Probability of BRCA1/2 mutation varies with ovarian histology: results from screening 442 ovarian cancer families

While there are many reports in the literature of mutation testing of BRCA1 and BRCA2 in breast/ovarian cancer families, the question of which type of ovarian cancers are relevant still pertains. We have undertaken whole gene screening including multiple ligation-dependent probe amplification in an affected individual within 442 unrelated non-Jewish families containing at least one reported ovarian cancer diagnosed less than 50 years or at any age with family history of breast or ovarian cancer for mutations in BRCA1 and BRCA2. A total of 166 mutations were identified 110 (25%) in BRCA1 and 56 (13%) in BRCA2. In families without confirmation of ovarian diagnosis, the detection rate drops significantly. In families fulfilling Breast Cancer Linkage Consortium (BCLC) criteria with confirmed ovarian cancer cases, the mutation detection frequency was 80%. If only BCLC families with unconfirmed ovarian cancers were included, the detection rate dropped to 36% when a relevant ovarian cancer diagnosis was not confirmed. In BCLC families containing only one ovarian cancer, BRCA2 accounted for 45% of identified mutations. No mutations were identified in affected individuals with borderline or mucinous tumours. Detection rates dropped below the 10/20% international thresholds in a number of families with unconfirmed ovarian cancers. Borderline/mucinous pathology substantially reduces the likelihood of identifying a BRCA1/2 mutation. Strenuous efforts should be made to confirm ovarian pathology if the lack of confirmation or refuting the diagnosis would decrease a family's likelihood of mutation detection below screening thresholds. In the UK, a higher proportion of families harbour BRCA2 pathogenic mutations than predicted from previous studies.

A detailed analysis of localized J-difference GABA editing: theoretical and experimental study at 4 T

The problem of low signal-to-noise ratio for gamma-aminobutyric acid (GABA) in vivo is exacerbated by inefficient detection schemes and non-optimal experimental parameters. To analyze the mechanisms for GABA signal loss of a MEGA-PRESS J-difference sequence at 4 T, numerical simulations were performed ranging from ideal to realistic experimental implementation, including volume selection and experimental radio frequency (RF) pulse shapes with a macromolecular minimization scheme. The simulations were found to be in good agreement with phantom and in vivo data from human brain. The overall GABA signal intensity for the simulations with realistic conditions for the MEGA-PRESS difference spectrum was calculated to be almost half of the signal simulated under ideal conditions (~43% signal loss). In contrast, creatine was reduced significantly less then GABA (~19% signal loss). The 'four-compartment' distribution due to J-coupling in the PRESS-based localization was one of the most significant sources of GABA signal loss, in addition to imperfect RF profiles for volume selection and editing. An alternative strategy that reduces signal loss due to the four-compartment distribution is suggested. In summary, a detailed analysis of J-difference editing is provided with estimates of the relative amounts of GABA signal losses due to various mechanisms. The numerical simulations presented in this study should facilitate both implementation of the more efficient acquisition and quantification process of J-coupled systems.

NBS1 is involved in DNA repair and plays a synergistic role with ATM in mediating meiotic homologous recombination in plants

The ability of plants to repair DNA double-strand breaks (DSBs) is essential for growth and fertility. The Arabidopsis DSB repair proteins AtRAD50 and AtMRE11 form part of an evolutionarily conserved complex that, in Saccharomyces cerevisiae and mammals, includes a third component termed XRS2 and NBS1, respectively. The MRN complex (MRX in yeast) has a direct role in DSB repair and is also required for DNA damage signaling and checkpoint activation in a pathway mediated by the protein kinase ATM. This study characterizes Arabidopsis and maize NBS1 orthologues that share conserved protein motifs with human NBS1. Both plant NBS1 proteins interact with the corresponding MRE11 orthologues, and deletion analysis of AtNBS1 defines a region towards the C-terminus (amino acids 465-500) that is required for interaction with AtMRE11. Arabidopsis lines homozygous for a T-DNA insertional mutation in AtNBS1 display hypersensitivity to the DNA cross-linking reagent mitomycin C, and this phenotype can be rescued by complementation with the wild-type gene, consistent with a function for AtNBS1 in plant DSB repair. Analysis of atnbs1-1 atatm double mutants revealed a role for AtNBS1 in meiotic recombination. While atatm mutants produce reduced seed numbers, plants deficient in both AtATM and AtNBS1 are completely infertile. Cytological analysis of these double mutants revealed incomplete chromosome pairing and synapsis in meiotic prophase, and extensive chromosome fragmentation in metaphase I and subsequent stages. These results suggest a novel role for AtNBS1 that is independent of AtATM-mediated signaling and functions in the very early stages of meiosis.

Mortality event in freshwater drum Aplodinotus grunniens from Lake Ontario, Canada, associated with viral haemorrhagic septicemia virus, type IV

A mortality event primarily affecting freshwater drum Aplodinotus grunniens was noted during April and May 2005 in the Bay of Quinte, Lake Ontario, Canada. A conservative estimate of the number of dead drum was approximately 100 metric tonnes. Large numbers of dead round goby Neogobius melanostomus were also seen, as well as a few muskellunge Esox masquinongy. In the drum, there was a consistent histological pattern of variably severe panvasculitis, a necrotising myocarditis, meningoencephalitis and a segmental enteritis. Moderate numbers of bullet-shaped viral particles consistent with a rhabdovirus were identified by transmission electron microscopy (TEM) in affected heart tissue. Following primary isolation from pooled tissues on fathead minnow (FHM) cells, a morphologically similar virus, approximately 165 x 60 nm in size, was visualised. Identification of the isolate as viral haemorrhagic septicemia virus (VHSV) was confirmed by enzyme immunoassay and by polymerase chain reaction. An appropriately sized product (468 bp) of the G-glycoprotein gene (nucleotides [nt] 340 to 807) was generated with RNA extracted from FHM cell supernatant. Analysis of a 360 nt partial glycoprotein gene sequence (nt 360 to 720) indicated a 96.4 to 97.2% nucleotide identity with known strains of North American (NA) VHSV. Analysis using Neighbour-joining distance methods assigned the isolate to the same lineage as the NA and Japanese isolates (Genogroup IV). However, there was sufficient sequence divergence from known NA VHSV isolates to suggest that this isolate may represent a distinct subgroup. The effects of ongoing mortality in freshwater drum and in multiple species during spring 2006 suggest that this newly recognised virus in the Great Lakes will have continued impact in the near future.

Use of atypical antipsychotic medications in adolescent psychiatric inpatients: a comparison with inpatients who did not receive antipsychotic medications during their stay

The use of atypical antipsychotic medications has been reported to be increased in adolescent psychiatric outpatients and to include many patients with non-psychotic disorders. This study examined the correlates of antipsychotic usage in adolescent inpatients and compared their characteristics with a sample of adolescent inpatients who did not receive antipsychotics during their hospitalisation. A total of 159 consenting consecutive patients treated with atypical antipsychotic medications were compared with 150 patients who were admitted during the same time period and not treated with antipsychotics. The samples were compared for demographic factors, clinical diagnoses, clinical symptoms at admission and other medications received during their inpatient stay. Sex and ethnicity did not differ significantly as a function of antipsychotic mediation status. Significantly few patients with an admission diagnosis of major depression received antipsychotic medications and more patients with admission diagnosis of bipolar and/or conduct disorder were treated with antipsychotic medications. Clinical symptom differences and additional medications received were consistent with the differences in admission diagnoses. Despite the fact that significantly fewer patients with major depression received antipsychotic medications, 47% of the patients who did receive antipsychotic medications in this study had an admission diagnosis of major depression. There are several differences between these inpatient data and previous studies of outpatient claims databases, the majority of adolescent inpatient cases treated with antipsychotic medications had admission diagnoses consistent with both adult indications and previous research with adolescent patients. These data suggest an urgent need to study the safety and efficacy of atypical antipsychotic medications on aspects of depression in adolescents.

Making health informatics competencies useful: an applied health informatics competency self-assessment system

Years ago we undertook to define Health Informatics (HI) competencies. This effort resulted in the creation of a document that articulated HI roles, the challenges faced by HI professionals, the high-level tasks that they needed to undertake to address these challenges and the competencies (skills, knowledge, and experience) they needed to complete these tasks. Unfortunately, in so doing we created what is arguably the most boring book in history, shoes contents are very difficult to extract, use, maintain and improve. We report here the completion of a pilot of a system that we believe corrects this situation. It is a webbased tool that incorporates all of the material, from roles to detailed competencies, enabling them to be accessed and used for a variety of purposes, the most notable of which is professional self-assessment.

Robust analysis of short echo time (1)H MRSI of human brain

Short echo time proton MR Spectroscopic Imaging (MRSI) suffers from low signal-to-noise ratio (SNR), limiting accuracy to estimate metabolite intensities. A method to coherently sum spectra in a region of interest of the human brain by appropriate peak alignment was developed to yield a mean spectrum with increased SNR. Furthermore, principal component (PC) spectra were calculated to estimate the variance of the mean spectrum. The mean or alternatively the first PC (PC(1)) spectrum from the same region can be used for quantitation of peak areas of metabolites in the human brain at increased SNR. Monte Carlo simulations showed that both mean and PC(1) spectra were more accurate in estimating regional metabolite concentrations than solutions that regress individual spectra against the tissue compositions of MRSI voxels. Back-to-back MRSI studies on 10 healthy volunteers showed that mean spectra markedly improved reliability of brain metabolite measurements, most notably for myo-inositol, as compared to regression methods.

Comprehensive processing, display and analysis for in vivo MR spectroscopic imaging

Image reconstruction for magnetic resonance spectroscopic imaging (MRSI) requires specialized spatial and spectral data processing methods and benefits from the use of several sources of prior information that are not commonly available, including MRI-derived tissue segmentation, morphological analysis and spectral characteristics of the observed metabolites. In addition, incorporating information obtained from MRI data can enhance the display of low-resolution metabolite images and multiparametric and regional statistical analysis methods can improve detection of altered metabolite distributions. As a result, full MRSI processing and analysis can involve multiple processing steps and several different data types. In this paper, a processing environment is described that integrates and automates these data processing and analysis functions for imaging of proton metabolite distributions in the normal human brain. The capabilities include normalization of metabolite signal intensities and transformation into a common spatial reference frame, thereby allowing the formation of a database of MR-measured human metabolite values as a function of acquisition, spatial and subject parameters. This development is carried out under the MIDAS project (Metabolite Imaging and Data Analysis System), which provides an integrated set of MRI and MRSI processing functions. It is anticipated that further development and distribution of these capabilities will facilitate more widespread use of MRSI for diagnostic imaging, encourage the development of standardized MRSI acquisition, processing and analysis methods and enable improved mapping of metabolite distributions in the human brain.

The Gross Anatomy of the Male Reproductive System of a Neotropical Rodent: the Agouti (Dasyprota leporina)

The literature available on the agouti (Dasyprocta leporina) is very limited. The agouti is a Neotropical rodent found in Trinidad and Tobago, Central and South America. This study focuses on one of the many unexplored areas relating to the species, the male reproductive system. The results showed that the mean testicular length, diameter and weight was 3.67 +/- 0.12 cm, 1.67 +/- 0.04 cm and 5.03 +/- 0.52 g respectively. The paired testes and epididymis were found in contact with the abdominal muscles within scrotal pouches, which are evaginations of the caudoventral abdominal wall. The caput epididymis is enclosed by a fat body. The ductus deferens has a mean length and diameter of 10.98 +/- 0.40 cm and 0.14 +/- 0.01 cm respectively. At the urethral end of the ductus deferens the diameter of each duct expends to form the ampulla. The mean diameter of each of the ampulla was 0.25 cm. The accessory sex organs of the male agouti (D. leporina) include the vesicular glands, the coagulating glands, the prostate glands and the bulbourethral glands. The penis of the agouti is U-shaped with a mean length of 9.90 +/- 0.43 cm. The glans penis contains an os penis, a pair of lateral penile cartilages and paired ventral keratinaceous styles.

WebSAT: a web-based competency self-assessment system linking to educational resources

We describe a web-based system that enables an individual to assess him/her self against the set of competencies required for a variety of roles in the area of Applied Health Informatics (AHI). The competencies themselves were developed by a multi-disciplinary team under the auspices of the Canadian Institute for Health Research (CIHR), and include the knowledge, skills, and experience necessary to fulfill specific roles as an applied health informatician. Both textual and graphical information is presented to the user and potential mechanisms for correcting competency gaps are presented in this online interactive system.

Follow-up and final results of the Oslo I Study comparing screen-film mammography and full-field digital mammography with soft-copy reading

PURPOSE

To compare cancer detection rates of screen-film (SFM) and full-field digital mammography (FFDM) with soft-copy reading in a screening program including the initial positive scores for interval cancers and cancers in the subsequent screening round, and to analyze the false-negative FFDM interpretations.

MATERIAL AND METHODS

Using a paired study design, 3683 women underwent SFM and FFDM in a population-based screening program. Two standard views of each breast were acquired. The images were interpreted without previous films for comparison. Independent double reading using a 5-point rating scale for probability of cancer was used for each modality. An examination was defined as positive if at least one of the two independent readers scored 2 or higher on the 5-point rating scale. SFM-positive cases were discussed in a SFM consensus meeting and FFDM-positive cases in a separate FFDM consensus meeting before recall. The study population was followed for more than 2 years so that interval cancers and screen-detected cancers in the subsequent screening round could be included. Cancer detection rates were compared using the McNemar test for paired proportions. The kappa statistic and Wilcoxon signed-rank test for matched pairs were used for comparing rating scores. The reading time was recorded for all FFDM interpretations.

RESULTS

A total of 31 cancers (detection rate 0.84%) were diagnosed initially, of which SFM detected 28 and FFDM 23 (McNemar test P=0.23, discordant pair 8 and 3). Two cancers with a positive score at initial SFM reading and three with a positive score at initial FFDM reading were dismissed at SFM and FFDM consensus meetings, respectively. The difference in cancer detection after recall (discordant pair 11 and 5) was not significant (McNemar test, P=0.21). Of the 10 interval cancers and 16 screen-detected cancers in the subsequent round, 3 had true-positive SFM scores while 4 had true-positive FFDM scores in the initial reading session. A total of 38 cancers therefore had a positive result at double reading at one or both modalities, 31 at SFM and 27 at FFDM (McNemar test, P=0.48). Comparison of SFM and FFDM interpretations using the mean score for each case revealed no statistically significant difference between the two modalities (Wilcoxon signed-rank test for matched pairs; P-value=0.228). Two initial round cancers (one tumor found incidentally at work-up for a mass proved to be a simple cyst with a positive score at FFDM but a negative score at SFM, and one tumor with positive score at SFM but negative score at FFDM due to positioning failure) were excluded from the further analysis. Excluding these two cancers from comparison, there were 31% (22 of 72) false-negative SFM and 47% (34 of 72) false-negative FFDM individual interpretations. The overall mean interpretation time for normal FFDM examinations was 45 s. For most false-negative FFDM results, the reading time was shorter or longer than for normal examinations. The recorded FFDM interpretation time was noticeably short for several overlooked cancers manifesting as microcalcifications (ductal carcinoma in situ).

CONCLUSION

There is no statistically significant difference in cancer detection rate between SFM and FFDM with soft-copy reading in a mammography screening program. Analysis of cancers missed at FFDM with soft-copy reading indicates that close attention has to be paid to systematic use of image display protocols.

Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response

Polyploidy, the inheritance of more than two genome copies per cell, has played a major role in the evolution of higher plants. Little is known about the transition from diploidy to polyploidy but in some species, triploids are thought to function as intermediates in this transition. In contrast, in other species triploidy is viewed as a block. We investigated the responses of Arabidopsis thaliana to triploidy. The role of genetic variability was tested by comparing triploids generated from crosses between Col-0, a diploid, and either a natural autotetraploid (Wa-1) or an induced tetraploid of Col-0. In this study, we demonstrate that triploids of A. thaliana are fertile, producing a swarm of different aneuploids. Propagation of the progeny of a triploid for a few generations resulted in diploid and tetraploid cohorts. This demonstrated that, in A. thaliana, triploids can readily form tetraploids and function as bridges between euploid types. Genetic analysis of recombinant inbred lines produced from a triploid identified a locus on chromosome I exhibiting allelic bias in the tetraploid lines but not in the diploid lines. Thus, genetic variation was subject to selection contingent on the final ploidy and possibly acting during the protracted aneuploid phase.

CONTRAST HARMONIC ULTRASOUND OF SPONTANEOUS LIVER NODULES IN 32 DOGS

Thirty-two dogs with spontaneous hepatic nodules were given intravenous ultrasound contrast medium (Definity or Sonovue) and imaged with contrast harmonic software on a conventional ultrasound machine system. Digital video images were initially reviewed to describe the perfusion pattern of malignant nodules. The images were reviewed again to test this pattern against all individual nodules. Subjectively, there was improved conspicuity of malignant nodules after contrast enhancement compared with conventional imaging and increased numbers of malignant nodules were often noted. There was decreased conspicuity of benign nodules and no additional nodules were seen after contrast enhancement. There was a highly significant (P < 0.0001) association of malignancy with a hypoechoic nodule at surrounding normal liver peak contrast enhancement. Benign nodules were isoechoic to the surrounding normal liver at peak contrast enhancement. Only one benign nodule (hepatoma) had regions of hypoechogenicity compared with the surrounding normal liver at peak liver contrast enhancement. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy were highly significant (P < 0.0001) (100%, 94.1%, 93.8%, 100%, and 96.9%, respectively). No complications or morbidity was noted throughout the course of the study. Contrast harmonic ultrasound appears to be accurate at discriminating between naturally occurring benign and malignant nodules in the liver of dogs.

A new scoring system for the chances of identifying a BRCA1/2 mutation outperforms existing models including BRCAPRO

PURPOSE

To develop a simple scoring system for the likelihood of identifying a BRCA1 or BRCA2 mutation.

METHODS

DNA samples from affected subjects from 422 non-Jewish families with a history of breast and/or ovarian cancer were screened for BRCA1 mutations and a subset of 318 was screened for BRCA2 by whole gene screening techniques. Using a combination of results from screening and the family history of mutation negative and positive kindreds, a simple scoring system (Manchester scoring system) was devised to predict pathogenic mutations and particularly to discriminate at the 10% likelihood level. A second separate dataset of 192 samples was subsequently used to test the model's predictive value. This was further validated on a third set of 258 samples and compared against existing models.

RESULTS

The scoring system includes a cut-off at 10 points for each gene. This equates to >10% probability of a pathogenic mutation in BRCA1 and BRCA2 individually. The Manchester scoring system had the best trade-off between sensitivity and specificity at 10% prediction for the presence of mutations as shown by its highest C-statistic and was far superior to BRCAPRO.

CONCLUSION

The scoring system is useful in identifying mutations particularly in BRCA2. The algorithm may need modifying to include pathological data when calculating whether to screen for BRCA1 mutations. It is considerably less time-consuming for clinicians than using computer models and if implemented routinely in clinical practice will aid in selecting families most suitable for DNA sampling for diagnostic testing.

Discovery of induced point mutations in maize genes by TILLING

BACKGROUND

Going from a gene sequence to its function in the context of a whole organism requires a strategy for targeting mutations, referred to as reverse genetics. Reverse genetics is highly desirable in the modern genomics era; however, the most powerful methods are generally restricted to a few model organisms. Previously, we introduced a reverse-genetic strategy with the potential for general applicability to organisms that lack well-developed genetic tools. Our TILLING (Targeting Induced Local Lesions IN Genomes) method uses chemical mutagenesis followed by screening for single-base changes to discover induced mutations that alter protein function. TILLING was shown to be an effective reverse genetic strategy by the establishment of a high-throughput TILLING facility and the delivery of thousands of point mutations in hundreds of Arabidopsis genes to members of the plant biology community.

RESULTS

We demonstrate that high-throughput TILLING is applicable to maize, an important crop plant with a large genome but with limited reverse-genetic resources currently available. We screened pools of DNA samples for mutations in 1-kb segments from 11 different genes, obtaining 17 independent induced mutations from a population of 750 pollen-mutagenized maize plants. One of the genes targeted was the DMT102 chromomethylase gene, for which we obtained an allelic series of three missense mutations that are predicted to be strongly deleterious.

CONCLUSIONS

Our findings indicate that TILLING is a broadly applicable and efficient reverse-genetic strategy. We are establishing a public TILLING service for maize modeled on the existing Arabidopsis TILLING Project.