 pts and 33% dose increments was utilized. Subsequently, pts received C-1311 at doses of 640 mg/m2 (3 pts), 850 mg/m2 (3 pts) and 1100 mg/m2 (5 pts); 2/5 pts treated at 1100 mg/m2 experienced an identical DLT (grade 4 neutropenia for ≥7 days with grade 4 thrombocytopenia), defining this as the MTD. The 850 mg/m2 cohort was expanded to confirm this as the RD. Neutropenia, thrombocytopenia, anemia and fatigue have been reported as drug-related grade 3 or 4 adverse events (AEs). Grade 1 or 2 AEs most commonly described as drug-related are fatigue, nausea, vomiting and diarrhea. Stable disease was observed in two patients with advanced malignancy. A pt had a stable disease over 8 cycles and one over 6 cycles. Plasma drug concentrations are linear and proportional to dose. Conclusions: A C-1311 dose of 850 mg/m2 administered once every 3 weeks offers a predictable and tolerable safety profile.

[Table: see text]

Phase I dose-escalation study of ZK 304709, an oral multi-target tumor growth inhibitor (MTGI), administered for 14 days of a 28-day cycle

2076

Background: ZK 304709 is a novel oral MTGI that induces cell cycle arrest and inhibits tumour angiogenesis by selectively inhibiting Cyclin Dependent Kinases (CDKs) 1, 2, 4, 7 and 9,VEGF-R 1, 2 and 3, and PDGF-Rβ tyrosine kinases. Methods: Adult patients (pts) (WHO PS ≤2) with a histologically or cytologically confirmed solid tumor, resistant or refractory to conventional therapy, were eligible. ZK304709 was administered orally, once daily, at a 15 mg starting dose, on days 1–14 of a 28-day cycle, then escalated by 33–100% depending on incidence of drug-related toxicity ≥ grade (gr) 2 (CTC v2.0). At least 3 pts were treated at each dose level. The primary objective was to identify the maximum tolerated dose (MTD) and dose-limiting toxicities (DLT). Secondary objectives were to determine the tolerability, pharmacokinetic (PK) profile, and preliminary efficacy. Results: Interim results were available for 24 pts (19 M/5 F; median age 56.5) at 5 dose levels (15–120 mg qd). Pts received a median of 2 cycles (range 0–10). Common drug related toxicities were nausea, vomiting, and fatigue. Two DLT were observed: dizziness and hypertension. However, the MTD has yet to be established. The PK profile for dose levels up to 90 mg demonstrated rapid absorption and a dose-dependent increase of exposure and Cmax. Disease stabilization for ≥4 cycles has been observed. Conclusions: ZK 304709 was rapidly absorbed and has been tolerated on this schedule at up to 120 mg qd. The MTD has not been reached and enrolment is ongoing. These preliminary data demonstrate that oral delivery on this schedule of an agent that inhibits both cell cycle and angiogenesis is feasible.

[Table: see text]

Tumor-specific correlation of tumor-type M2 pyruvate kinase (Tu M2-PK) in patients with cervical carcinoma

5044

Background: Pyruvate kinase is a key enzyme in glycosis. Proliferating cells express the tetrameric isoenzyme pyruvate kinase type M2 (M2-PK), which decomposes to the dimeric form during tumor development (Tu M2-PK). This suggests that Tu M2-PK can be used as a tumor marker. The goal of the present study was to investigate the diagnostic value of Tu M2-PK in patients with cervix carcinoma and in patients with preinvasive lesions (CIN I-III). Methods: Plasma samples were investigated from a total of 116 patients using the quantitative sandwich enzyme immunoassay for Tu M2-PK (ScheBo, Tech GmbH). The patients were divided up into 3 groups depending on the severity of their condition: Group 1 (n = 43): CIN I-III; Group2 (n = 49): cervix carcinoma FIGO stage I-IV; Group3 (n = 24): relapse of cervical cancer. Results: The differentiation into three groups depending on the severity of the condition gave significant results, with the group of patients with relapsed cervix carcinoma having the highest concentration of Tu M2-PK (p < 0.001) (mean rank: Group 1 - 33.67, Group 2 - 62.48, Group 3 - 94.85 U/ml). In addition, there was a significant differentiation with respect to the FIGO stage, with increasing concentration for increasing stages (p < 0.001). In contrast with this there was no significant differentiation in patients with preinvasive lesions (p < 0.99). In the evaluation of the correlation with prognosis factors of cervix carcinoma (lymph-node status: N(+), N(−); lymphangioinvasion: L1;L0; angioinvasion: V1, V0 and grading G1–3) there were significantly higher values with positive lymph nodes (N+) (p < 0.0001). No significant differences were determined in the analysis of different tumor sub-types (squamous cell carcinoma, adenocarcinoma, adeno-squamous cell carcinoma) (p = 0.076). Conclusions: These are first results which indicate that Tu M2-PK can be used as a marker to differentiate between malignant and premalignant lesions for patients with cervical cancer. In addition, the concentration correlates with the stage of the disease.

No significant financial relationships to disclose.

Influence of palliative surgical resection on overall survival in patients with Advanced Colorectal Cancer: A retrospective single institutional study

13532

Background: The role of palliative surgical resection in patients presenting with locally advanced or metastatic colorectal cancer (CRC) is unclear. Resection is often limited to symptomatic management of bleeding, obstruction, perforation or for relief of pain, in patients with an adequate performance status and an expected life span of over several weeks. An exploratory analysis to evaluate the influence of a palliative surgical resection on survival outcome in patients with advanced CRC is reported. Methods: A retrospective review of medical records of all patients diagnosed with advanced CRC at our institution between the years 1998–2003 was undertaken. Tumor registry data were reviewed to identify age, gender, modalities of therapy (i.e. surgery (S), chemotherapy (C), radiation), and overall survival. IRB approval was obtained for this study. Results: 185 patients were identified. Mean age was 67 years (range 30–99). M: F ratio was 1:1. 62% of patients (115/185) underwent a palliative surgical intervention. Mean survival of patients who underwent S and those that did not undergo S was 27.7 months (mo) and 8.7 mo respectively (p<0.0001). 48% of patients (79/185) underwent systemic C. Mean survival of patients who received C + S, and patients who received C alone was 39 mo and 17.3 mo respectively (p<0.0004). 51% of patients who underwent S, received C; 30% of patients who did not undergo S, received C. Chemotherapy data were available on 46 of 79 patients. Patients treated with S + C, and C without S, received a median of 9 mo and 6 mo of therapy respectively. The median number of regimens used were similar in both. Conclusions: These exploratory data suggest a positive influence of a palliative resection performed during the disease course of patients with advanced CRC. The increased frequency of utilization and the more prolonged duration of C in the surgically treated patients may in part contribute to this improved survival . This may also be reflective of performance status at the time of diagnosis. Future trials enrolling patients with advanced CRC should prospectively stratify for surgical intervention to further clarify the influence of this modality on the outcome of systemic therapy in this disease.

No significant financial relationships to disclose.

Improved differentiation of 300 breast lesions using real-time elastography

10608

Background: Differences in tissue elasticity are useful in the diagnosis of breast tumors. With elastography the elastic properties of breast tissue can be imaged in real time by means of color-coded superimposition on the B image and then used for evaluating focal lesions. The goal of the present study was to compare the sensitivity and specificity of elastography with that of B-mode sonography. Methods: A total of 300 patients with histologically confirmed breast lesions (168 benign, 132 malignant) were included in the study. The patients’ average age was 51 years, the range 16 to 86 years. Evaluation was by means of the 3D finite-element method. The data is color-coded and superimposed on the B-mode ultrasound scan (HITACHI EUB 8500). A second examiner was employed to improve the objectivity of the method. The results were compared with histology and the data obtained by previous ultrasound investigations. Sensitivities and specificities were calculated. Results: B-mode sonography yielded a sensitivity of 95.5% and a specificity of 84%. The two examiners were almost in complete agreement in their evaluation of the elastography images (McNemar Test: weighted kappa: 0.86): elastography yielded a sensitivity of 82%, a specificity of 88%. Conclusion: The diagnostic results for elastography in breast lesions showed a higher specificity and a somewhat lower sensitivity in comparision with B-mode sonography.

No significant financial relationships to disclose.

Analysis of the VEGF family and their receptors in serum/plasma of patients with pre-invasive and invasive cervical cancer

5016

Background: The vascular endothelial growth factor (VEGF) family and their receptors are essential regulators of angiogenesis and lymphangiogenesis. This study examined the significance of circulating VEGF, VEGF-C, VEGF-D and their receptors VEGFR-1 and VEGFR-2 in patients with preinvasive and invasive cancer in relation to conventional prognostic parameters. Methods: Blood samples were obtained from 125 women before initial treatment (CIN I-III n = 50; FIGO stage I-IV n = 51; relapse n = 24). Plasma (p) and serum(s) levels of pVEGF, sVEGF-D, sVEGFR-1, sVEGFR-2 (R&D Systems, USA) and sVEGF-C (IBL, Japan) were determined by using a quantitative sandwich enzyme-linked immunosorbent assay (ELISA). Results: The highest level of pVEGF (p = 0.007) and sVEGFR-2 (p = 0.014) were detected in patients with recurrent disease, whereas the highest level of sVEGF-D (p = 0.046) were measured in patients with preinvasive lesions (CIN I-III). Furthermore, significantly elevated levels of sVEGF-C (p = 0.021) were detected in early stages (FIGO I-II) in comparison with advanced stages (FIGO III-IV) of cervical cancer. No significant difference in concentration was observed between the various grades of cervical intraepithelial neoplasia (CIN I-III). Correlations between conventional prognostic markers such as lymph node status (N0/N1), lymphangioinvasion (L0/L1), angioinvasion (V0/V1) and grading (G1/G2/G3) were investigated. Increased plasma levels of VEGF (p = 0.036) correlate with the dissemination of tumor cells to regional lymph nodes (N1),whereas serum VEGF-D levels were significantly decreased in women with lymph-node involvement (N1) (p = 0.045) and vascular invasion (L1) (p = 0.019). None of these members of the VEGF family were found to correlate significantly with histological subtype (squamous cell carcinoma, adenocarcinoma, adeno-squamous cell carcinoma) or grading of the tumor cells (G1/G2/G3). Conclusions: These results show that circulating concentrations of VEGF are associated with the stage of disease. In an early stage of cervical cancer a switch to a lymphangiogenic phenotype (VEGF-D, VEGF-C) might be possible.

No significant financial relationships to disclose.

Lipid-destabilising properties of a peptide with structural plasticity

The Chameleon peptide (Cham) is a peptide designed from two regions of the GB1 protein, one folded as an alpha-helix and the other as a beta structure. Depending on the environment, the Cham peptide adopts an alpha or a beta conformation when inserted in different locations of GB1. This environment dependence is also observed for tilted peptides. These short protein fragments, able to destabilise organised system, are mainly folded in beta structure in water and in alpha helix in a hydrophobic environment, like the lipid bilayer. In this paper, we tested whether the Cham peptide can be qualified as a tilted peptide. For this, we have compared the properties of Cham peptide (hydrophobicity, destabilising properties, conformation) to those of tilted peptides. The results suggest that Cham is a tilted peptide. Our study, together the presence of tilted fragments in transconformational proteins, suggests a relationship between tilted peptides and structural lability.

Association of conversion & cure with initial smear grading among new smear positive pulmonary tuberculosis patients treated with Category I regimen

BACKGROUND & OBJECTIVES

Early diagnosis of tuberculosis (TB) is important for initiating treatment to gain cure. The present investigation was undertaken to study the association of conversion and cure with initial smear grading among pulmonary tuberculosis (TB) patients registered in a directly observed treatment - short course (DOTS) programme in Tiruvallur district, south India.

METHODS

All new smear positive cases registered from May, 1999 to December, 2002 were analysed for conversion and cure related to initial smear grading.

RESULTS

Of the 1463 patients, 1206(82.4%) were converted at the end of the intensive phase and 1109 (75.8%) were declared 'cured' after the completion of treatment. The cure rate decreased as the initial smear grading increased and the decrease in trend was statistically significant (P=0.01). Similarly, a significant decrease in conversion rate was also observed with increase in initial smear grading (P<0.001). In multivariate analysis, lower cure rate was significantly associated with patient's age (AOR=1.5, 95% CI=1.1-2.1), alcoholism (AOR=1.7, 95% CI 1.2- 2.4) and conversion at the end of intensive phase (AOR=3.5, 95% CI= 2.6-4.8).

INTERPRETATION & CONCLUSION

Cure and conversion rates were linearly associated with initial smear grading. High default and death rates were responsible for low cure and conversion. The proportion of patients who required extension of treatment and those who had an unfavourable treatment outcome were significantly higher among patients with a 3+ initial smear grading. This reiterates the need to pay more attention in motivating these patients to return to regular treatment and sustained commitment in the control of tuberculosis. There is a need to extend the treatment for one more month in the intensive phase of treatment.

The N-terminal 12 Residue Long Peptide of HIV gp41 is the Minimal Peptide Sufficient to Induce Significant T-cell-like Membrane Destabilization in Vitro

Here, we predicted the minimal N-terminal fragment of gp41 required to induce significant membrane destabilization using IMPALA. This algorithm is dedicated to predict peptide interaction with a membrane. We based our prediction of the minimal fusion peptide on the tilted peptide theory. This theory proposes that some protein fragments having a peculiar distribution of hydrophobicity adopt a tilted orientation at a hydrophobic/hydrophilic interface. As a result of this orientation, tilted peptides should disrupt the interface. We analysed in silico the membrane-interacting properties of gp41 N-terminal peptides of different length derived from the isolate BRU and from an alignment of 710 HIV strains available on the Los Alamos National Laboratory. Molecular modelling results indicated that the 12 residue long peptide should be the minimal fusion peptide. We then assayed lipid-mixing and leakage of T-cell-like liposomes with N-terminal peptides of different length as first challenge of our predictions. Experimental results confirmed that the 12 residue long peptide is necessary and sufficient to induce membrane destabilization to the same extent as the 23 residue long fusion peptide. In silico analysis of some fusion-incompetent mutants presented in the literature further revealed that they cannot insert into a modelled membrane correctly tilted. According to this work, the tilted peptide model appears to explain at least partly the membrane destabilization properties of HIV fusion peptide.

Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral

BACKGROUND

Genetic testing for hereditary cancer syndromes contributes to the medical management of patients who may be at increased risk of one or more cancers. BRCA1 and BRCA2 testing for hereditary breast and ovarian cancer is one such widely used test. However, clinical testing methods with high sensitivity for deleterious mutations in these genes also detect many unclassified variants, primarily missense substitutions.

METHODS

We developed an extension of the Grantham difference, called A-GVGD, to score missense substitutions against the range of variation present at their position in a multiple sequence alignment. Combining two methods, co-occurrence of unclassified variants with clearly deleterious mutations and A-GVGD, we analysed most of the missense substitutions observed in BRCA1.

RESULTS

A-GVGD was able to resolve known neutral and deleterious missense substitutions into distinct sets. Additionally, eight previously unclassified BRCA1 missense substitutions observed in trans with one or more deleterious mutations, and within the cross-species range of variation observed at their position in the protein, are now classified as neutral.

DISCUSSION

The methods combined here can classify as neutral about 50% of missense substitutions that have been observed with two or more clearly deleterious mutations. Furthermore, odds ratios estimated for sets of substitutions grouped by A-GVGD scores are consistent with the hypothesis that most unclassified substitutions that are within the cross-species range of variation at their position in BRCA1 are also neutral. For most of these, clinical reclassification will require integrated application of other methods such as pooled family histories, segregation analysis, or validated functional assay.

HLA class I diversity among rural rainforest inhabitants in Cameroon: identification of A*2612-B*4407 haplotype

The population distribution of alleles of the classical HLA class I loci in Cameroon has not been well studied but is of particular interest given the AIDS and malarial epidemics afflicting this population. We investigated the genetic diversity of HLA-A, HLA-B and HLA-C alleles in remote populations of Cameroon. Subjects from seven small, isolated, indigenous populations (N = 274) in the rainforest of southern Cameroon were typed for HLA-A, HLA-B and HLA-C alleles using a polymerase chain reaction/sequence-specific oligonucleotide probe assay and sequence analysis. Multiple alleles of the HLA-A (N = 28), HLA-B (N = 41) and HLA-C (N = 21) loci were identified, of which A*2301[allele frequency (AF) = 12.8%], B*5802 (AF = 10.9%) and Cw*0401 (AF = 16.6%) were the most frequent individual alleles and A*02 (AF = 19.0%), B*58 (AF = 15.9%) and Cw*07 (AF = 22.4%) the most common serologically defined groups of alleles. Twenty-six (28.9%) alleles with a frequency of less than 1% (AF < 1%), 39 (43%) with a frequency of 2.0-15.0% (AF = 2.0-15.0%), three globally uncommon alleles [A*2612 (AF = 2.0%), B*4016 (AF = 0.7%) and B*4407 (AF = 1.4%)], and the A*2612-Cw*0701/06/18-B*4407 haplotype (haplotype frequency = 1.3%) were also identified. Heterozygosity values of 0.89, 0.92 and 0.89 were determined for HLA-A, HLA-B and HLA-C, respectively. The extensive allelic and haplotypic diversity observed in this population may have resulted from varied natural selective pressures on the population, as well as intermingling of peoples from multiple origins. Thus, from an anthropologic perspective, these data highlight the challenges in T-cell-based vaccine development, the identification of allogeneic transplant donors and the understanding of infectious disease patterns in different populations.