Bead-linked transposomes enable a normalization-free workflow for NGS library preparation.

BACKGROUND: Transposome-based technologies have enabled the streamlined production of sequencer-ready DNA libraries; however, current methods are highly sensitive to the amount and quality of input nucleic acid. RESULTS: We describe a new library preparation technology (Nextera DNA Flex) that utilizes a known concentration of transposomes conjugated directly to beads to bind a fixed amount of DNA, and enables direct input of blood and saliva using an integrated extraction protocol. We further report results from libraries generated outside the standard parameters of the workflow, highlighting novel applications for Nextera DNA Flex, including human genome builds and variant calling from below 1 ng DNA input, customization of insert size, and preparation of libraries from short fragments and severely degraded FFPE samples. Using this bead-linked library preparation method, library yield saturation was observed at an input amount of 100 ng. Preparation of libraries from a range of species with varying GC levels demonstrated uniform coverage of small genomes. For large and complex genomes, coverage across the genome, including difficult regions, was improved compared with other library preparation methods. Libraries were successfully generated from amplicons of varying sizes (from 50 bp to 11 kb), however, a decrease in efficiency was observed for amplicons smaller than 250 bp. This library preparation method was also compatible with poor-quality DNA samples, with sequenceable libraries prepared from formalin-fixed paraffin-embedded samples with varying levels of degradation. CONCLUSIONS: In contrast to solution-based library preparation, this bead-based technology produces a normalized, sequencing-ready library for a wide range of DNA input types and amounts, largely obviating the need for DNA quantitation. The robustness of this bead-based library preparation kit and flexibility of input DNA facilitates application across a wide range of fields.

Novel therapeutic approaches in polycythemia vera.

Polycythemia vera (PV) is the most common Philadelphia chromosome-negative myeloproliferative neoplasm. Whereas low-risk patients are treated with aspirin and phlebotomy, high-risk patients receive cytoreductive therapy, which most commonly consists of hydroxyurea in the United States. Concerns about the long-term safety of hydroxyurea, as well as a desire for more efficacious and targeted therapy, have led to the development of novel therapies for high-risk patients with PV. Pegylated interferon (IFN) has shown promise in phase 2 studies of PV, and preliminary data from ongoing phase 3 studies suggest noninferiority as a frontline therapy. Efficient count control, tolerability, and even molecular responses as a salvage therapy have been demonstrated. Ropeginterferon-α-2b, a monopegylated IFN with a longer half-life and less frequent dose interval compared with recombinant or pegylated IFN, is an impressive agent in development. Ruxolitinib has a proven role as second-line therapy for PV, but an ongoing trial combining ruxolitinib and IFN as salvage therapy is under way. Early-phase clinical trials have also suggested that MDM2 inhibitors such as idasanutlin and histone deacetylase inhibitors should continue in their development. If these novel agents are able to modify the natural history of PV, the treatment paradigm in newly diagnosed patients will evolve from risk-adapted or reactive treatment toward early interventions.

3 mm can save your case: Making beauty function.

Understanding esthetic design is not enough if restorations are to withstand the forces of function. Dentists also must understand the relationships of incisal tables, the interincisal angle, disclusion forces, and the implications of changing those parameters when restoring the anterior dentition. While canine-protected occlusion is often a goal, it may not always be appropriate or attainable. This article describes the details of creating a functional anterior design that will not only be beautiful but will have the best chance of withstanding parafunctional activity and abnormal force.

Polycythemia Vera-Associated Complications: Pathogenesis, Clinical Manifestations, And Effects On Outcomes.

Polycythemia vera is a Philadelphia-negative chronic myeloproliferative neoplasm, characterized by erythrocytosis, which is unique, compared to essential thrombocytosis and primary myelofibrosis. Though longevity can usually be expected, vascular morbidity is associated with this condition, as well as a propensity to evolve into myelofibrosis (post-PV MF) and acute myeloid leukemia. In addition, patients can have a pronounced symptom burden. Herein, contributors to the symptomatic burden, as well as the thrombotic and transformative tendencies are reviewed. From a symptom perspective, some are explained by cytokine release, others by microvascular complications, whereas certain symptoms can herald disease evolution. Thrombosis has multifactorial contributors, including but not limited to gender, and inflammatory stress; investigators have recently hypothesized that microparticles and Neutrophil Extracellular Trap Formations may add to thrombotic burden. Finally, we examine the progression to post-PV MF as well as leukemic transformation, highlighting well-established risk factors including age and leukocytosis, certain treatments, and the presence of "non-driver" mutations.

Therapy-associated leukemic transformation in myeloproliferative neoplasms - What do we know?

Myeloproliferative Neoplasms (MPNs) are a group of progressive diseases that share a common pathogenesis, clinical and laboratory features, as well as a spontaneous risk of secondary AML. Certain MPN therapies have been associated with an increased risk of leukemic conversion, with robust data highlighting the highest rates with 32P, chlorambucil, and pipobroman. Herein, we review risk factors for leukemic transformation, including therapy-related MPN-BP, with a focus on the debate surrounding the potential leukemogenicity of hydroxyurea. Lastly, we discuss emerging studies on the association between ruxolitinib and high grade B-cell lymphomas. We conclude that statistical associations have not implicated hydroxyurea monotherapy as leukemogenic. However, it is difficult to definitely disprove an association, as large prospective, controlled studies with decades of follow-up would be needed to draw conclusions. Overall, the concept of therapy-related neoplasms remains important to the field, and mandates judicious selection and sequencing of therapies for MPN patients.

Splanchnic Vein Thrombosis in the Myeloproliferative Neoplasms.

PURPOSE OF REVIEW: To review the epidemiology, diagnostic challenges, pathogenesis, and treatment strategies for patients with myeloproliferative neoplasm-associated splanchnic vein thrombosis. RECENT FINDINGS: The epidemiology of myeloproliferative neoplasm-associated splanchnic vein thrombosis (MPN-SVT) has been well characterized. While typical MPN-associated thrombosis affects older patients and involves the arterial circulation, MPN-SVT mostly impacts younger women. An association with JAK2 V617F is well-known; recent studies have demonstrated only a weak association with CALR mutations. JAK inhibition may represent a novel treatment strategy, complementing anticoagulation, and management of portal hypertension. While the epidemiology has been well characterized, more work is needed to identify novel contributors to disease pathogenesis, beyond the JAK2 V617F mutation itself, and endothelial compromise. Testing for MPN mutations in the setting of non-cirrhotic SVT is commonplace; JAK2 V617F is the most likely to be identified. Testing for CALR or MPL mutations requires clinical judgement, though not unreasonable. The mainstay of therapy is indefinite anticoagulation; the role of direct oral anticoagulants is unclear. JAK inhibition may play a role in addressing associated splenomegaly and portal hypertension.

Contemporary Use of Interferon Therapy in the Myeloproliferative Neoplasms.

PURPOSE OF REVIEW: The purpose of this article is to review the current evidence behind interferon therapy in patients with myeloproliferative neoplasms. RECENT FINDINGS: Preliminary analysis suggests that interferon may be non-inferior to hydroxyurea in patients with polycythemia vera and essential thrombocytosis. Responses have been observed regardless of JAK2 mutational status, but the presence of non-JAK2 somatic mutations may negatively influence response rates. Pegylated interferon has proven efficacy for patients with myeloproliferative neoplasms. Both newly diagnosed and previously treated patients with polycythemia vera and essential thrombocytosis exhibit high hematologic response rates, and some of these patients achieve molecular responses as well. Interferon therapy leads to lower rates of hematologic response in MF patients, but patients earlier on in their disease course have a better chance of responding. There are ongoing trials comparing pegylated interferon to hydroxyurea in essential thrombocytosis (ET) and polycythemia vera (PV), and early analysis suggests non-inferiority. However, longer follow-up is needed before drawing any conclusions. Future research is needed to better define characteristics of the best responders and to determine whether novel forms of interferon therapy or combination therapy with interferon can enhance efficacy and tolerability.

Identification of genome-wide targets of Olig2 in the adult mouse spinal cord using ChIP-Seq.

In jawed vertebrates, oligodendrocytes (OLs) are the myelin-producing glial cells responsible for ensheathment of axons within the central nervous system and are also crucial for remyelination following injury or disease. Olig2 is a crucial factor in the specification and differentiation of oligodendrocyte precursor cells (OPCs) that give rise to mature, myelin-producing OLs in the developing and postnatal CNS; however, its role in adulthood is less well understood. To investigate the role Olig2 plays in regulating gene expression in the adult OL lineage in a physiologically-relevant context, we performed chromatin immunoprecipitation followed by next generation sequencing analysis (ChIP-Seq) using whole spinal cord tissue harvested from adult mice. We found that many of the Olig2-bound sites were associated with genes with biological processes corresponding to OL differentiation (Nkx2.2, Nkx6.2, and Sip1), myelination and ensheathment (Mbp, Cldn11, and Mobp), as well as cell cycle and cytoskeletal regulation. This suggests Olig2 continues to play a critical role in processes related to OL differentiation and myelination well into adulthood.

Extinction risks and the conservation of Madagascar's reptiles.

BACKGROUND: An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. METHODOLOGY/PRINCIPAL FINDINGS: Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. CONCLUSIONS/SIGNIFICANCE: With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and western regions of Madagascar and this study highlights the importance of these arid regions to conserving the island's biodiversity.

High throughput tissue preparation for large-scale genotyping experiments.

A fast, efficient technique is described for the extraction of DNA from a large number of samples. The applications of this method include population genetics, plant breeding, and genetic screening. In the field, samples are collected in premeasured silica gel aliquots in polypropylene blocks, which are later used to grind the dried tissue. This permits naturalists, breeders, and collaborators to collect a large number of samples in a short amount of time and allows the samples to dry quickly during shipping. No phenol or chloroform steps are required to obtain high-quality DNA. Samples representing 12 plant families, three invertebrates, and a mammal were included. Quantities of DNA obtained were consistent with or better than other techniques. The quality of samples was tested by amplification of the internal transcribed spacer region. Test amplifications were successful, confirming the quality of extracted DNA.