A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings

"Sequencing-grade" screening for BRCA1 variants by oligo-arrays

The need for fast, efficient, and less costly means to screen genetic variants associated with disease predisposition led us to develop an oligo-nucleotide array-based process for gene-specific single nucleotide polymorphism (SNP) genotyping. This cost-effective, high-throughput strategy has high sensitivity and the same degree of accuracy as direct sequencing, the current gold standard for genetic screening. We used the BRCA1 breast and ovarian cancer predisposing gene model for the validation of the accuracy and efficiency of our strategy. This process could detect point mutations, insertions or deletions of any length, of known and unknown variants even in heterozygous conditions without affecting sensitivity and specificity. The system could be applied to other disorders and can also be custom-designed to include a number of genes related to specific clinical conditions. This system is particularly useful for the screening of long genomic regions with relatively infrequent but clinically relevant variants, while drastically cutting time and costs in comparison to high-throughput sequencing.

Leukocyte antigen and antibody detection assays: tools for assessing and preventing pulmonary transfusion reactions

Antibodies to neutrophil and HLA antigens can cause pulmonary transfusion reactions, and in some cases acute lung injury. When evaluating cases of pulmonary transfusion reactions, it is often necessary to test donors for neutrophil and HLA antibodies and also type the recipient for neutrophil and HLA antigens. A variety of enzyme-linked immunosorbent assay (ELISA) and flow cytometry-based solid phase assays are available to test for HLA class I and class II antibodies, but not neutrophil antibodies. Screening for neutrophil antibodies requires the preparation of panels of fresh neutrophils and testing in agglutination, immunofluorescence, or flow cytometry assays. Genotyping of HLA class I and II antigens is performed with a variety of sequence-specific primers, sequenced-specific oligonucleotide probe, and sequence-based typing assays. Neutrophil-specific antigens HNA-1a, -1b, -1c, -4a, and -5a can be genotyped, but not HNA-2a or -3a. Phenotyping of HNA-2a can be performed with CD177 monoclonal antibodies, but the gene encoding HNA-3a has not been identified, and the genomic basis for the HNA-2a-negative phenotype is not known. In conclusion, patients and donors involved with pulmonary transfusion reactions can be quickly typed for HLA antigens and tested for HLA antibodies, but testing for neutrophil antibodies and antigens requires the use of a reference laboratory.

Overview of melanoma vaccines and promising approaches

It is difficult to envision anything better than melanoma vaccines to exemplify the effectiveness of modern biotechnology in developing biologically rational therapeutics. Melanoma vaccines can reproducibly induce cytotoxic T lymphocyte (CTL) responses better than any other anticancer therapy. Anticancer vaccines have been labeled by some as ineffective for the simple reason that they only rarely lead to cancer regression. This oxymoron stems from the naïve expectation that CTLs are all that is needed to reject cancer. Little is known about requirements for CTL localization and effector function within the tumor microenvironment. In the future, more attention should be given to events downstream of immunization (afferent arm of immune response) to identify combination therapies likely to facilitate localization and activation of CTL at the receiving end (efferent arm).

SNP and Mutation Analysis

Genetic variation and SNP analysis starts with generation of sequence-specific signal, followed by the collection of that signal. The final step is extensive data analysis, which starts with conversion of quantifiable raw data and ends up with identified SNPs, frequencies, and sometimes tissue-specific expression patterns (levels). In this chapter we describe and compare the mechanisms of signal generation of several representative SNP analysis platforms. DNA microarray no doubt has its advantage in applications involving the classification and identification of tumor classes, gene discovery, drug dependent transcription mechanisms, as well as prediction of drug response. PCR, xMAP, invader assay, mass spectrometry, and pyrosequencing, on the other hand, are alternative methods of genotyping employed following the large scale screening and discovery of genetic variations. In addition, they offer higher specificity and sensitivity in analysis of both genomic DNA, as well as RNA. By exploiting these technologies, correlative study of the effects of putative genetic variations on cells, tissue-specific and developmentally specific expression is possible. Of extreme value are the many forms of Mass Spectrometry in the areas of sensitive, early cancer diagnosis. Finally, microarray and xMAP are suitable for protein analysis. While protein array offers higher throughput, xMAP is more amendable to the native 3D structure of protein molecules.

Vaccination with T cell-defined antigens

Tumour immunology encompasses a broad array of biological phenomena including interactions between neoplastic cells and the innate and adaptive immune response. Among immune cells, T cells have taken the centre stage because they can be easily demonstrated to specifically recognise autologous cancer cells. As most tumour-associated antigens are intracellular proteins, T cells appear to be the most suitable tool for cancer-specific attack, as antibodies do not cross the cell membrane and the innate immune response lacks the same level of specificity. Finally, the relative ease in which T cells can be educated through antigen-specific immunisation to recognise cancer cells has elevated them to an even higher stature. In this review, it will be argued that T cells represent a unique anticancer agent, characterised by absolute specificity. Although other therapeutic modalities (antibody-based) have been effectively implemented, a comparison of T cell-based approaches with other modalities goes beyond the purposes of this review and will not be included in the discussion. However, it is obvious that the role of the T cell is limited and other components of the immune response (effector mononuclear phagocytes, natural killer cells, cytokines, chemokines, soluble factors), genetic background and tumour heterogeneity are likely to be necessary for the completion of cancer rejection.

HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people

Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods-sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GF=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.

Understanding the response to immunotherapy in humans

Whether the efforts of the last decade aimed at the development of vaccines against tumor-specific antigens encountered success or failure is a matter of expectations. On the bright side, we could optimistically observe that anti-cancer-vaccines stand as an outstanding example of the successful implementation of modern biotechnology tools for the development of biologically sound therapeutics. In particular, vaccines against melanoma (the prototype model of tumor immunology in humans) can reproducibly induce cytotoxic T cell (CTL) responses exquisitely specific for cancer cells. This achievement trespasses the specificity of any other anti-cancer therapy. The skeptics, on the other end, might point out that immunization only rarely leads to cancer regression, labeling, therefore, this approach is ineffective. In our opinion this judgment stems from the naïve expectation that CTL induction is sufficient for an effective immune response. Here we propose that more needs to be understood about the mechanisms required for the induction of a therapeutically relevant immune response in humans. In particular, we will discuss the variables related to cancer heterogeneity, the weight of individual patients' polymorphism(s), the role of the T cell activation and differentiation and, finally, the complex relationship between immune and cancer cells within the tumor microenvironment.

From bench to clinic and back: Perspective on the 1st IQPC Translational Research conference

Translational Research (TR) provides a set of tools and communication context for scientists and clinicians to optimize the drug discovery and development process. In the proceedings of a Princeton conference on this timely topic, the strengths and needs of this developing field were debated. Outcomes and key points from these discussions are summarized in this article which covers the topics of defining what we mean by translational research (both theoretically and in operational terms), ways in which to engender the TR mindset and embed it in organizations such as the pharmaceutical industry in order to optimize the impact of available technologies (including imaging methods), the scientific basis and under-pinnings of TR including genomics knowledge, information sharing, as well as examples of application to drug discovery and development. Importantly, it should be noted that collaborations and communications between the stakeholders in this field, namely academia, industry and regulatory authorities, must be strengthened in order for the promise of TR to be delivered as better therapies to patients.

Active-specific immunization against melanoma: Is the problem at the receiving end?

The recent progress in tumor immunology is a striking example of the successful application of modern biotechnology to understand the complex phenomenon of immune-mediated cancer rejection. Tumor antigens were identified and successfully utilized in active immunization trials to induce tumor antigen-specific T cells. This achievement has left, however, clinicians and researchers perplexed by the paradoxical observation that immunization-induced T cells can recognize tumor cells in standard assays but cannot induce tumor regression. A closer look at T cell physiology and tumor biology suggests that this observation is not so surprising. Here, we argue that successful immunization is one of several steps required for tumor clearance while more needs to be understood about how T cells localize and are effective within a tumor microenvironment impervious to the execution of their effector function.

Pyrosequencing trade mark : A one-step method for high resolution HLA typing

While the use of high-resolution molecular typing in routine matching of human leukocyte antigens (HLA) is expected to improve unrelated donor selection and transplant outcome, the genetic complexity of HLA still makes the current methodology limited and laborious. Pyrosequencing™ is a gel-free, sequencing-by-synthesis method. In a Pyrosequencing reaction, nucleotide incorporation proceeds sequentially along each DNA template at a given nucleotide dispensation order (NDO) that is programmed into a pyrosequencer. Here we describe the design of a NDO that generates a pyrogram unique for any given allele or combination of alleles. We present examples of unique pyrograms generated from each of two heterozygous HLA templates, which would otherwise remain cis/trans ambiguous using standard sequencing based typing (SBT) method. In addition, we display representative data that demonstrate long read and linear signal generation. These features are prerequisite of high-resolution typing and automated data analysis. In conclusion Pyrosequencing is a one-step method for high resolution DNA typing.

Polymorphism in clinical immunology - From HLA typing to immunogenetic profiling

The pathology of humans, in contrast to that of inbred laboratory animals faces the challenge of diversity addressed in genetic terms as polymorphism. Thus, unsurprisingly, treatment modalities that successfully can be applied to carefully-selected pre-clinical models only sporadically succeed in the clinical arena. Indeed, pre-fabricated experimental models purposefully avoid the basic essence of human pathology: the uncontrollable complexity of disease heterogeneity and the intrinsic diversity of human beings. Far from pontificating on this obvious point, this review presents emerging evidence that the study of complex system such as the cytokine network is further complicated by inter-individual differences dictated by increasingly recognized polymorphisms. Polymorphism appears widespread among genes of the immune system possibly resulting from an evolutionary adaptation of the organism facing an ever evolving environment. We will refer to this high variability of immune-related genes as immune polymorphism. In this review we will briefly highlight the possible clinical relevance of immune polymorphism and suggest a change in the approach to the study of human pathology, from the targeted study of individual systems to a broader view of the organism as a whole through immunogenetic profiling.