Despite developments in targeted gene sequencing and whole-genome analysis techniques, the robust detection of all genetic variation, including structural variants, in and around genes of interest and in an allele-specific manner remains a challenge. Here we present targeted locus amplification (TLA), a strategy to selectively amplify and sequence entire genes on the basis of the crosslinking of physically proximal sequences. We show that, unlike other targeted re-sequencing methods, TLA works without detailed prior locus information, as one or a few primer pairs are sufficient for sequencing tens to hundreds of kilobases of surrounding DNA. This enables robust detection of single nucleotide variants, structural variants and gene fusions in clinically relevant genes, including BRCA1 and BRCA2, and enables haplotyping. We show that TLA can also be used to uncover insertion sites and sequences of integrated transgenes and viruses. TLA therefore promises to be a useful method in genetic research and diagnostics when comprehensive or allele-specific genetic information is needed.

Purpose: To predict the invasiveness of urothelial bladder carcinoma using a logistic regression model on preoperative peripheral blood samples. Patients and Methods: Hospital data of patients operated for urothelial carcinoma were reviewed retrospectively. Preoperative blood samples were collected before the first cystoscopic examination. Any kind of infection or inflammation was an exclusion criterion. Patients were grouped as having a non-muscle-invasive or muscle-invasive urothelial carcinoma. The mean age was 69 years and was determined as the cut-off value. According to receiver operating characteristic curves, threshold points were determined for lymphocytes, neutrophil count, neutrophil-to-lymphocyte ratio (NLR), thrombocytes and mean platelet volume. Demographic specialties, parameters obtained from blood samples, tumor size and multiplicity were evaluated and significant parameters were put into a logistic regression model. Results: The study group consisted of 80 non-muscle-invasive and 102 muscle-invasive patients. Age (≤69 vs. >69), female gender, NLR (2.57), mean platelet volume (7.9/fl) and platelet count (400,000/µl) were significant parameters and put in a model. Using odds ratios, the probability of tumor invasiveness was calculated by a formula. Conclusion: Age, female gender, NLR and platelet count were found to be the predictors of invasiveness of urothelial carcinoma.

This study examined the diagnostic accuracy of nine indices to discriminate between patients with mild-to-moderate (haemoglobin 8.5 -11 g/dl) or moderateto-severe (haemoglobin < 8.

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In routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens.

Transporter associated with antigen presenting (TAP) 1 and TAP2 genes are localized in the major histocompatability complex (MHC) class II region and form a heterodimer playing a key role in endogenous pathways for antigen presentation. Defects of these genes have been reported to be common in different types of cancer. Polymorphisms identified in these loci have also been investigated and reported to be associated with several autoimmune disorders, viral infections and neoplasms. In the present study, for the first time, the allele and genotype frequencies of TAP1-333, TAP2-565, TAP2-651 and TAP2-665 were determined in patients with hematological malignancies (HM) using a PCR-RFLP method and compared with the frequencies in the control group. Our results suggested an association of TAP1-333 polymorphism with multiple myeloma-MM and TAP2-565 polymorphism with chronic lymphoid leukemia-CLL. In addition, it could be concluded that the TAP2-665 GG genotype might be a risk factor for all types of hematological malignancies included in this study.

Background: Metastases to the parotid and thyroid glands from breast cancer are rare and have a poor prognosis. Case Report: We present the case of a patient with breast carcinoma and synchronous involvement of both the parotid and thyroid gland, and review the literature on this subject. Conclusion: Metastatic malignancy in clinically suspect thyroid and parotid nodules could be detected more frequently with routine use of fine needle aspiration biopsy.

Multiplex TLA shows promising results as an acute leukemia screening test. It can detect cryptic and other translocations in selected genes. Further optimization may make this assay suitable for diagnostic use.