Linked read technology for assembling large complex and polyploid genomes

Background: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly. Results: Here we describe a de novo maize B73 genome assembly generated via linked read technology which contains ~ 172,000 scaffolds with an N50 of 89 kb that cover 50% of the genome. Based on comparisons to the B73 reference genome, 91% of linked read contigs are accurately assembled. Because it was possible to identify errors with \u3e 76% accuracy using machine learning, it may be possible to identify and potentially correct systematic errors. Complex polyploids represent one of the last grand challenges in genome assembly. Linked read technology was able to successfully resolve the two subgenomes of the recent allopolyploid, proso millet (Panicum miliaceum). Our assembly covers ~ 83% of the 1 Gb genome and consists of 30,819 scaffolds with an N50 of 912 kb. Conclusions: Our analysis provides a framework for future de novo genome assemblies using linked reads, and we suggest computational strategies that if implemented have the potential to further improve linked read assemblies, particularly for repetitive genomes

Whole-exome sequencing identifies novel MPL and JAK2 mutations in triple-negative myeloproliferative neoplasms.

Essential thrombocythemia (ET) and primary myelofibrosis (PMF) are chronic diseases characterized by clonal hematopoiesis and hyperproliferation of terminally differentiated myeloid cells. The disease is driven by somatic mutations in exon 9 of CALR or exon 10 of MPL or JAK2-V617F in >90% of the cases, whereas the remaining cases are termed "triple negative." We aimed to identify the disease-causing mutations in the triple-negative cases of ET and PMF by applying whole-exome sequencing (WES) on paired tumor and control samples from 8 patients. We found evidence of clonal hematopoiesis in 5 of 8 studied cases based on clonality analysis and presence of somatic genetic aberrations. WES identified somatic mutations in 3 of 8 cases. We did not detect any novel recurrent somatic mutations. In 3 patients with clonal hematopoiesis analyzed by WES, we identified a somatic MPL-S204P, a germline MPL-V285E mutation, and a germline JAK2-G571S variant. We performed Sanger sequencing of the entire coding region of MPL in 62, and of JAK2 in 49 additional triple-negative cases of ET or PMF. New somatic (T119I, S204F, E230G, Y591D) and 1 germline (R321W) MPL mutation were detected. All of the identified MPL mutations were gain-of-function when analyzed in functional assays. JAK2 variants were identified in 5 of 57 triple-negative cases analyzed by WES and Sanger sequencing combined. We could demonstrate that JAK2-V625F and JAK2-F556V are gain-of-function mutations. Our results suggest that triple-negative cases of ET and PMF do not represent a homogenous disease entity. Cases with polyclonal hematopoiesis might represent hereditary disorders

Comparative Evaluation of the Bruker Biotyper and Vitek MS Matrix-Assisted Laser Desorption Ionization-Time Of Flight (MALDI-TOF) Mass Spectrometry Systems for Identification of Yeasts of Medical Importance

We report the first comparative evaluation between the Bruker Biotyper MS (BMS) and the Vitek MS (VMS) for the identification of yeasts. The rate of correct identifications at the species level was comparable using the commercial databases (89.8% versus 84.3%; P = 0.712), but higher for BMS using an in-house-extended database (100% versus 84.3%; P = 0.245). Importantly, the rate of misidentification was significantly higher for VMS (1% versus 12.1%; P < 0.0001), including the rate of major errors (0% versus 4.5%; P = 0.0036)

Evaluating the effectiveness and risks of oral anticoagulant treatments in multimorbid frail older subjects with atrial fibrillation using the multidimensional prognostic index: the EURopean study of older subjects with atrial fibrillation\u2014EUROSAF

Background: Previous studies suggested that a different risk of mortality may influence the oral anticoagulant prescription in older patients with atrial fibrillation (AF). Recently, the Multidimensional Prognostic Index (MPI) demonstrated a high grade of accuracy, calibration and feasibility to predict mortality in hospitalized and community-dwelling older people. Prognostic information, as calculated by the MPI, however, is not included in the decision algorithm of treatments in older patients with AF Purpose: The aim of this international multicenter prospective observational study was to evaluate whether a different prognostic profile, as determined by the MPI, is associated with different treatments for AF (no treatment vs oral anticoagulants) and differences in the main outcomes, i.e., mortality, major thromboembolic events and side effects. Materials and methods: Older hospitalized patients (age 65\ua065\ua0years) with non-valvular AF will be consecutively enrolled in an European, cross-national, prospective, observational study. At baseline, functional and clinical information will be collected to calculate the MPI, CHA2DS2-VASc score, HAS-BLED score, pharmacological treatments (and the compliance during follow-up) and main and secondary diagnoses. During the 12-month follow-up period, information on survival, major thromboembolic events and major bleeding will be collected. For these aims, a sample size of 3000 people was deemed as sufficient. Conclusions: The EUROSAF study has the main objective of evaluating in a population of hospitalized older subjects with AF the clinical benefit/risk ratio of the oral anticoagulant treatments in terms of mortality, major thromboembolic events and bleeding side-effects, giving important information regarding the appropriate prescription of anticoagulant therapy in this population. ClinicalTrials.gov Identifier: NCT02973984