Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan

Multiple displacement amplification (MDA) has emerged as a promising new method of whole genome amplification (WGA) with the potential to generate virtually unlimited genome-equivalent DNA from only a small amount of seed DNA. To date, genome-wide high marker density assessments of MDA–DNA have focussed mainly upon suitability for single nucleotide polymorphism (SNP) genotyping applications. Suitability for short tandem repeat (STR) genotyping has not been investigated in great detail, despite their inherent instability during DNA replication, and the obvious challenge that this presents to WGA techniques. Here, we aimed to assess the applicability of MDA in STR genotyping by conducting a genome-wide scan of 768 STR markers for MDAs of 15 high quality genomic DNAs. We found that MDA genotyping call and accuracy rates were only marginally lower than for genomic DNA. Pooling of three replicate MDAs resulted in a small increase in both call rate and genotyping accuracy. We identified 34 STRs (4.4% of total markers) of which five essentially failed with MDA samples, and 29 of which showed elevated genotyping failures/discrepancies in the MDAs. We emphasise the importance of DNA and MDA quality checks, and the use of appropriate controls to identify problematic STR markers.     

Likelihood-based disequilibrium mapping for two-marker haplotype data

We report a theory that gives the sampling distribution of two-marker haplotypes that are linked to a rare disease mutation. The sampling distribution is generated with successive Monte Carlo realizations of the coalescence of the disease mutation having recombination and marker mutation events placed along the lineage. Given a sample of mutation-bearing, two-marker haplotypes, the maximum likelihood estimate of the location of the disease mutation can be calculated from the generated sampling distribution, provided that one knows enough about the population history in order to model it. The two-marker likelihood method is compared to a single-marker likelihood and a composite likelihood. The two-marker maximum likelihood gives smaller confidence intervals for the location of the disease locus than a comparable single-marker maximum likelihood. The composite likelihood can give biased results and the bias increases as the extent of linkage disequilibrium on mutation-bearing chromosomes decreases. Haplotype configurations exist for which the composite likelihood will fail to place the disease locus in the correct marker interval.     

A vectorized method of importance sampling with applications to models of mutation and migration

An importance-sampling method is presented for computing the likelihood of the configuration of population genetic data under general assumptions about population history and transitions among states. The configuration of the data is the number of chromosomes sampled that are in each of a finite set of states. Transitions among states are governed by a Markov chain with transition probabilities dependent on one or more parameters. The method assumes that the joint distribution of coalescence times of the underlying gene genealogy is independent of the genetic state of each lineage. Given a set of coalescence times, the probability that a pair of lineages is chosen to coalesce in each replicate is proportional to the contribution that the coalescence event makes to the probability of the data. This method can be applied to gene genealogies generated by the neutral coalescent process and to genealogies generated by other processes, such as a linear birth-death process which provides a good approximation to the dynamics of low-frequency alleles. Two applications are described. In the first, the fit of allele frequencies at two microsatellite loci sampled in a Sardinian population to the one-step mutation model is tested. The one-step model is rejected for one locus but not for the other. The second application is to low-frequency alleles in a geographically subdivided population. The geographic location is the allelic state, and the alleles are assumed to be sufficiently rare that their dynamics can be approximated by a linear birth-death process in which the birth and death rates are independent of geographic location. The analysis of eight low-frequency allozyme alleles found in the glaucous-winged gull, Larus glaucescens, illustrates how geographically restricted dispersal can be detected.     

Multiplex relative risk and estimation of the number of loci underlying an inherited disease

Knowledge of the number of causative loci is necessary to estimate the power of mapping studies of complex diseases. In the present article, we reexamine a theory developed by Risch and its implications for estimating the number L of causative loci affecting a complex inherited disease. We first show that methods based on Risch's analysis can produce estimates of L that are inconsistent with the observed population prevalence of the disease. We demonstrate this point by showing that the maximum-likelihood estimate for L produced by the method of Farrall and Holder for cleft lip/cleft palate data is not consistent with the prevalence under the multiplicative model. We show how to incorporate disease prevalence and develop a maximum-likelihood method for estimating L that uses the entire distribution of numbers of affected individuals in families containing an affected individual. This method avoids the potential inconsistencies of the Risch method and has greater precision. We apply our method to data on cleft lip/cleft palate and schizophrenia.     

Effect of different protocols of caffeine intake on metabolism and endurance performance.

Competitive athletes completed two studies of 2-h steady-state (SS) cycling at 70% peak O(2) uptake followed by 7 kJ/kg time trial (TT) with carbohydrate (CHO) intake before (2 g/kg) and during (6% CHO drink) exercise. In Study A, 12 subjects received either 6 mg/kg caffeine 1 h preexercise (Precaf), 6 x 1 mg/kg caffeine every 20 min throughout SS (Durcaf), 2 x 5 ml/kg Coca-Cola between 100 and 120 min SS and during TT (Coke), or placebo. Improvements in TT were as follows: Precaf, 3.4% (0.2-6.5%, 95% confidence interval); Durcaf, 3.1% (-0.1-6.5%); and Coke, 3.1% (-0.2-6.2%). In Study B, eight subjects received 3 x 5 ml/kg of different cola drinks during the last 40 min of SS and TT: decaffeinated, 6% CHO (control); caffeinated, 6% CHO; decaffeinated, 11% CHO; and caffeinated, 11% CHO (Coke). Coke enhanced TT by 3.3% (0.8-5.9%), with all trials showing 2.2% TT enhancement (0.5-3.8%; P < 0.05) due to caffeine. Overall, 1) 6 mg/kg caffeine enhanced TT performance independent of timing of intake and 2) replacing sports drink with Coca-Cola during the latter stages of exercise was equally effective in enhancing endurance performance, primarily due to low intake of caffeine (approximately 1.5 mg/kg).     

Spontaneous and engineered mutant mice as models for experimental and comparative pathology: history, comparison, and developmental technology

During the last half-century pathologists have explored the biologic mechanisms associated with inherited human and veterinary diseases by using inbred and inbred mutant (spontaneous) strains of mice. The first successful gene transfer to mice by pronuclear injection of the herpes simplex virus thymidine kinase gene and rabbit and human beta-globulin genes was achieved in the early 1980s. This accomplishment was followed a few years later with the creation of a mouse bearing a disrupted hypoxanthine phosphoribosyl transferase (hrpt) gene (targeted mutation based on ES cell blastocyst injection). Since then, hundreds of genetically engineered models of biomedical importance have been created. The unprecedented scale and scope of development of engineered models present great opportunities as well as experimental challenges to the investigator. The aim of the present review is to provide a framework of information on engineered mouse models from the perspective of experimental and comparative pathology research. Sections include: 1) a brief historical account of the development of mouse models of disease, with increasing progression of genetic refinement as represented by inbred (spontaneous) and congenic (targeted) mutant strains of mice; 2) a synopsis of spontaneous and targeted mutations, with anecdotal examples of expression of individual genes and interactions between multiple mutant genes; 3) selected examples of targeted mutations of interest to developmental and cancer biologists and immunologists; 4) an overview of the technology of development of transgenic mice; and 5) an introduction to on-line database resources of current multi-species genomic information.     

Extracellular polysaccharides of modified strains of Erwinia spp.

The structure of the extracellular polysaccharide (EPS) produced by Erwinia chrysanthemi strain A2148 has been determined using low pressure size-exclusion and anion-exchange chromatographies, high pH anion-exchange chromatography, glycosyl-linkage analysis, and 1D 1H NMR spectroscopy. The polysaccharide is structurally similar, if not identical, to the EPS produced by E. chrysanthemi strain A350. A streptomycin-resistant strain of E. chrysanthemi Ech6 (Ech6S(+)) has been generated and has an elevated production of EPS, as does a streptomycin-resistant strain (Ech9Sm6) of E. chrysanthemi Ech9. These modified E. chrysanthemi spp. have been ribotyped and found to be closely related to their parent strains.     

Two parallel,pragmatic, UK multicentre,randomised controlled trials comparing surgical options for upper compartment (vault or uterine) pelvic organ prolapse (the VUE Study): study protocol for a randomised controlled trial

BackgroundOne in three women who have a prolapse operation will go on to have another operation, though not necessarily in the same compartment. Surgery can result in greater impairment of quality of life than the original prolapse itself (such as the development of new-onset urinary incontinence, or prolapse at a different site). Anterior and posterior prolapse surgery is most common (90 % of operations), but around 43 % of women also have a uterine (34 %) or vault (9 %) procedure at the same time. There is not enough evidence from randomised controlled trials (RCTs) to guide management of vault or uterine prolapse. The Vault or Uterine prolapse surgery Evaluation (VUE) study aims to assess the surgical management of upper compartment pelvic organ prolapse (POP) in terms of clinical effectiveness, cost-effectiveness and adverse events.Methods/designVUE is two parallel, pragmatic, UK multicentre, RCTs (Uterine Trial and Vault Trial). Eligible for inclusion are women with vault or uterine prolapse: requiring a surgical procedure, suitable for randomisation and willing to be randomised. Randomisation will be computer-allocated separately for each trial, minimised on: requiring concomitant anterior and/or posterior POP surgery or not, concomitant incontinence surgery or not, age (under 60 years or 60 years and older) and surgeon. Participants will be randomly assigned, with equal probability to intervention or control arms in either the Uterine Trial or the Vault Trial. Uterine Trial participants will receive either a vaginal hysterectomy or a uterine preservation procedure. Vault Trial participants will receive either a vaginal sacrospinous fixation or an abdominal sacrocolpopexy. Participants will be followed up by postal questionnaires (6 months post surgery and 12 months post randomisation) and also reviewed in clinic 12 months post surgery. The primary outcome is the participant-reported Pelvic Organ Prolapse Symptom Score (POP-SS) at 12 months post randomisation.DiscussionDemonstrating the efficacy of vault and uterine prolapse surgeries is relevant not only to patients and clinicians but also to health care providers, both in the UK and globally.

Trial registration

Current controlled trials ISRCTN86784244 (assigned 19 October 2012), and the first subject was randomly assigned on 1 May 2013 

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-016-1576-x) contains supplementary material, which is available to authorized users.