Use Of Multiple Markers Research Articles

Only a single implanted marker is needed for tracking lung cancers for IGRT

Only a single implanted marker is needed for tracking lung cancers for IGRT

The diagnosis of Sézary syndrome on peripheral blood by flow cytometry requires the use of multiple markers

The diagnosis of Sézary syndrome on peripheral blood by flow cytometry requires the use of multiple markers

Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura)

Cospeciation between hosts and parasites offers a unique opportunity to use information from parasites to infer events in host evolutionary history. Although lice (Insecta: Phthiraptera) are known to cospeciate with their hosts and have frequently served as important markers to infer host evolutionary history, most molecular studies are based on only one or two markers. Resulting phylogenies may, therefore, represent gene histories (rather than species histories), and analyses of multiple molecular markers are needed to increase confidence in the results of phylogenetic analyses. Herein, we phylogenetically examine nine molecular markers in primate sucking lice (Phthiraptera: Anoplura) and we use these markers to estimate divergence times among louse lineages. Individual and combined analyses of these nine markers are, for the most part, congruent, supporting relationships hypothesized in previous studies. Only one marker, the nuclear protein-coding gene Histone 3, has a significantly different tree topology compared to the other markers. The disparate evolutionary history of this marker, however, has no significant effect on topology or nodal support in the combined phylogenetic analyses. Therefore, phylogenetic results from the combined data set likely represent a solid hypothesis of species relationships. Additionally, we find that simultaneous use of multiple markers and calibration points provides the most reliable estimates of louse divergence times, in agreement with previous studies estimating divergences among species. Estimates of phylogenies and divergence times also allow us to verify the results of [Reed, D.L., Light, J.E., Allen, J.M., Kirchman, J.J., 2007. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5, 7.]; there was probable contact between gorilla and archaic hominids roughly 3 Ma resulting in a host switch of Pthirus lice from gorillas to archaic hominids. Thus, these results provide further evidence that data from cospeciating organisms can yield important information about the evolutionary history of their hosts.

The diagnosis of Sézary syndrome on peripheral blood by flow cytometry requires the use of multiple markers

Diagnosis of Sézary syndrome (SS)-defining blood involvement is hampered by the lack of Sézary cell-specific markers and nonspecific morphology of the tumour cells. To identify the most reliable and easy to use markers for the diagnosis of SS-defining blood involvement. We studied 17 patients with SS and 11 control patients. We used flow cytometry for the detection of T-cell antigens (CD3, CD4, CD7 and CD8), expression of the Sézary cell-associated marker CD158k and T-cell receptor (TCR)-Vbeta chain. Additionally, Sézary cells were identified by peripheral blood smear for lymphocytes with cerebriform nuclei. It was not possible to diagnose blood involvement in all patients with SS by a single marker or method, although none of the markers was increased in the control population. Sézary cells were detected by blood smears in 13 of 17 (76%), by flow cytometry by their CD4+ CD7- CD3(dim) phenotype (> 1000 cells microL(-1)) in 13 of 17 (76%) and by expression of CD158k in 11 of 17 (65%) patients with SS. A specific T-cell clone was identified by identical TCR-Vbeta chain expression in 12 of 17 (71%) patients with SS. The identification of Sézary cells in individual patients varied for the different markers investigated. The combination of identifying CD4+ CD7- CD3(dim) cells, TCR-Vbeta chain and CD158k expression allowed a definite identification of SS-defining blood involvement in every individual patient. All of these markers can be measured by flow cytometry which would avoid time-consuming analysis of blood smears. These markers would also be suitable to monitor tumour cell load during therapy.

Nutrition Support in Burns—Is there Consistency in Practice?

Nutrition support is an integral part of the multidisciplinary management of a burn. However, the large body of research has lead to some confusion regarding optimal feeding practices. This review examines nutrition support practices in six United States (U.S.) and seven Australian burns units and compares practice to common themes and options in the literature. The review focuses on the consistency of practice in: managing the hormonal and metabolic changes resulting from a burn injury and their relationship to nutrition; techniques of estimating energy requirements; changes in macronutrient requirements; the use of specialized immune enhancing nutrition; methods of optimizing nutrition support; and methods of monitoring nutritional status and progress. In general, dietitians had a good understanding of the hypermetabolic response and increased nutritional requirements of burns patients. There were several areas where consistency was not seen, such as the fat and carbohydrate content of enteral formulas, the indications for use of total parenteral nutrition, the use of immunonutrition in enteral nutrition, and the most appropriate strategies for peri-operative feeding. This is a reflection of inconclusive research outcomes. There was more consistency in the techniques used for estimation of energy requirements, although more widespread use of indirect calorimetry would be beneficial. The need for high energy and high protein enteral feeds was also recognized across all units studied. The limitations of common nutritional markers was understood and managed by the use of multiple markers.

Multiple-marker screening for Down's syndrome: a method of assessing the statistical robustness of proposed tests

Antenatal screening for Down's syndrome relies on the use of multiple markers in combination. Markers that are highly correlated can cause statistical instability. We used the maximum variance inflation factor (VIF(max)) to determine whether a screening test using multiple markers was robust to imprecision in the estimation of the marker distribution parameters. The VIF(max) for a specified screening test was calculated from the correlations between markers in Down's syndrome pregnancies for six tests: integrated and serum integrated tests without repeat measurements, both tests with repeat measurements across trimesters analysed in the standard way, and both tests with repeat measurements analysed as cross-trimester (CT) marker ratios. The screening performance of each test using published parameter values, in terms of the false-negative rates for a 3% false-positive rate (FN(3)), were calculated for simulated populations with medians 0.2 standard deviations (SD) higher or lower than the published values (to reflect imprecision in parameter estimation) for pregnancy-associated plasma protein A and unconjugated oestriol in affected pregnancies. For each test, the VIF(max) value was compared with the coefficient of variation of the FN(3) (FN(3) CV). An independent set of 27 Down's syndrome pregnancies was used to determine how many had meaningless low risks (<1 in 10,000) with each test. Tests with VIF(max) values greater than 5 had FN(3)CV values over 50%, but those with VIF(max) values less than 5 had FN(3) CV values less than 21%. The numbers of Down's syndrome pregnancies with meaningless low risk estimates in the independent set were 18 (64%) in tests with VIF(max) values > or =5 and none for those with values <5. VIF(max) values of 5 or more suggest instability. The tests using CT marker ratios were stable (VIF(max) < 3), but the tests using repeat measurements in the standard manner were not (VIF(max) > 5).

Markers for Microscopic Imaging of Lymphangiogenesis and Angiogenesis

Imaging of lymphangiogenesis and angiogenesis requires robust and unambiguous markers of lymphatic and blood vessels. Although much progress has been made in recent years in identifying molecules specifically expressed on lymphatic and blood vessels, no perfect marker has been found that works reliably in all species, tissues, vascular beds, and in all physiological and pathologic conditions. The heterogeneity of expression of markers in both blood and lymphatic vessels reflects underlying differences in the phenotype of endothelial cells. Use of only one marker can lead to misleading interpretations, but these pitfalls can usually be avoided by use of multiple markers and three-dimensional whole-mount preparations. LYVE-1, VEGFR-3, Prox1, and podoplanin are among the most useful markers for microscopic imaging of lymphatic vessels, but, depending on histologic location, each marker can be expressed by other cell types, including vascular endothelial cells. Other markers, including CD31, junctional proteins, and receptors, such as VEGF-2, are shared by lymphatic and blood vessels.

Quality performance of newborn screening systems: Strategies for improvement

Newborn metabolic screening is a public health activity with the potential to realize significant health gains for infants affected with a range of congenital conditions. Many of these are inborn errors of metabolism. The activities required to achieve the gains are diverse and carried out by a number of organizations, by families and by many health care professionals. Laboratories have the best-developed quality strategies, which include quality assurance programmes, guidelines, protocols and standards. Two-tier testing and use of multiple markers improve sensitivity and specificity. There are international initiatives to harmonize assay materials and definitions to allow better benchmarking between programmes. Outside the laboratory, standards, education and protocols improve the quality of specimen collection, diagnosis and treatment, which together produce the health gains.

Insights on speciation patterns in the genus Iberochondrostoma (Cyprinidae): Evidence from mitochondrial and nuclear data

In this paper, the patterns of cladogenesis in the cyprinid fish genus Iberochondrostoma were analysed using a mitochondrial (cytochrome b) and a nuclear (beta-actin) gene fragment. The two genes yielded discordant results. While the cytochrome b gene yielded a fully dichotomous tree, where all species of the genus are monophyletic, the much slower beta-actin gene yielded star-like relationships. However, when information from both genes was considered together, the data suggested the persistence of a very large central unit from which at least two peripheral clades arose at different times. This pattern which is akin to peripatric speciation was shown to be compatible with the paleogeographical information available. It is suggested that combining the techniques of phylogeny and phylogeography and the use of multiple markers varying in their rate of evolution may enrich our understanding of speciation and evolution of clades beyond species level.

Multiple biomarkers in molecular oncology. II. Molecular diagnostics applications in breast cancer management

In recent years, the application of genomic and proteomic technologies to the problem of breast cancer prognosis and the prediction of therapy response have begun to yield encouraging results. Independent studies employing transcriptional profiling of primary breast cancer specimens using DNA microarrays have identified gene expression profiles that correlate with clinical outcome in primary breast biopsy specimens. Recent advances in microarray technology have demonstrated reproducibility, making clinical applications more achievable. In this regard, one such DNA microarray device based upon a 70-gene expression signature was recently cleared by the US FDA for application to breast cancer prognosis. These DNA microarrays often employ at least 70 gene targets for transcriptional profiling and prognostic assessment in breast cancer. The use of PCR-based methods utilizing a small subset of genes has recently demonstrated the ability to predict the clinical outcome in early-stage breast cancer. Furthermore, protein-based immunohistochemistry methods have progressed from using gene clusters and gene expression profiling to smaller subsets of expressed proteins to predict prognosis in early-stage breast cancer. Beyond prognostic applications, DNA microarray-based transcriptional profiling has demonstrated the ability to predict response to chemotherapy in early-stage breast cancer patients. In this review, recent advances in the use of multiple markers for prognosis of disease recurrence in early-stage breast cancer and the prediction of therapy response will be discussed.

Genetic differentiation and history of populations of the Italian treefrog Hyla intermedia: lack of concordance between mitochondrial and nuclear markers

The genetic differentiation among 33 populations of the Italian treefrog, Hyla intermedia (Anura: Hylidae), was investigated using both biparentally (23 allozyme loci) and maternally (partial mitochondrial cytochrome b gene) inherited markers. Two main population groups were evidenced by both markers, located north and south of the northern Apennines. However, the pattern of differentiation between these two groups was much less pronounced at allozymes than at mtDNA, leading to gene flow estimates that were 25 times lower at mitochondrial than at nuclear level. Also, the mtDNA divergence between the two groups was particularly marked for two cospecific lineages of anuran amphibians (the P-distance being on average 9.04%), while their average genetic distance at allozymes was comparatively low (D (NEI) = 0.07). This contrasting pattern of nuclear versus mitochondrial genetic variation is discussed in the context of: (1) marker specific selection, (2) secondary contact and sex-biased gene flow and (3) ancestral polymorphism and colonization from north to south. Finally we emphasize how, for population genetic studies, the use of multiple markers having distinct evolutionary properties can help unravel the existence of more complex evolutionary histories.

Estimation of the day‐specific probabilities of conception: current state of the knowledge and the relevance for epidemiological research

Conception, as defined by the fertilisation of an ovum by a sperm, marks the beginning of human development. Currently, a biomarker of conception is not available; as conception occurs shortly after ovulation, the latter can be used as a proxy for the time of conception. In the absence of serial ultrasound examinations, ovulation cannot be readily visualised leaving researchers to rely on proxy measures of ovulation that are subject to error. The most commonly used proxy measures include: charting basal body temperature, monitoring cervical mucus, and measuring urinary metabolites of oestradiol and luteinising hormone. Establishing the timing of the ovulation and the fertile window has practical utility in that it will assist couples in appropriately timing intercourse to achieve or avoid pregnancy. Identifying the likely day of conception is clinically relevant because it has the potential to facilitate more accurate pregnancy dating, thereby reducing the iatrogenic risks associated with uncertain gestation. Using data from prospective studies of couples attempting to conceive, several researchers have developed models for estimating the day-specific probabilities of conception. Elucidating these will allow researchers to more accurately estimate the day of conception, thus spawning research initiatives that will expand our current limited knowledge about the effect of exposures at critical periconceptional windows. While basal body temperature charting and cervical mucus monitoring have been used with success in field-based studies for many years, recent advances in science and technology have made it possible for women to get instant feedback regarding their daily fertility status by monitoring urinary metabolites of reproductive hormones in the privacy of their own homes. Not only are innovations such as luteinising hormone test kits and digital fertility monitors likely to increase study compliance and participation rates, they provide valuable prospective data that can be used in epidemiological research. Although we have made great strides in estimating the timing and length of the fertile window, more work is needed to elucidate the day-specific probabilities of conception using proxy measures of ovulation that are inherently subject to error. Modelling approaches that incorporate the use of multiple markers of ovulation offer great promise to fill these important data gaps.

Quantitative Analysis of the Relationship between Intra- Axonal Neurofilament Compaction and Impaired Axonal Transport following Diffuse Traumatic Brain Injury

Traumatic axonal injury (TAI) following traumatic brain injury (TBI) contributes to morbidity and mortality. TAI involves intra-axonal changes assumed to progress to impaired axonal transport (IAT), disconnection, and axonal bulb formation. Immunocytochemical studies employing antibodies to amyloid precursor protein (APP), a marker of IAT and RMO14, a marker of neurofilament compaction (NFC), have shown that TAI involves both NFC and IAT, with the suggestion that NFC leads to IAT. Recently, new data has suggested that NFC may occur independently of IAT. The objective of this study was to determine quantitatively the precise relationship between NFC and IAT. Following TBI, rats were studied at 30 min, 3 h, and 24 h. Using single-label immunocytochemistry employing the antibodies RM014, APP, or a combined labeling strategy targeting APP/RMO14 in aggregate, the immunoreactive (IR) profiles were counted in the corticospinal tract (CSpT) and medial lemniscus (ML). In the CSpT, the number of axons demonstrating RMO14-IR approximated the number of axons showing APP-IR, with the APP-IR population showing a significant increase over 24 h (p < 0.05). The sum of both single-label counts equaled the aggregate APP/RMO14 numbers, demonstrating little relationship between NFC and IAT. In the ML, 75% of fibers demonstrated a separation of APP-IR and NFC-IR; however, 25% of the ML fibers showed co-localization of APP-IR and RMO14. The results of these studies indicate that, in the majority of damaged axons, NFC is not associated with IAT. Our findings argue for the use of multiple markers when evaluating the extent of TAI or the efficacy of therapies targeting the treatment of TAI.

Prediction of preeclampsia: can it be achieved?

In this review, the various biochemical tests that have been proposed for the prediction of preeclampsia are described and evaluated. Placenta hormone markers do not predict future disease. They denounce the early placental changes that are part of the evolving disease and only predict the imminent of preeclamptic syndrome. This explains why tests are better predictors when preeclampsia supervenes shortly, and why screening in the first trimester is unlikely to work as well as in the second trimester. The use of multiple markers in the screening should reflect different aspects of the disease process and could increase the specificity and sensitivity of the screening and work on different etiologic factors. The possible use of second-trimester biochemical screening to predict the risk of preeclampsia remains to be investigated in the high-risk population. Obstetricians & Gynecologists, Family Physicians After completion of this article, the reader should be able to list the various theories on the etiology of preeclampsia, to relate the various risk factors for the development of preeclampsia, and to describe the various screening tests for preeclampsia.

Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis.

Advanced-stage epithelial ovarian cancer has a poor prognosis with long-term survival in less than 30% of patients. When the disease is detected in stage I, more than 90% of patients can be cured by conventional therapy. Screening for early-stage disease with individual serum tumor markers, such as CA125, is limited by the fact that no single marker is up-regulated and shed in adequate amounts by all ovarian cancers. Consequently, use of multiple markers in combination might detect a larger fraction of early-stage ovarian cancers. To identify potential candidates for novel markers, we have used Affymetrix human genome arrays (U95 series) to analyze differences in gene expression of 41,441 known genes and expressed sequence tags between five pools of normal ovarian surface epithelial cells (OSE) and 42 epithelial ovarian cancers of different stages, grades, and histotypes. Recursive descent partition analysis (RDPA) was performed with 102 probe sets representing 86 genes that were up-regulated at least 3-fold in epithelial ovarian cancers when compared with normal OSE. In addition, a panel of 11 genes known to encode potential tumor markers [mucin 1, transmembrane (MUC1), mucin 16 (CA125), mesothelin, WAP four-disulfide core domain 2 (HE4), kallikrein 6, kallikrein 10, matrix metalloproteinase 2, prostasin, osteopontin, tetranectin, and inhibin] were similarly analyzed. The 3-fold up-regulated genes were examined and four genes [Notch homologue 3 (NOTCH3), E2F transcription factor 3 (E2F3), GTPase activating protein (RACGAP1), and hematological and neurological expressed 1 (HN1)] distinguished all tumor samples from normal OSE. The 3-fold up-regulated genes were analyzed using RDPA, and the combination of elevated claudin 3 (CLDN3) and elevated vascular endothelial growth factor (VEGF) distinguished the cancers from normal OSE. The 11 known markers were analyzed using RDPA, and a combination of HE4, CA125, and MUC1 expression could distinguish tumor from normal specimens. Expression at the mRNA level in the candidate markers was examined via semiquantitative reverse transcription-PCR and was found to correlate well with the array data. Immunohistochemistry was performed to identify expression of the genes at the protein level in 158 ovarian cancers of different histotypes. A combination of CLDN3, CA125, and MUC1 stained 157 (99.4%) of 158 cancers, and all of the tumors were detected with a combination of CLDN3, CA125, MUC1, and VEGF. Our data are consistent with the possibility that a limited number of markers in combination might identify >99% of epithelial ovarian cancers despite the heterogeneity of the disease.

A novel rapid single nucleotide polymorphism (SNP)–based method for assessment of hematopoietic chimerism after allogeneic stem cell transplantation

AbstractA major end point of nonmyeloablative hematopoietic stem cell transplantation is the attainment of either mixed chimerism or full donor hematopoiesis. Because the majority of human genetic disparity is generated by single nucleotide polymorphisms (SNPs), direct measurement of SNPs should provide a robust tool for the detection and quantitation of chimerism. Using pyrosequencing, a rapid quantitative sequencing technology, we developed a SNP-based assay for hematopoietic chimerism. Based on 14 SNPs with high allele frequencies, we were able to identify at least 1 informative SNP locus in 55 patients with HLA-identical donors. The median number of informative SNPs in related pairs was 5 and in unrelated pairs was 8 (P< .0001). Assessment of hematopoietic chimerism in posttransplantation DNA was shown to be quantitative, accurate, and highly reproducible. The presence of 5% donor cells was reliably detected in replicate assays. Compared with current measures of engraftment based on identification of short tandem repeats (STRs), variable number of tandem repeats (VNTRs), or microsatellite polymorphisms, this SNP-based method provides a more rapid and quantitative assessment of chimerism. A large panel of SNPs enhances the ability to identify an informative marker in almost all patient/donor pairs and also facilitates the simultaneous use of multiple markers to improve the statistical validity of chimerism measurements. The inclusion of SNPs that encode minor histocompatibility antigens or other genetic polymorphisms that may influence graft-versus-host disease or other transplantation outcomes can provide additional clinically relevant data. SNP-based assessment of chimerism is a promising technique that will assist in the analysis of outcomes following transplantation.

The Alpha Dx POINT-OF-NEED System

The Alpha Dx POINT-OF-NEED System

The Evaluation of Multiple Surrogate Endpoints

Surrogate endpoints are desirable because they typically result in smaller, faster efficacy studies compared with the ones using the clinical endpoints. Research on surrogate endpoints has received substantial attention lately, but most investigations have focused on the validity of using a single biomarker as a surrogate. Our paper studies whether the use of multiple markers can improve inferences about a treatment's effects on a clinical endpoint. We propose a joint model for a time to clinical event and for repeated measures over time on multiple biomarkers that are potential surrogates. This model extends the formulation of Xu and Zeger (2001, in press) and Fawcett and Thomas (1996, Statistics in Medicine 15, 1663-1685). We propose two complementary measures of the relative benefit of multiple surrogates as opposed to a single one. Markov chain Monte Carlo is implemented to estimate model parameters. The methodology is illustrated with an analysis of data from a schizophrenia clinical trial.

Hepatic fibrosis: are any of the serum markers useful?

There is a clinical need for noninvasive measurement of liver fibrosis both to diagnose significant liver fibrosis and to monitor the effects of therapy on fibrogenesis and fibrolysis. Multiple clinical markers have been evaluated over the years, and as our understanding of the molecular process of liver scarring has advanced, newer markers have appeared. Serum markers include extracellular matrix proteins such as the N-terminal propeptide of collagen III, hyaluronan, YKL-40, laminin, metalloproteinases, and their inhibitors. Use of multiple markers has led to 90% sensitivity in diagnosing cirrhosis, but specificity is variable at about 60%. Automated systems to measure these markers are under development and are being evaluated for their ability to monitor fibrosis during and after therapy in multiple liver diseases, including hepatitis B and C. Although no individual fibrosis marker is clinically applicable today, we foresee a future in which monitoring fibrosis markers will replace sequential liver biopsy as a standard of care.

Quantitative trait locus mapping based on selective DNA pooling

Concepts of a simple method to map quantitative trait loci (QTL) based on selective DNA pooling in half-sib family, backcross, and F2 designs were developed. It is shown that the position of a QTL can be estimated from differences in allele frequencies for two flanking markers between individuals with high and low phenotypes and does not depend on the phenotypic means of the selected groups. An estimate of the QTL effect was obtained by relating group differences in phenotypic means to differences in QTL frequencies, which can be estimated from the QTL position and marker allele frequencies. Simulation of a half-sib family and a F2 family of 2000 individuals showed that the method gives close to unbiased results when power is high. Biases increased when measurement errors on marker allele frequencies increased and when the effect of the QTL was small. Similarities of QTL mapping based on selective DNA pooling data and on individual genotyping data are discussed, as are opportunities to extend the selective DNA pooling method to the use of multiple markers and multiple half-sib family designs. This study shows that the use of selective DNA pooling can be extended from the detection of marker associations to the mapping of QTL. Selective DNA pooling can greatly reduce the number of genotypings required.