High Sensitivity and Specificity of Digital Infrared Imaging for Breast Cancer Detection in Younger Women Undergoing Breast Biopsy

Background and aim: Recent published evidence suggests that digital infrared breast scanning may be a useful adjunctive tool for breast cancer detection. In this study we have assessed the effectiveness of digital infrared imaging captured using Sentinel BreastScan (Infrared Sciences Corp., Bohemia, NY, USA) and compared the computer-generated reports from this system with expert manual review of the images as well as a new software programme currently under development called NoTouch BreastScan.Methods: A total of 100 patients scheduled for breast biopsy (n=106), following detection of an abnormality via clinical examination or breast imaging were recruited to this research ethics committee-approved study. After obtaining informed consent all patients were imaged using Sentinel BreastScan, prior to their scheduled biopsy procedure in the Cambridge Breast Unit. The data for each patient was analysed in four different ways for comparison with final pathology findings as follows: 1. Sentinel screening report (score 0 = normal, 1-5 = abnormal); 2.Sentinel neural network (positive or negative); 3. Independent expert review (positive or negative); 4. NoTouch BreastScan artificial intelligence (score 0-3 = normal, 4-10 abnormal).Results: Sensitivity for the whole group using Sentinel screening (53%) and neural network (48%) was low compared to recently published data (97%), expert review (78%) and NoTouch (70%).Sensitivity and specificity results for NoTouch BreastScan by age group are shown in table1Sensitivity and specificity results for NoTouch BreastScan by age group <50 years, n=2150-70 years, n=73>70 years, n=12All patients, n=106Sensitivity78%72%42%70%Specificity75%37%N/A48% Conclusion: This study confirms acceptable sensitivity (72%) for breast cancer detection using NoTouch BreastScan in women under 70 years of age despite the data being captured with Sentinel. This sensitivity increases to 78% for women <50 years old and is combined with a marked increase in specificity (75%) in this group. These encouraging figures may increase even further when data is captured by the NoTouch software and studies are ongoing with this novel imaging system.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5025.

The replicase gene of avian coronavirus infectious bronchitis virus is a determinant of pathogenicity

We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene.

Incidental breast lesions detected on CT: what is their significance?

An increasing number of breast lesions are being detected incidentally on CT. The aim of this study was to investigate the rate of referrals to the breast unit for assessment of lesions identified on CT and the resulting yield of previously undiagnosed breast malignancies from this pathway. A retrospective review was undertaken of CT examinations conducted over a period of 14 years. All patients (with no previous history of breast cancer) whose report contained the keyword "breast" and who were referred to a specialist breast unit for assessment were reviewed. CT lesion morphology and enhancement pattern were identified and compared with the final diagnostic outcome. 70 patients were identified by retrospective analysis, yielding 78 incidental breast lesions, of which 22 (28.2%) were malignant (category B5). This gave a positive predictive value (PPV) for malignancy of 28.2%. The best morphological predictor of malignancy was spiculation (PPV, 76%) and irregularity (PPV, 58%), whereas calcification patterns (PPV, 36%) were diagnostically unhelpful. Malignant lesions were likely to be larger (mean, 28.5 mm) than benign lesions (mean, 20.2 mm; p<0.05). In conclusion, 30% of incidental breast lesions in this large series of patients proved to be unsuspected breast cancers, particularly irregular spiculated masses. Referral for formal triple assessment of CT-diagnosed breast lesions is worthwhile, and careful examination of the breast should be a routine part of CT examinations.

One-stop diagnostic breast clinics: how often are breast cancers missed?

The aim of this study was to estimate the number of patients discharged from a symptomatic breast clinic who subsequently develop breast cancer and to determine how many of these cancers had been ‘missed’ at initial assessment. Over a 3-year period, 7004 patients were discharged with a nonmalignant diagnosis. Twenty-nine patients were subsequently diagnosed with breast cancer over the next 36 months. This equates to a symptomatic ‘interval’ cancer rate of 4.1 per 1000 women in the 36 months after initial assessment (0.9 per 1000 women within 12 months, 2.6 per 1000 women within 24 months). The lowest sensitivity of initial assessment was seen in patients of 40–49 years of age, and these patients present the greatest imaging and diagnostic challenge. Following multidisciplinary review, a consensus was reached on whether a cancer had been missed or not. No delay occurred in 10 patients (35%) and probably no delay in 7 patients (24%). Possible delay occurred in three patients (10%) and definite delay in diagnosis (i.e., a ‘missed’ cancer) occurred in only nine patients (31%). The overall diagnostic accuracy of ‘triple’ assessment is 99.6% and the ‘missed’ cancer rate is 1.7 per 1000 women discharged.

Sequence of the spike protein of the Belgian B164S isolate of nephropathogenic infectious bronchitis virus

The sequence of the gene encoding the spike glycoprotein (S) of the 1984 Belgian nephropathogenic isolate B1648 has been determined and shown to encode a protein of 1171 amino acids. Comparison of the deduced amino acid sequence of the S1 (amino-terminal half) of S, which induces virus-neutralizing antibodies, with that of vaccinal strains D274, H120 and D1466 revealed that it differed from them by 21, 25 and 49%, respectively, and by 24 to 25% from the North American nephropathogenic isolates Gray and Holte. The deduced amino add sequence of the S2 (carboxy-terminal) half of S differed by 10 to 12% (25% from D1466).

Role of phosphorylation clusters in the biology of the coronavirus infectious bronchitis virus nucleocapsid protein

The coronavirus infectious bronchitis virus (IBV) nucleocapsid (N) protein is an RNA binding protein which is phosphorylated at two conserved clusters. Kinetic analysis of RNA binding indicated that the C-terminal phosphorylation cluster was involved in the recognition of viral RNA from non-viral RNA. The IBV N protein has been found to be essential for the successful recovery of IBV using reverse genetics systems. Rescue experiments indicated that phosphorylated N protein recovered infectious IBV more efficiently when compared to modified N proteins either partially or non-phosphorylated. Our data indicate that the phosphorylated form of the IBV N protein plays a role in virus biology.

Manipulation of the infectious bronchitis coronavirus genome for vaccine development and analysis of the accessory proteins

Infectious bronchitis coronavirus (IBV) is the cause of the single most economically costly infectious disease of domestic fowl in the UK—and probably so in many countries that have a developed poultry industry. A major reason for its continued dominance is its existence as many serotypes, determined by the surface spike protein (S), cross-protection being poor. Although controlled to some degree by live and inactivated vaccines, a new generation of IB vaccines is called for. Reverse genetic or ‘infectious clone’ systems, which allow the manipulation of the IBV genome, are key to this development. New vaccines would ideally be: genetically stable (i.e. maintain a stable attenuated phenotype); administered in ovo; and be flexible with respect to the source of the spike protein gene. Rational attenuation of IBV requires the identification of genes that are simultaneously not essential for replication and whose absence would reduce pathogenicity. Being able to modify a ‘core’ vaccine strain to make it applicable to a prevailing serotype requires a procedure for doing so, and the demonstration that ‘spike-swapping’ is sufficient to induce good immunity.

We have demonstrated that four small IBV proteins, encoded by genes 3 and 5, are not essential for replication; failure to produce these proteins had little detrimental affect on the titre of virus produced. Our current molecularly cloned IBV, strain Beaudette, is non-pathogenic, so we do not know what effect the absence of these proteins would have on pathogenicity. That said, plaque size and composition of various gene 3/5 recombinant IBVs in cell culture, and reduced output and ciliostasis in tracheal organ cultures, shows that they are less aggressive than the wild-type Beaudette. Consequently these genes remain targets for rational attenuation. We have recently obtained evidence that one or more of the 15 proteins encoded by gene 1 are also determinants of pathogenicity. Hence gene 1 is also a target for rational attenuation.

Replacing the S protein gene of Beaudette with that from the pathogenic M41 strain resulted in a recombinant virus that was still non-pathogenic but which did induce protection against challenge with M41. We have since made other ‘spike-swapped’ recombinants, including ones with chimaera S genes. Uniquely, our molecular clone of Beaudette is benign when administered to 18-day-old embryos, even at high doses, and induces immunity after this route of vaccination.

Taken together, our results point to the creation of a new generation of IB vaccines, based on rational modification of the genome, as being a realisable objective.

Neither the RNA nor the proteins of open reading frames 3a and 3b of the coronavirus infectious bronchitis virus are essential for replication

Gene 3 of infectious bronchitis virus is tricistronic; open reading frames (ORFs) 3a and 3b encode two small nonstructural (ns) proteins, 3a and 3b, of unknown function, and a third, structural protein E, is encoded by ORF 3c. To determine if either the 3a or the 3b protein is required for replication, we first modified their translation initiation codons to prevent translation of the 3a and 3b proteins from recombinant infectious bronchitis viruses (rIBVs). Replication in primary chick kidney (CK) cells and in chicken embryos was not affected. In chicken tracheal organ cultures (TOCs), the recombinant rIBVs reached titers similar to those of the wild-type virus, but in the case of viruses lacking the 3a protein, the titer declined reproducibly earlier. Translation of the IBV E protein is believed to be initiated by internal entry of ribosomes at a structure formed by the sequences corresponding to ORFs 3a and 3b. To assess the necessity of this mechanism, we deleted most of the sequence representing 3a and 3b to produce a gene in which ORF 3c (E) was adjacent to the gene 3 transcription-associated sequence. Western blot analysis revealed that the recombinant IBV produced fivefold less E protein. Nevertheless, titers produced in CK cells, embryos, and TOCs were similar to those of the wild-type virus, although they declined earlier in TOCs, probably due to the absence of the 3a protein. Thus, neither the tricistronic arrangement of gene 3, the internal initiation of translation of E protein, nor the 3a and 3b proteins are essential for replication per se, suggesting that these proteins are accessory proteins that may have roles in vivo.

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data

DNA microarrays offer the possibility of testing for the presence of thousands of micro-organisms in a single experiment. However, there is a lack of reliable bioinformatics tools for the analysis of such data. We have developed DetectiV, a package for the statistical software R. DetectiV offers powerful yet simple visualization, normalization and significance testing tools. We show that DetectiV performs better than previously published software on a large, publicly available dataset.

Sequence of the nucleoprotein gene from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae

Subgenomic mRNA from a virulent isolate of porcine transmissible gastroenteritis virus (TGEV) was used to produce cDNA which was sequenced. Two non‐overlapping open reading frames (ORFs) were identified. The largest, encoding a polypeptide of 382 amino acids (relative molecular mass (M_r) 43 483), was shown to be the viral nucleoprotein gene. The second ORF, found 3’to the larger ORF, encodes a polypeptide of 78 amino acids (M_r 9068) which has yet to be assigned to a viral product. The nucleoprotein gene was expressed in yeast cells under the control of two types of yeast promoters: the constitutive PGK promoter, and the inducible GAL1 promoter. Yeast cells containing recombinant plasmids, with the nucleoprotein gene in the correct orientation, produced a polypeptide of M, 47000, identical to the viral product, that reacted with a specific monoclonal antibody.

Safety and efficacy of an infectious bronchitis virus used for chicken embryo vaccination

Commercial vaccines for in ovo vaccination have not yet been developed for infectious bronchitis virus (IBV), the major coronavirus in the poultry industry. Recombinant IBVs based on the Beaudette strain expressing the Beaudette spike protein (Beau-R) or that from the virulent M41 strain (BeauR-M41(S)) were assessed for their potential as prototype vaccines for application to 18-day-old embryos. Pathogenicity was assessed by observing the effect on hatchability, and/or the production of nasal discharge and/or the effects on ciliary activity in the trachea at various time points post hatch. In contrast to commercial IBV vaccines given in ovo, the Beau-R and BeauR-M41(S) strains did not reduce hatchability or cause nasal discharge, and caused minimal damage to the ciliated epithelium of the trachea. The presence of the spike protein from a virulent virus did not increase the pathogenicity of the virus according to the criteria used. Assessment of the BeauR-M41(S) strain for efficacy showed that it protected up to 90% of chicks against challenge with virulent IB virus (M41) in a dose dependent manner. Further egg passage of the BeauR-M41(S) strain (BeauR-M41(S) EP10) did not increase its pathogenicity though it did improve its efficacy, based on serology and protection against a virulent challenge. BeauR-M41(S) EP10 was more efficacious than BeauR-M41(S) protecting more birds against virulent challenge and providing a better serological antibody response. BeauR-M41(S) EP10 induced a serological response similar to that of a commercial vaccine given at day-old though the commercial vaccine provided slightly higher efficacy. These results are promising for the development of embryo safe efficacious IBV vaccines for in ovo application.

Isolation of a coronavirus from a green-cheeked Amazon parrot (Amazon viridigenalis Cassin)

A virus (AV71/99) was isolated from a green-cheeked Amazon parrot by propagation and passage in both primary embryo liver cells derived from blue and yellow macaw (Ara ararauna) embryos and chicken embryo liver cells. Electron microscopic examination of cytopathic agents derived from both types of cell cultures suggested that it was a coronavirus. This was confirmed using a pan-coronavirus reverse transcriptase polymerase chain reaction that amplified part of gene 1 that encodes the RNA-dependent RNA polymerase. The deduced sequence of 66 amino acids had 66 to 74% amino acid identity with the corresponding sequence of coronaviruses in groups 1, 2 and 3. Several other oligonucleotide primer pairs that give PCR products corresponding to genes 3, 5, N and the 3'-untranslated region of infectious bronchitis virus, turkey coronavirus and pheasant coronavirus (all in group 3) failed to do so with RNA from the parrot coronavirus. This is the first demonstration of a coronavirus in a psittacine species.

Gene 5 of the avian coronavirus infectious bronchitis virus is not essential for replication

The avian coronavirus Infectious bronchitis virus (IBV), like other coronaviruses, expresses several small nonstructural (ns) proteins in addition to those from gene 1 (replicase) and the structural proteins. These coronavirus ns genes differ both in number and in amino acid similarity between the coronavirus groups but show some concordance within a group or subgroup. The functions and requirements of the small ns gene products remain to be elucidated. With the advent of reverse genetics for coronaviruses, the first steps in elucidating their role can be investigated. We have used our reverse genetics system for IBV (R. Casais, V. Thiel, S. G. Siddell, D. Cavanagh, and P. Britton, J. Virol. 75:12359-12369, 2001) to investigate the requirement of IBV gene 5 for replication in vivo, in ovo, and ex vivo. We produced a series of recombinant viruses, with an isogenic background, in which complete expression of gene 5 products was prevented by the inactivation of gene 5 following scrambling of the transcription-associated sequence, thereby preventing the expression of IBV subgenomic mRNA 5, or scrambling either separately or together of the translation initiation codons for the two gene 5 products. As all of the recombinant viruses replicated very similarly to the wild-type virus, Beau-R, we conclude that the IBV gene 5 products are not essential for IBV replication per se and that they are accessory proteins.

Variation in the spike protein of the 793/B type of infectious bronchitis virus, in the field and during alternate passage in chickens and embryonated eggs

The degree of variation exhibited within the 793/B serotype (also known as 4/91 and CR88 serotypes) was investigated with nine French and 10 British isolates, collected between 1985 and 1994. The S1 part (1644 nucleotides) of the spike protein gene of the first known isolate of this serotype, FR/CR85131/85, had 95.9% to 97% nucleotide identity with the other isolates. Partial sequencing of isolates from Iran and Saudi Arabia, isolated in 2000, revealed approximately 95% nucleotide identity with European isolates, including the two live 793/B vaccinal strains, showing that they were not re-isolations of vaccinal virus. The data indicates that strains within the 793/B serotype have > or =96% nucleotide identity within the whole S1 gene and > or =93% nucleotide identity within the first 560 nucleotides, and > or =92% and > or =86% amino acid identities in the corresponding protein regions. This is similar to the identities exhibited within the Massachusetts serotype. Sequence analysis of a 793/B field isolate after passage in embryonated eggs, then in chickens and then again in eggs revealed selection for a serine and alanine at S1 amino acid position 95 in chicken-passaged and egg-passaged virus, respectively. There was no change in pathogenicity. This is the first demonstration at gene sequence level of host-driven selection for infectious bronchitis virus.