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Motivation Low-copy repeats (LCRs) or segmental duplications are long segments of duplicated DNA that cover > 5% of the human genome. Existing tools for variant calling using short reads exhibit low accuracy in LCRs due to ambiguity in read mapping and extensive copy number variation. Variants in more than 150 genes overlapping LCRs are associated with risk for human diseases. Methods We describe a short-read variant calling method, ParascopyVC, that performs variant calling jointly across all repeat copies and utilizes reads independent of mapping quality in LCRs. To identify candidate variants, ParascopyVC aggregates reads mapped to different repeat copies and performs polyploid variant calling. Subsequently, paralogous sequence variants that can differentiate repeat copies are identified using population data and used for estimating the genotype of variants for each repeat copy. Results On simulated whole-genome sequence data, ParascopyVC achieved higher precision (0.997) and recall (0.807) than three state-of-the-art variant callers (best precision = 0.956 for DeepVariant and best recall = 0.738 for GATK) in 167 LCR regions. Benchmarking of ParascopyVC using the genome-in-a-bottle high-confidence variant calls for HG002 genome showed that it achieved a very high precision of 0.991 and a high recall of 0.909 across LCR regions, significantly better than FreeBayes (precision = 0.954 and recall = 0.822), GATK (precision = 0.888 and recall = 0.873) and DeepVariant (precision = 0.983 and recall = 0.861). ParascopyVC demonstrated a consistently higher accuracy (mean F 1 = 0.947) than other callers (best F 1 = 0.908) across seven human genomes. Availability and implementation ParascopyVC is implemented in Python and is freely available at https://github.com/tprodanov/ParascopyVC. [ABSTRACT FROM AUTHOR]

Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g. schizophrenia (SCZ)], suggestive of brain functionality, here we characterize piggyBac transposable element-derived 1 (PGBD1). PGBD1 is nonmonotreme mammal-specific and under purifying selection, consistent with functionality. The gene body of human PGBD1 retains much of the original DNA transposon but has additionally captured SCAN and KRAB domains. Despite gene body retention, PGBD1 has lost transposition abilities, thus transposase functionality is absent. PGBD1 no longer recognizes piggyBac transposon-like inverted repeats, nonetheless PGBD1 has DNA binding activity. Genome scale analysis identifies enrichment of binding sites in and around genes involved in neuronal development, with association with both histone activating and repressing marks. We focus on one of the repressed genes, the long noncoding RNA NEAT1 , also dysregulated in SCZ, the core structural RNA of paraspeckles. DNA binding assays confirm specific binding of PGBD1 both in the NEAT1 promoter and in the gene body. Depletion of PGBD1 in neuronal progenitor cells (NPCs) results in increased NEAT1/paraspeckles and differentiation. We conclude that PGBD1 has evolved core regulatory functionality for the maintenance of NPCs. As paraspeckles are a mammal-specific structure, the results presented here show a rare example of the evolution of a novel gene coupled to the evolution of a contemporaneous new structure. [ABSTRACT FROM AUTHOR]

Background: Patients with good renal function receiving intermittent-infusion vancomycin (IIV) may require total daily doses ≥4 g to achieve trough concentrations of 15-20 mg/L, increasing the risk of vancomycin-associated nephrotoxicity. Continuous-infusion vancomycin (CIV) may be associated with a lower risk of vancomycin-associated nephrotoxicity compared with IIV, but studies comparing safety of both dosing strategies are lacking.Objectives: To compare the risk of nephrotoxicity with CIV versus IIV when target concentration ranges were the same with both dosing modalities.Methods: A retrospective multicentre matched cohort study of admitted patients between 1 January 2010 and 31 December 2016 was completed. Adult patients who received ≥48 h of vancomycin with at least one steady-state vancomycin concentration were eligible. The primary outcome was to compare the rates of nephrotoxic risk and renal injury, defined by the RIFLE criteria, between CIV and IIV.Results: Of 2136 patients who received vancomycin during the study period, 146 CIV patients were eligible and matched to 146 IIV patients. After adjustment of potential confounders, CIV was found to have a lower odds of developing nephrotoxic risk (OR 0.42, 95% CI 0.21-0.98, P = 0.025) and renal injury (OR 0.19, 95% CI 0.05-0.59, P = 0.004).Conclusions: CIV is associated with a lower odds of nephrotoxicity compared with IIV when targeting the same concentration range and should be an alternative dosing strategy for patients who will receive prolonged therapy or require >4 g/day to achieve therapeutic levels. [ABSTRACT FROM AUTHOR]

Motivation Reconstruction of haplotypes for human genomes is an important problem in medical and population genetics. Hi-C sequencing generates read pairs with long-range haplotype information that can be computationally assembled to generate chromosome-spanning haplotypes. However, the haplotypes have limited completeness and low accuracy. Haplotype information from population reference panels can potentially be used to improve the completeness and accuracy of Hi-C haplotyping. Results In this paper, we describe a likelihood based method to integrate short-range haplotype information from a population reference panel of haplotypes with the long-range haplotype information present in sequence reads from methods such as Hi-C to assemble dense and highly accurate haplotypes for individual genomes. Our method leverages a statistical phasing method and a maximum spanning tree algorithm to determine the optimal second-order approximation of the population-based haplotype likelihood for an individual genome. The population-based likelihood is encoded using pseudo-reads which are then used as input along with sequence reads for haplotype assembly using an existing tool, HapCUT2. Using whole-genome Hi-C data for two human genomes (NA19240 and NA12878), we demonstrate that this integrated phasing method enables the phasing of 97–98% of variants, reduces the switch error rates by 3–6-fold, and outperforms an existing method for combining phase information from sequence reads with population-based phasing. On Strand-seq data for NA12878, our method improves the haplotype completeness from 71.4 to 94.6% and reduces the switch error rate 2-fold, demonstrating its utility for phasing using multiple sequencing technologies. Availability and implementation Code and datasets are available at https://github.com/vibansal/IntegratedPhasing. [ABSTRACT FROM AUTHOR]

Motivation: The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention. Results: We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25-30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets. [ABSTRACT FROM AUTHOR]

Discontinuing routine processing of screening urine cultures prior to elective joint arthroplasty resulted in substantial reduction in urine cultures ordered and antimicrobial prescriptions for asymptomatic bacteriuria, without any significant impact on incidence of prosthetic joint infection. This simple change would be scalable across institutions with potential for significant healthcare savings. [ABSTRACT FROM AUTHOR]

Motivation: High-throughput sequencing technologies have made population-scale studies of human genetic variation possible. Accurate and comprehensive detection of DNA sequence variants is crucial for the success of these studies. Small insertions and deletions represent the second most frequent class of variation in the human genome after single nucleotide polymorphisms (SNPs). Although several alignment tools for the gapped alignment of sequence reads to a reference genome are available, computational methods for discriminating indels from sequencing errors and genotyping indels directly from sequence reads are needed.Results: We describe a probabilistic method for the accurate detection and genotyping of short indels from population-scale sequence data. In this approach, aligned sequence reads from a population of individuals are used to automatically account for context-specific sequencing errors associated with indels. We applied this approach to population sequence datasets from the 1000 Genomes exon pilot project generated using the Roche 454 and Illumina sequencing platforms, and were able to detect a significantly greater number of indels than reported previously. Comparison to indels identified in the 1000 Genomes pilot project demonstrated the sensitivity of our method. The consistency in the number of indels and the fraction of indels whose length is a multiple of three across different human populations and two different sequencing platforms indicated that our method has a low false discovery rate. Finally, the method represents a general approach for the detection and genotyping of small-scale DNA sequence variants for population-scale sequencing projects.Availability: A program implementing this method is available at http://polymorphism.scripps.edu/~vbansal/software/piCALL/Contact: vbansal@scripps.eduSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]

A thermal model has been developed to investigate the potential of using the storage capacity of the ground for cooling with the help of an earth to air heat exchanger (EAHE) system integrated with evaporative cooler. Parametric studies performed for the EAHE coupled with the evaporative cooler illustrate the effects of buried pipe length, pipe diameter, volumetric flow rate of air, number of pipes and surface-to-volume (S/V) ratio on the outlet temperature of the EAHE. An analytical solution has been derived by considering the fundamental equation of energy, heat transfer and psychrometry, for predicting the temperature at the outlet of EAHE. The results of the EAHE coupled with evaporative cooling are compared with that of EAHE without evaporative cooling for different S/V ratio and bypass factor. It is observed that the length of the EAHE pipe is reduced significantly as much as 93.5% for obtaining desired temperature at the outlet of the EAHE by the integration of evaporative cooling with EAHE. Reduction in the length of buried pipe is also noted with decrease in bypass factor of evaporator cooler. [ABSTRACT FROM PUBLISHER]

Motivation: Next-generation sequencing technologies have enabled the sequencing of several human genomes in their entirety. However, the routine resequencing of complete genomes remains infeasible. The massive capacity of next-generation sequencers can be harnessed for sequencing specific genomic regions in hundreds to thousands of individuals. Sequencing-based association studies are currently limited by the low level of multiplexing offered by sequencing platforms. Pooled sequencing represents a cost-effective approach for studying rare variants in large populations. To utilize the power of DNA pooling, it is important to accurately identify sequence variants from pooled sequencing data. Detection of rare variants from pooled sequencing represents a different challenge than detection of variants from individual sequencing. [ABSTRACT FROM PUBLISHER]