Statistical colour models: an automated digital image analysis method for quantification of histological biomarkers.

BACKGROUND: Colour is the most important feature used in quantitative immunohistochemistry (IHC) image analysis; IHC is used to provide information relating to aetiology and to confirm malignancy. METHODS: Statistical modelling is a technique widely used for colour detection in computer vision. We have developed a statistical model of colour detection applicable to detection of stain colour in digital IHC images. Model was first trained by massive colour pixels collected semi-automatically. To speed up the training and detection processes, we removed luminance channel, Y channel of YCbCr colour space and chose 128 histogram bins which is the optimal number. A maximum likelihood classifier is used to classify pixels in digital slides into positively or negatively stained pixels automatically. The model-based tool was developed within ImageJ to quantify targets identified using IHC and histochemistry. RESULTS: The purpose of evaluation was to compare the computer model with human evaluation. Several large datasets were prepared and obtained from human oesophageal cancer, colon cancer and liver cirrhosis with different colour stains. Experimental results have demonstrated the model-based tool achieves more accurate results than colour deconvolution and CMYK model in the detection of brown colour, and is comparable to colour deconvolution in the detection of pink colour. We have also demostrated the proposed model has little inter-dataset variations. CONCLUSIONS: A robust and effective statistical model is introduced in this paper. The model-based interactive tool in ImageJ, which can create a visual representation of the statistical model and detect a specified colour automatically, is easy to use and available freely at http://rsb.info.nih.gov/ij/plugins/ihc-toolbox/index.html . Testing to the tool by different users showed only minor inter-observer variations in results.

Comparative phylogeographic summary statistics for testing simultaneous vicariance.

Testing for simultaneous vicariance across comparative phylogeographic data sets is a notoriously difficult problem hindered by mutational variance, the coalescent variance, and variability across pairs of sister taxa in parameters that affect genetic divergence. We simulate vicariance to characterize the behaviour of several commonly used summary statistics across a range of divergence times, and to characterize this behaviour in comparative phylogeographic datasets having multiple taxon-pairs. We found Tajima's D to be relatively uncorrelated with other summary statistics across divergence times, and using simple hypothesis testing of simultaneous vicariance given variable population sizes, we counter-intuitively found that the variance across taxon pairs in Nei and Li's net nucleotide divergence (pi(net)), a common measure of population divergence, is often inferior to using the variance in Tajima's D across taxon pairs as a test statistic to distinguish ancient simultaneous vicariance from variable vicariance histories. The opposite and more intuitive pattern is found for testing more recent simultaneous vicariance, and overall we found that depending on the timing of vicariance, one of these two test statistics can achieve high statistical power for rejecting simultaneous vicariance, given a reasonable number of intron loci (> 5 loci, 400 bp) and a range of conditions. These results suggest that components of these two composite summary statistics should be used in future simulation-based methods which can simultaneously use a pool of summary statistics to test comparative the phylogeographic hypotheses we consider here.

Comparison of methods for assessment of minimal residual disease in childhood B-lineage acute lymphoblastic leukemia.

The level of minimal residual disease (MRD) early in treatment of acute lymphoblastic leukemia (ALL) strongly predicts the risk of marrow relapse. As a variety of methods of varying complexity have been separately used for detecting and quantifying MRD, we compared the prognostic utility of three methods measurement of blast percentage on day 14 of treatment, detection of monoclonality on day 14 or day 35, and measurement of MRD by PCR-based limiting dilution analysis on day 14 or day 35. The study group comprised 38 children aged 1-15 with Philadelphia-negative B-lineage ALL who were uniformly treated and followed until relapse or for a minimum of 5 years. We also studied some of the technical factors which influence the ability to detect MRD. Measurement of blast percentage on day 14 by an expert morphologist, detection of monoclonality on day 35, and PCR-based measurement of MRD levels on days 14 and 35 all showed significant ability to divide patients into prognostic groups. Measurement of blast percentage on day 14 by routine morphology or detection of monoclonality on day 14 were not useful. The quality of DNA samples varied greatly, as determined by amplifiability in the PCR. However, virtually all amplifiable leukemic targets in a sample were detectable which suggests that the level of detection achieved by limiting dilution analysis is essentially determined by the amount of DNA which it is practicable to study. We conclude that quantification of MRD at the end of induction provides the full range of prognostic information for marrow relapse but is complex; detection of monoclonality on day 35 is simple and has good positive predictive value; and quantification of MRD on day 14 merits further study. PCR-based methods for measurement of MRD levels should incorporate a correction for variation in DNA amplifiability.

An orphaned mammalian beta-globin gene of ancient evolutionary origin.

Mammals possess multiple, closely linked beta-globin genes that differ in the timing of their expression during development. These genes have been thought to be derived from a single ancestral gene, by duplication events that occurred after the separation of the mammals and birds. We report the isolation and characterization of an atypical beta-like globin gene (omega-globin) in marsupials that appears to be more closely related to avian beta-globin genes than to other mammalian beta-globin genes, including those previously identified in marsupials. Phylogenetic analyses indicate that omega-globin evolved from an ancient gene duplication event that occurred before the divergence of mammals and birds. Furthermore, we show that omega-globin is unlinked to the previously characterized beta-globin gene cluster of marsupials, making this the first report of an orphaned beta-like globin gene expressed in a vertebrate.

Early resistance to therapy during induction in childhood acute lymphoblastic leukemia.

Many patients with acute lymphoblastic leukemia (ALL) are not cured by current therapy because of the development of drug resistance. It is not clear when resistance develops during the growth of the leukemic clone and whether resistant cells are already present at diagnosis or develop later during treatment. Twenty-two uniformly treated children with ALL were studied throughout induction treatment. The size of the leukemic clone in blood and marrow was estimated by limiting dilution PCR analysis, using the rearranged immunoglobulin heavy chain gene as a molecular marker. The decline in the number of leukemic cells was biphasic in virtually all patients. For both marrow and blood, the logarithmic mean of the number of leukemic cells fell by approximately four orders of magnitude during the first 2 weeks, one order of magnitude during the third week, and not at all during the last two weeks of induction treatment. For marrow, the median of the fraction of leukemic cells in each patient that survived per week of treatment was 0.008 for the first 2 weeks, 0.12 for the third week, and 1.4 for the last 2 weeks; for blood, the corresponding figures were 0.003, 0.14, and 0.69, respectively. In individual patients, the results for marrow and blood showed good correlation. The biphasic decline of leukemic cell number suggests that most leukemic cells were sensitive to treatment and were rapidly killed, leaving behind a minor but substantial population of drug-resistant cells. The most likely explanation for this phenomenon is that these resistant cells were already present at diagnosis, their resistance having originated from genetic or epigenetic mutations during prior growth of the leukemic clone.

Minimal residual disease in childhood acute lymphoblastic leukaemia quantified by aspirate and trephine: is the disease multifocal?

The level of minimal residual disease (MRD) in marrow early in treatment strongly predicts outcome in childhood acute lymphoblastic leukaemia (ALL). Using PCR we studied 30 pairs of aspirates and trephines taken during induction treatment. Consensus PCR primers showed a monoclonal gene rearrangement in eight pairs, polyclonal rearrangement in 18 pairs and a monoclonal rearrangement only in the trephine in four pairs. MRD was quantified by leukaemia-specific primers in 22 pairs. There was a linear relationship between the logarithms of MRD levels of aspirate and trephine, with a residual variance which increased as the level of MRD fell. The mean level of MRD in the trephines was 4.1-fold greater than that in the aspirates, probably due to greater dilution of the aspirates with peripheral blood. The high variance at low levels of MRD could not be explained by measurement variation, which had an MRD-independent value of 0.42 log10 units, and was attributed to sampling variation due to patchiness of disease at low MRD levels. The magnitude of the variation was such that predictions of outcome could well be confounded for many patients. We suggest that MRD sampling variability could be minimized either by taking multiple marrow samples or by measuring MRD in peripheral blood.

Monitoring minimal residual disease in peripheral blood in B-lineage acute lymphoblastic leukaemia.

The use of peripheral blood rather than marrow has potential advantages for monitoring minimal residual disease during the treatment of leukaemia. To determine the feasibility of using blood, we used a sensitive polymerase chain reaction method to quantify leukaemia in the blood and marrow in 35 paired samples from 15 children during induction treatment. Leukaemic cells in the blood ranged from 1.1 x 10(-2) to < 9.4 x 10(-7) leukaemic cells/total cells, corresponding to 1.3 x 10(7) to < 2 x 10(3) leukaemic cells/l. In 15 paired samples, leukaemia could be quantified in both tissues and in 20 paired samples, leukaemia was not detected in one or both tissues so that only upper level limits could be set. In the former 15 pairs, the level of leukaemia in peripheral blood was directly proportional to that in marrow but was a mean of 11.7-fold lower. Leukaemia in blood was detected in 10/12 pairs in which the level in marrow was > 10(-4), but in only two of 13 pairs in which the level in marrow was < 10(-5). Patients studied at multiple time-points showed parallel declines in the number of leukaemic cells in both tissues. The results showed that leukaemia could be monitored in peripheral blood during induction therapy, and quantitative considerations based on the results suggest that monitoring of blood during post-induction therapy may be of value in detecting molecular relapse.

Effect of the Philadelphia chromosome on minimal residual disease in acute lymphoblastic leukemia.

The Philadelphia translocation is associated with a poor prognosis in adults and children with acute lymphoblastic leukemia, even though the majority of patients achieve remission. To test the hypothesis that the translocation leads to drug resistance in vivo, we studied 61 children and 20 adults with acute lymphoblastic leukemia and used the level of minimal residual disease at the end of induction as the measure of drug resistance in vivo. In children the presence of the translocation was associated with a significant increase in residual disease, indicating higher drug resistance in vivo; five of seven Philadelphia-positive children but only five of 54 Philadelphia-negative children had a minimal residual disease level >10(-3), a level which is associated with a high risk of relapse in childhood acute lymphoblastic leukemia of standard risk. By contrast, in adults, residual disease and hence drug resistance was already higher than in children, and the presence of the Philadelphia translocation in seven patients had no obvious additional effect. We conclude that the Philadelphia chromosome may increase resistance to drugs in vivo in children, but not detectably in adults.

The use of monoclonal gene rearrangement for detection of minimal residual disease in acute lymphoblastic leukemia of childhood.

Sensitive quantification of minimal residual disease (MRD) using the polymerase chain reaction (PCR) is strongly predictive of outcome in childhood acute lymphoblastic leukemia (ALL), with MRD levels at the end of induction therapy of >10(-3) predicting a poor outcome. Methods for sensitive quantification are, however, complicated and time-consuming. Detection by PCR of monoclonal immunoglobulin heavy chain (IgH) and T cell receptor (TCR) gene rearrangements is simple and can be used in routine laboratories but is non-quantitative and of lower but uncertain sensitivity. The aim of this study was to determine the value of detection of monoclonality in identification of different levels of MRD. We looked for monoclonality in 64 bone marrow aspirates which had been obtained from 31 patients with B lineage ALL at various times during induction therapy and for which levels of MRD had been determined by limiting dilution analysis using patient-specific PCR primers. Detection of monoclonality identified levels of MRD of > or =10(-3) during induction with a sensitivity of 78% and a specificity of 93%. The positive and negative predictive values were 0.86 and 0.88, respectively. The sensitivity of detection of a monoclonal IgH rearrangement was greater than that for the TCRgamma locus during induction as an IgH rearrangement was detected more often than a TCRgamma rearrangement in patients who had both IgH and TCRgamma rearrangement at diagnosis. Detection of monoclonality is therefore a simple and quick test applicable to the majority of patients with ALL and it may be useful in identifying high-risk patients at the end of induction and in identifying relapsing patients later during therapy.

A molecular and evolutionary study of the beta-globin gene family of the Australian marsupial Sminthopsis crassicaudata.

Beta-globin gene families in eutherians (placental mammals) consist of a set of four or more developmentally regulated genes which are closely linked and, in general, arranged in the order 5'-embryonic/fetal genes-adult genes-3'. This cluster of genes is proposed to have arisen by tandem duplication of ancestral beta-globin genes, with the first duplication occurring 200 to 155 MYBP just prior to a period in mammalian evolution when eutherians and marsupials diverged from a common ancestor. In this paper we trace the evolutionary history of the beta-globin gene family back to the origins of these mammals by molecular characterization of the beta-globin gene family of the Australian marsupial Sminthopsis crassicaudata. Using Southern and restriction analysis of total genomic DNA and bacteriophage clones of beta-like globin genes, we provide evidence that just two functional beta-like globin genes exist in this marsupial, including one embryonic-expressed gene (S.c-epsilon) and one adult-expressed gene (S.c-beta), linked in the order 5'-epsilon-beta-3'. The entire DNA sequence of the adult beta-globin gene is reported and shown to be orthologous to the adult beta-globin genes of the North American marsupial Didelphis virginiana and eutherian mammals. These results, together with results from a phylogenetic analysis of mammalian beta-like globin genes, confirm the hypothesis that a two-gene cluster, containing an embryonic- and an adult-expressed beta-like globin gene, existed in the most recent common ancester of marsupials and eutherians. Northern analysis of total RNA isolated from embryos and neonatals indicates that a switch from embryonic to adult gene expression occurs at the time of birth, coinciding with the transfer of the marsupial from a uterus to a pouch environment.

Molecular cytogenetic characterisation of a small ring X chromosome in a Turner patient and in a male patient with congenital abnormalities: role of X inactivation.

The association of small accessory marker chromosomes in man with specific abnormalities has been difficult to define owing to variations in the chromosome origin and the size of the markers. In a patient with typical Turner phenotype and a 45,X/46,X, + mar karyotype the marker was shown to be a small portion of the long arm of the X chromosome which included the centromere and XIST, a candidate gene for the X inactivation centre. Therefore the lack of any additional abnormalities was attributed to inactivation of the portion of the X chromosome in the marker. In a patient with a 47,XY, + mar karyotype the mar was a small ring X chromosome which did not contain the XIST gene. For both markers the short arm breakpoints were localised between UBE1 and DXS423E. The congenital abnormalities of the male patient were attributed to the lack of X inactivation of the small ring and therefore disomic expression of normal genes possessed by the marker.

The structure of the roof of the fourth ventricle in pigeon and chick brains by light and electron microscopy.

The hindbrains and meninges of the pigeon and chick have been examined by light and electron microscopy. Serial section histology of the skull with the brain and meninges intact has shown that the caudal end of the roof of the fourth ventricle consists of an extensive membranous pouch which projects caudally and dorsally into the subarachnoid space. Electron microscopy of selected areas of the membranous pouch in pigeon has shown it to consist of two components: ependymal cells and pial tissue. The membrane ependymal cells are squamous, adjacent cells being linked by intermediate junctions. At the junction with the surface of the medulla the ependymal cells are continuous with the ventricular ependyma, and at the choroid plexus they are continuous with the choroid plexus epithelium. These results are discussed in relation to the fluid spaces in and around the hindbrain.