BackgroundDouble minute chromosomes are circular fragments of DNA whose presence is associated with the onset of certain cancers. Double minutes are lethal, as they are highly amplified and typically contain oncogenes. Locating double minutes can supplement the process of cancer diagnosis, and it can help to identify therapeutic targets. However, there is currently a dearth of computational methods available to identify double minutes. We propose a computational framework for the idenfication of double minute chromosomes using next-generation sequencing data. Our framework integrates predictions from algorithms that detect DNA copy number variants, and it also integrates predictions from algorithms that locate genomic structural variants. This information is used by a graph-based algorithm to predict the presence of double minute chromosomes.ResultsUsing a previously published copy number variant algorithm and two structural variation prediction algorithms, we implemented our framework and tested it on a dataset consisting of simulated double minute chromosomes. Our approach uncovered double minutes with high accuracy, demonstrating its plausibility.ConclusionsAlthough we only tested the framework with three programs (RDXplorer, BreakDancer, Delly), it can be extended to incorporate results from programs that 1) detect amplified copy number and from programs that 2) detect genomic structural variants like deletions, translocations, inversions, and tandem repeats.The software that implements the framework can be accessed here: https://github.com/mhayes20/DMFinder

BackgroundUndaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida.ResultsA total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region.ConclusionsA high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.

BackgroundTo promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq™ Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer.ResultsHere, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3 % in four samples, whereas the concordance of co-detected variant loci reached 99 %. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5 %) was higher than the SNPs specific to TargetSeq-Proton (60.0 %) or specific to SureSelect-HiSeq (88.3 %). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0 %) and SureSelect-HiSeq-specific (89.6 %) were higher than those of TargetSeq-Proton-specific (15.8 %).ConclusionsIn the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the sequencing of platform-specific variants, the accuracy of variant calling by HiSeq 2000 was higher than that of Ion Proton, specifically for the InDel detection. Moreover, the variant calling software also influences the detection of SNPs and, specifically, InDels in Ion Proton exome sequencing.

BackgroundChina is experiencing increasing burden of acute myocardial infarction (AMI) in the face of limited medical resources. Hospital length of stay (LOS) is an important indicator of resource utilization.MethodsWe used data from the Retrospective AMI Study within the China Patient-centered Evaluative Assessment of Cardiac Events, a nationally representative sample of patients hospitalized for AMI during 2001, 2006, and 2011. Hospital-level variation in risk-standardized LOS (RS-LOS) for AMI, accounting for differences in case mix and year, was examined with two-level generalized linear mixed models. A generalized estimating equation model was used to evaluate hospital characteristics associated with LOS. Absolute differences in RS-LOS and 95% confidence intervals were reported.ResultsThe weighted median and mean LOS were 13 and 14.6 days, respectively, in 2001 (n = 1,901), 11 and 12.6 days in 2006 (n = 3,553), and 11 and 11.9 days in 2011 (n = 7,252). There was substantial hospital level variation in RS-LOS across the 160 hospitals, ranging from 9.2 to 18.1 days. Hospitals in the Central regions had on average 1.6 days (p = 0.02) shorter RS-LOS than those in the Eastern regions. All other hospital characteristics relating to capacity for AMI treatment were not associated with LOS.ConclusionsDespite a marked decline over the past decade, the mean LOS for AMI in China in 2011 remained long compared with international standards. Inter-hospital variation is substantial even after adjusting for case mix. Further improvement of AMI care in Chinese hospitals is critical to further shorten LOS and reduce unnecessary hospital variation.