Haplotype reconstruction for genetically complex regions with ambiguous genotype calls: Illustration by the KIR gene region.

Advances in DNA sequencing technologies have enabled genotyping of complex genetic regions exhibiting copy number variation and high allelic diversity, yet it is impossible to derive exact genotypes in all cases, often resulting in ambiguous genotype calls, that is, partially missing data. An example of such a gene region is the killer-cell immunoglobulin-like receptor (KIR) genes. These genes are of special interest in the context of allogeneic hematopoietic stem cell transplantation. For such complex gene regions, current haplotype reconstruction methods are not feasible as they cannot cope with the complexity of the data. We present an expectation-maximization (EM)-algorithm to estimate haplotype frequencies (HTFs) which deals with the missing data components, and takes into account linkage disequilibrium (LD) between genes. To cope with the exponential increase in the number of haplotypes as genes are added, we add three components to a standard EM-algorithm implementation. First, reconstruction is performed iteratively, adding one gene at a time. Second, after each step, haplotypes with frequencies below a threshold are collapsed in a rare haplotype group. Third, the HTF of the rare haplotype group is profiled in subsequent iterations to improve estimates. A simulation study evaluates the effect of combining information of multiple genes on the estimates of these frequencies. We show that estimated HTFs are approximately unbiased. Our simulation study shows that the EM-algorithm is able to combine information from multiple genes when LD is high, whereas increased ambiguity levels increase bias. Linear regression models based on this EM, show that a large number of haplotypes can be problematic for unbiased effect size estimation and that models need to be sparse. In a real data analysis of KIR genotypes, we compare HTFs to those obtained in an independent study. Our new EM-algorithm-based method is the first to account for the full genetic architecture of complex gene regions, such as the KIR gene region. This algorithm can handle the numerous observed ambiguities, and allows for the collapsing of haplotypes to perform implicit dimension reduction. Combining information from multiple genes improves haplotype reconstruction.

Validation of transcriptome signature reversion for drug repurposing in oncology.

Transcriptome signature reversion (TSR) has been extensively proposed and used to discover new indications for existing drugs (i.e. drug repositioning, drug repurposing) for various cancer types. TSR relies on the assumption that a drug that can revert gene expression changes induced by a disease back to original, i.e. healthy, levels is likely to be therapeutically active in treating the disease. Here, we aimed to validate the concept of TSR using the PRISM repurposing data set, which is-as of writing-the largest pharmacogenomic data set. The predictive utility of the TSR approach as it has currently been used appears to be much lower than previously reported and is completely nullified after the drug gene expression signatures are adjusted for the general anti-proliferative downstream effects of drug-induced decreased cell viability. Therefore, TSR mainly relies on generic anti-proliferative drug effects rather than on targeting cancer pathways specifically upregulated in tumor types.

A 12-gene pharmacogenetic panel to prevent adverse drug reactions: an open-label, multicentre, controlled, cluster-randomised crossover implementation study.

BACKGROUND: The benefit of pharmacogenetic testing before starting drug therapy has been well documented for several single gene-drug combinations. However, the clinical utility of a pre-emptive genotyping strategy using a pharmacogenetic panel has not been rigorously assessed. METHODS: We conducted an open-label, multicentre, controlled, cluster-randomised, crossover implementation study of a 12-gene pharmacogenetic panel in 18 hospitals, nine community health centres, and 28 community pharmacies in seven European countries (Austria, Greece, Italy, the Netherlands, Slovenia, Spain, and the UK). Patients aged 18 years or older receiving a first prescription for a drug clinically recommended in the guidelines of the Dutch Pharmacogenetics Working Group (ie, the index drug) as part of routine care were eligible for inclusion. Exclusion criteria included previous genetic testing for a gene relevant to the index drug, a planned duration of treatment of less than 7 consecutive days, and severe renal or liver insufficiency. All patients gave written informed consent before taking part in the study. Participants were genotyped for 50 germline variants in 12 genes, and those with an actionable variant (ie, a drug-gene interaction test result for which the Dutch Pharmacogenetics Working Group [DPWG] recommended a change to standard-of-care drug treatment) were treated according to DPWG recommendations. Patients in the control group received standard treatment. To prepare clinicians for pre-emptive pharmacogenetic testing, local teams were educated during a site-initiation visit and online educational material was made available. The primary outcome was the occurrence of clinically relevant adverse drug reactions within the 12-week follow-up period. Analyses were irrespective of patient adherence to the DPWG guidelines. The primary analysis was done using a gatekeeping analysis, in which outcomes in people with an actionable drug-gene interaction in the study group versus the control group were compared, and only if the difference was statistically significant was an analysis done that included all of the patients in the study. Outcomes were compared between the study and control groups, both for patients with an actionable drug-gene interaction test result (ie, a result for which the DPWG recommended a change to standard-of-care drug treatment) and for all patients who received at least one dose of index drug. The safety analysis included all participants who received at least one dose of a study drug. This study is registered with ClinicalTrials.gov, NCT03093818 and is closed to new participants. FINDINGS: Between March 7, 2017, and June 30, 2020, 41 696 patients were assessed for eligibility and 6944 (51·4 % female, 48·6% male; 97·7% self-reported European, Mediterranean, or Middle Eastern ethnicity) were enrolled and assigned to receive genotype-guided drug treatment (n=3342) or standard care (n=3602). 99 patients (52 [1·6%] of the study group and 47 [1·3%] of the control group) withdrew consent after group assignment. 652 participants (367 [11·0%] in the study group and 285 [7·9%] in the control group) were lost to follow-up. In patients with an actionable test result for the index drug (n=1558), a clinically relevant adverse drug reaction occurred in 152 (21·0%) of 725 patients in the study group and 231 (27·7%) of 833 patients in the control group (odds ratio [OR] 0·70 [95% CI 0·54-0·91]; p=0·0075), whereas for all patients, the incidence was 628 (21·5%) of 2923 patients in the study group and 934 (28·6%) of 3270 patients in the control group (OR 0·70 [95% CI 0·61-0·79]; p <0·0001). INTERPRETATION: Genotype-guided treatment using a 12-gene pharmacogenetic panel significantly reduced the incidence of clinically relevant adverse drug reactions and was feasible across diverse European health-care system organisations and settings. Large-scale implementation could help to make drug therapy increasingly safe. FUNDING: European Union Horizon 2020.

The impact of autoantibodies on the efficacy of biological disease-modifying anti-rheumatic drugs in rheumatoid arthritis: meta-analysis of randomized controlled trials.

OBJECTIVE: To investigate the efficacy of bDMARDs in patients with RA with RF/ACPA compared with patients without these autoantibodies. METHODS: Previous systematic literature reviews performed by EULAR RA management task forces were searched for qualifying RCTs. RCTs investigating the efficacy of bDMARDs and including both autoantibody-positive (≤80% of total population) and -negative RA patients were eligible. For trials comparing bDMARD+csDMARD vs csDMARD, relative risks (RR) comparing two groups (RF + vs RF-, ACPA+ vs ACPA-) were calculated for efficacy outcomes for each arm. Subsequently, relative risk ratios (RRRs) were computed, as the ratio of RR of the bDMARD-arm and the RR from the non-bDMARD-arm. Pooled effects were obtained with random effect meta-analyses. RESULTS: Data from 28 eligible RCTs were analyzed, pooling 23 studies in three subgroups: 6 including csDMARD-naïve patients, 14 csDMARD-IR, and 3 TNFi-IR patients. In csDMARD-naïve and csDMARD-IR patients, seropositivity was not associated with a better response to bDMARDs: pooled 6-month ACR20 RRRs 1.02 (0.88-1.18) and 1.09 (0.90-1.32), respectively. Other outcomes showed no difference between groups either. In TNFi-IR patients, based on 3 trials, the 6-month ACR20 RRR was 2.28 (1.31-3.95), favoring efficacy in seropositive patients. Other outcomes mostly showed no significant difference between the groups. Based on the mode of action, efficacy was comparable between RF-positive and RF-negative patients for both TNFi and non-TNFi treatment and also for the individual bDMARDs. CONCLUSION: The effect of bDMARDs is generally comparable in patients with and without RF/ACPA, regardless of the patient population, the mechanism of action or individual drug used.

Intervention with methotrexate in patients with arthralgia at risk of rheumatoid arthritis to reduce the development of persistent arthritis and its disease burden (TREAT EARLIER): a randomised, double-blind, placebo-controlled, proof-of-concept trial.

BACKGROUND: Rheumatoid arthritis is the most common autoimmune disease worldwide and requires long-term treatment to suppress inflammation. Currently, treatment is started when arthritis is clinically apparent. We aimed to evaluate whether earlier intervention, in the preceding phase of arthralgia and subclinical joint inflammation, could prevent the development of clinical arthritis or reduce the disease burden. METHODS: We conducted a randomised, double-blind, placebo-controlled, proof-of-concept-trial at the Leiden University Medical Centre, Leiden, Netherlands. Adults aged 18 years or older with arthralgia clinically suspected of progressing to rheumatoid arthritis and MRI-detected subclinical joint inflammation were eligible for enrolment across 13 rheumatology outpatient clinics in the southwest region of the Netherlands and randomly assigned (1:1) to a single intramuscular glucocorticoid injection (120 mg) and a 1-year course of oral methotrexate (up to 25 mg/week), or placebo (single injection and tablets for 1 year). Participants and investigators were masked to group assignment. Follow-up continued for 1 year after the end of the 1-year treatment period. The primary endpoint was development of clinical arthritis (fulfilling the 2010 rheumatoid arthritis classification criteria or involving two or more joints) that persisted for at least 2 weeks. Patient-reported physical functioning, symptoms, and work productivity were secondary endpoints, which were measured every 4 months. Additionally, the course of MRI-detected inflammation was studied. All participants entered the intention-to-treat analysis. This trial is registered with EudraCT, 2014-004472-35, and the Netherlands Trial Register, NTR4853-trial-NL4599. FINDINGS: Between April 16, 2015, and Sept 11, 2019, 901 patients were assessed for eligibility and 236 were enrolled and randomly assigned to active treatment (n=119) or placebo (n=117). At 2 years, the frequency of the primary endpoint was similar between the groups (23 [19%] of 119 participants in the treatment group vs 21 [18%] of 117 in the placebo group; hazard ratio 0·81, 95% CI 0·45 to 1·48). Physical functioning improved more in the treatment group during the first 4 months and remained better than in the placebo group (mean between-group difference in Health Assessment Questionnaire disability index over 2 years: -0·09, 95% CI -0·16 to -0·03; p=0·0042). Similarly, pain (on scale 0-100, mean between-group difference: -8, 95% CI -12 to -4; p<0·0001), morning stiffness of joints (-12, -16 to -8; p<0·0001), presenteeism (-8%, -13 to -3; p=0·0007), and MRI-detected joint inflammation (-1·4 points, -2·0 to -0·9; p<0·0001) showed sustained improvement in the treatment group compared with the placebo group. The number of serious adverse events was equal in both groups; adverse events were consistent with the known safety profile for methotrexate. INTERPRETATION: Methotrexate, the cornerstone treatment of rheumatoid arthritis, initiated at the pre-arthritis stage of symptoms and subclinical inflammation, did not prevent the development of clinical arthritis, but modified the disease course as shown by sustained improvement in MRI-detected inflammation, related symptoms, and impairments compared with placebo. FUNDING: Dutch Research Council (NWO; Dutch Arthritis Society).

Choosing and changing the analysis scale in non-inferiority trials with a binary outcome.

BACKGROUND: The size of the margin strongly influences the required sample size in non-inferiority and equivalence trials. What is sometimes ignored, however, is that for trials with binary outcomes, the scale of the margin - risk difference, risk ratio or odds ratio - also has a large impact on power and thus on sample size requirement. When considering several scales at the design stage of a trial, these sample size consequences should be taken into account. Sometimes, changing the scale may be needed at a later stage of a trial, for example, when the event proportion in the control arm turns out different from expected. Also after completion of a trial, a switch to another scale is sometimes made, for example, when using a regression model in a secondary analysis or when combining study results in a meta-analysis that requires unifying scales. The exact consequences of such switches are currently unknown. METHODS AND RESULTS: This article first outlines sample size consequences for different choices of analysis scale at the design stage of a trial. We add a new result on sample size requirement comparing the risk difference scale with the risk ratio scale. Then, we study two different approaches to changing the analysis scale after the trial has commenced: (1) mapping the original non-inferiority margin using the event proportion in the control arm that was anticipated at the design stage or (2) mapping the original non-inferiority margin using the observed event proportion in the control arm. We use simulations to illustrate consequences on type I and type II error rates. Methods are illustrated on the INES trial, a non-inferiority trial that compared single birth rates in subfertile couples after different fertility treatments. Our results demonstrate large differences in required sample size when choosing between risk difference, risk ratio and odds ratio scales at the design stage of non-inferiority trials. In some cases, the sample size requirement is twice as large on one scale compared with another. Changing the scale after commencing the trial using anticipated proportions mainly impacts type II error rate, whereas switching using observed proportions is not advised due to not maintaining type I error rate. Differences were more pronounced with larger margins. CONCLUSIONS: Trialists should be aware that the analysis scale can have large impact on type I and type II error rates in non-inferiority trials.

A prediction model for recurrence after translabyrinthine surgery for vestibular schwannoma: toward personalized postoperative surveillance.

PURPOSE: The aim of this study is to compute and validate a statistical predictive model for the risk of recurrence, defined as regrowth of tumor necessitating salvage treatment, after translabyrinthine removal of vestibular schwannomas to individualize postoperative surveillance. METHODS: The multivariable predictive model for risk of recurrence was based on retrospectively collected patient data between 1995 and 2017 at a tertiary referral center. To assess for internal validity of the prediction model tenfold cross-validation was performed. A 'low' calculated risk of recurrence in this study was set at < 1%, based on clinical criteria and expert opinion. RESULTS: A total of 596 patients with 33 recurrences (5.5%) were included for analysis. The final prediction model consisted of the predictors 'age at time of surgery', 'preoperative tumor growth' and 'first postoperative MRI outcome'. The area under the receiver operating curve of the prediction model was 89%, with a C-index of 0.686 (95% CI 0.614-0.796) after cross-validation. The predicted probability for risk of recurrence was low (< 1%) in 373 patients (63%). The earliest recurrence in these low-risk patients was detected at 46 months after surgery. CONCLUSION: This study presents a well-performing prediction model for the risk of recurrence after translabyrinthine surgery for vestibular schwannoma. The prediction model can be used to tailor the postoperative surveillance to the estimated risk of recurrence of individual patients. It seems that especially in patients with an estimated low risk of recurrence, the interval between the first and second postoperative MRI can be safely prolonged.

Blood pressure, antihypertensive medication and neuropsychiatric symptoms in older people with dementia: The COSMOS study.

OBJECTIVES: Neuropsychiatric symptoms (NPS) are very common in older patients with dementia. There is increasing evidence that hypoperfusion of the brain plays a role in the development of NPS. The aim of this study is to assess whether there is an association between low systolic blood pressure (SBP) and NPS and if NPS are more prevalent in older people with dementia using antihypertensive medication. METHODS: We studied the baseline data from participants in the Communication, Systematic pain treatment, Medication review, Organized activities and Safety study, a multicenter clustered trial with 765 participants from 72 nursing home units from 37 nursing homes in Norway. SBP (lowest quartile vs rest) and use of antihypertensive medication were predictors and Neuropsychiatric Inventory-Nursing Home version (NPI-NH) score (total and clusters) was the outcome. Missing data were imputed, except for missing data in predictors. We used a mixed model analysis adjusted for age, sex and Minimal Mental State Examination (MMSE) score. In a sensitivity analysis, continuous SBP values were used. RESULTS: In total, 412 patients were included with a mean age of 86.9 years, 53.9% had a MMSE score of <11. There was no difference in total NPI-NH score between low and high SBP (difference -1.07, Pdj = 0.62). There was no difference between high and low SBP and the NPI clusters. The use of antihypertensive medication was not associated with a different total or cluster NPI-NH score compared to no use (difference -0.99, Padj = 0.95, Pall = 0.37-0.99, respectively). In the sensitivity analyses with the continuous SBP levels, there was no association between SBP and NPI-NH score (estimate 1.00, 95%CI 0.98-1.01, P = 0.25). CONCLUSION: We found no association between low SBP and NPS, nor between antihypertensive use and NPS.

Modelling growth curves of the normal infant's mandible: 3D measurements using computed tomography.

OBJECTIVES: Data on normal mandibular development in the infant is lacking though essential to understand normal growth patterns and to discriminate abnormal growth. The aim of this study was to provide normal linear measurements of the mandible using computed tomography performed in infants from 0 to 2 years of age. MATERIAL AND METHODS: 3D voxel software was used to calculate mandibular body length, mandibular ramus length, bicondylar width, bigonial width and the gonial angle. Intra- and inter-rater reliability was assessed for these measurements. They were found to be sufficient for all distances; intra-class correlation coefficients were all above 0.9. Regression analysis for growth modelling was performed. RESULTS: In this multi-centre retrospective study, 109 CT scans were found eligible that were performed for various reasons (e.g. trauma, craniosynostosis, craniofacial abscesses). Craniosynostosis patients had larger mandibular measurements compared to non-craniosynostosis patients and were therefore excluded. Fifty-one CT scans were analysed. CONCLUSIONS: Analysis showed that the mandible increases more in size vertically (the mandibular ramus) than horizontally (the mandibular body). Most of the mandibular growth occurs in the first 6 months. CLINICAL RELEVANCE: These growth models provide insight into normal mandibular development in the first 2 years of life. This reference data facilitates discrimination between normal and abnormal mandibular growth.

Septorhinoplasty and Septoplasty: Outcomes of a Large Cohort Using Autologous Versus Homologous Cartilage, 1999-2019.

This study describes the complication rate and use of autologous and/or homologous cartilage in a large 20-year cohort of septo(rhino)plasty surgeries in a Dutch hospital, in relation to postoperative complications of septo(rhino)plasty surgery described in previous studies. A retrospective medical chart review was conducted. 2606 patients, mean age 34.7 (± 13.2) and 59.9% male, underwent primary or revision septo(rhino)plasty surgery from 01/01/1999 to 01/09/2019. Follow-up was known in 1384 of 2606 patients (53.1%) with a mean duration of 47.5 months. Complication registration was complete for 1774 patients. The overall complication rate was 270 out of 1774 (15.2%). The use of autologous costal cartilage (ACC) was a risk factor for overall complication with an odds ratio (OR) of 11.1 (95% CI 0.03-0.30; P < 0.01) as compared to 5.9 (95% CI 0.06-0.45; P < 0.01) when using homologous costal cartilage (HCC). Infections were more likely when ACC (5/26 [19.2%]) was used than when HCC (1/28 [3.6%]) was used. Notable resorption of cartilage was more likely when HCC (9/28 [32.1%]) was used than when ACC (1/26 [3.8%]) was used. Both the use of autologous costal cartilage grafts (OR 11.1) and homologous costal cartilage grafts (OR 5.9) lead to an increased risk of complications. When choosing cartilage type for reconstruction in septo(rhino)plasty, it should be taken into account that both ACC and HCC are associated with a higher risk of complications. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Changes in healthcare utilisation for paediatric tonsillectomy and adenoidectomy in the Netherlands: a population-based study.

OBJECTIVES: Tonsillectomy and adenoidectomy in children are controversial subjects with large regional variation in surgical rates, partly explained by cultural differences and lack of high-quality evidence on indications for surgery. A quality of care cycle was executed on this topic in the Netherlands. The objective of this study was to estimate changes in healthcare utilisation for paediatric tonsil surgery in the Netherlands. METHODS: Population-based data on tonsillectomies and adenoidectomies in children up to age 10 were retrieved retrospectively from Dutch administrative databases between 2005 and 2018. A change point analysis was performed to detect the most pivotal change point in surgical rates. We performed univariate analyses to compare surgical patients' characteristics before and after the pivotalpoint . Impact on healthcare budget and societal costs were estimated using current prices and data from cost-effectiveness analyses. RESULTS: The annual number of adenotonsillectomies reduced by 10 952 procedures (-39%; from 129 per 10 000 children to 87 per 10 000 children) between 2005 and 2018, and the number of adenoidectomies by 14 757 procedures (-49%; from 138 per 10 000 children to 78 per 10 000 children). The most pivotal change point was observed around 2012, accompanied by small changes in patient selection for surgery before and after 2012. An estimated €5.3 million per year was saved on the healthcare budget and €10.4 million per year on societal costs. CONCLUSION: The quality of care cycle resulted in fewer operations, with a concomitant reduction of costs. We suggest that part of these savings be invested in new research to maintain the quality of care cycle.

Generating evidence for precision medicine: considerations made by the Ubiquitous Pharmacogenomics Consortium when designing and operationalizing the PREPARE study.

OBJECTIVES: Pharmacogenetic panel-based testing represents a new model for precision medicine. A sufficiently powered prospective study assessing the (cost-)effectiveness of a panel-based pharmacogenomics approach to guide pharmacotherapy is lacking. Therefore, the Ubiquitous Pharmacogenomics Consortium initiated the PREemptive Pharmacogenomic testing for prevention of Adverse drug Reactions (PREPARE) study. Here, we provide an overview of considerations made to mitigate multiple methodological challenges that emerged during the design. METHODS: An evaluation of considerations made when designing the PREPARE study across six domains: study aims and design, primary endpoint definition and collection of adverse drug events, inclusion and exclusion criteria, target population, pharmacogenomics intervention strategy, and statistical analyses. RESULTS: Challenges and respective solutions included: (1) defining and operationalizing a composite primary endpoint enabling measurement of the anticipated effect, by including only severe, causal, and drug genotype-associated adverse drug reactions; (2) avoiding overrepresentation of frequently prescribed drugs within the patient sample while maintaining external validity, by capping drugs of enrolment; (3) designing the pharmacogenomics intervention strategy to be applicable across ethnicities and healthcare settings; and (4) designing a statistical analysis plan to avoid dilution of effect by initially excluding patients without a gene-drug interaction in a gatekeeping analysis. CONCLUSION: Our design considerations will enable quantification of the collective clinical utility of a panel of pharmacogenomics-markers within one trial as a proof-of-concept for pharmacogenomics-guided pharmacotherapy across multiple actionable gene-drug interactions. These considerations may prove useful to other investigators aiming to generate evidence for precision medicine.

Results of a 6-week treatment with 10 mg prednisolone in patients with hand osteoarthritis (HOPE): a double-blind, randomised, placebo-controlled trial.

BACKGROUND: Hand osteoarthritis is a prevalent joint condition that has a high burden of disease and an unmet medical need for effective therapeutic options. Since local inflammation is recognised as contributing to osteoarthritic complaints, the Hand Osteoarthritis Prednisolone Efficacy (HOPE) study aimed to investigate the efficacy and safety of short-term prednisolone in patients with painful hand osteoarthritis and synovial inflammation. METHODS: The HOPE study is a double-blind, randomised, placebo-controlled trial. We recruited eligible adults from rheumatology outpatient clinics at two sites in the Netherlands. Patients were considered eligible if they had symptomatic hand osteoarthritis and signs of inflammation in their distal and proximal interphalangeal (DIP/PIP) joints. For inclusion, patients were required to have four or more DIP/PIP joints with osteoarthritic nodes; at least one DIP/PIP joint with soft swelling or erythema; at least one DIP/PIP joint with a positive power Doppler signal or synovial thickening of at least grade 2 on ultrasound; and finger pain of at least 30 mm on a 100-mm visual analogue scale (VAS) that flared up during a 48-h non-steroidal anti-inflammatory drug (NSAID) washout (defined as worsening of finger pain by at least 20 mm on the VAS). Eligible patients were randomly assigned (1:1) to receive 10 mg prednisolone or placebo orally once daily for 6 weeks, followed by a 2-week tapering scheme, and a 6-week follow-up without study medication. The patients and study team were masked to treatment assignment. The primary endpoint was finger pain, assessed on a VAS, at 6 weeks in participants who had been randomly assigned to groups and attended the baseline visit. This study is registered with the Netherlands Trial Registry, number NTR5263. FINDINGS: We screened patients for enrolment between Dec 3, 2015, and May 31, 2018. Patients completed baseline visits and started treatment between Dec 14, 2015, and July 2, 2018, and the last study visit of the last patient was Oct 4, 2018. Of 149 patients assessed for eligibility, 57 (38%) patients were excluded (predominantly because they did not meet one or several inclusion criteria, most often because of an absence of synovial inflammation or of flare-ups after NSAID washout) and 92 (62%) patients were eligible for inclusion. We randomly assigned 46 (50%) patients to receive prednisolone and 46 (50%) patients to receive placebo, all of whom were included in the modified intention-to-treat analysis of the primary endpoint. 42 (91%) patients in the prednisolone group and 42 (91%) in the placebo group completed the 14-week study. The mean change between baseline and week 6 on VAS-reported finger pain was -21·5 (SD 21·7) in the prednisolone group and -5·2 (24·3) in the placebo group, with a mean between-group difference (of prednisolone vs placebo) of -16·5 (95% CI -26·1 to -6·9; p=0·0007). The number of non-serious adverse events was similar between the groups. Five serious adverse events were reported during our study: one serious adverse event in the prednisolone group (a myocardial infarction) and four serious adverse events in the placebo group (an infected traumatic leg haematoma that required surgery, bowel surgery, atrial fibrillation that required a pacemaker implantation, and symptomatic uterine myomas that required a hysterectomy). Four (4%) patients discontinued the study because of an adverse event: one (2%) patient receiving prednisolone (for a myocardial infarction) and three (7%) patients receiving placebo (for surgery of the bowel and for an infected leg haematoma and for Lyme disease arthritis of the knee). INTERPRETATION: Treatment with 10 mg prednisolone for 6 weeks is efficacious and safe for the treatment of patients with painful hand osteoarthritis and signs of inflammation. The results of our study provide clinicians with a new short-term treatment option for patients with hand osteoarthritis who report a flare-up of their disease. FUNDING: Dutch Arthritis Society.

Suppression of compensatory erythropoiesis in hemolytic disease of the fetus and newborn due to intrauterine transfusions.

BACKGROUND: Infants with severe hemolytic disease of the fetus and newborn often require 1 or multiple intrauterine transfusions to treat fetal anemia. Intrauterine transfusions may have an inhibiting effect on fetal and neonatal erythropoiesis. OBJECTIVE: To quantify the effect of 1 or multiple intrauterine transfusions on the fetal erythropoiesis by assessing the fetal reticulocyte counts in a population with severe hemolytic disease of the fetus and newborn. STUDY DESIGN: This was an observational cohort study in infants admitted to the Leiden University Medical Center who received 1 or multiple intrauterine transfusions for hemolytic disease of the fetus and newborn caused by (Rh)D or Kell antibodies and were born between January 2005 and December 2018. RESULTS: A total of 235 patients were included, of whom 189 were patients with D-mediated hemolytic disease of the fetus and newborn and 46 with Kell-mediated hemolytic disease of the fetus and newborn. Absolute fetal reticulocyte count in D-mediated hemolytic disease of the fetus and newborn declined exponentially over the course of consecutive intrauterine transfusions, with a 62% decline after 1 intrauterine transfusion (95% confidence interval, 56-67). A similar exponential decline was observed in Kell-mediated hemolytic disease of the fetus and newborn, with 32% (95% confidence interval, 19-45) decline after 1 intrauterine transfusion. This decline was not associated with the varying gestational age at the time of the first intrauterine transfusion or the total number of intrauterine transfusions. The number of red blood cell transfusions for postnatal anemia was greater for infants with D and Kell-mediated hemolytic disease of the fetus and newborn with >2 intrauterine transfusions (median of 3 [interquartile range, 2-3] vs 2 [interquartile range, 1-3], P=.035, in D-mediated disease and median of 2 [interquartile range, 1-2] vs 1 [interquartile range, 1-1], P<.001, in Kell-mediated disease). Infants born after >2 intrauterine transfusions less often required exchange transfusion in D-mediated hemolytic disease of the fetus and newborn (19/89 [21%] vs 31/100 [31%], P=.039), compared with infants with 1-2 intrauterine transfusions. CONCLUSION: Treatment with intrauterine transfusions causes an exponential decrease in fetal reticulocyte counts in both D- and Kell-mediated hemolytic disease of the fetus and newborn. Suppression of the compensatory erythropoiesis leads to prolonged postnatal anemia and an increased requirement of red blood cell transfusions after birth.

Effectiveness of Phantom Stimulation in Shifting the Pitch Percept in Cochlear Implant Users.

OBJECTIVES: Phantom electrode stimulation was developed for cochlear implant (CI) systems to provide a lower pitch percept by stimulating more apical regions of the cochlea, without inserting the electrode array deeper into the cochlea. Phantom stimulation involves simultaneously stimulating a primary and a compensating electrode with opposite polarity, thereby shifting the electrical field toward the apex and eliciting a lower pitch percept. The current study compared the effect sizes (in shifts of place of excitation) of multiple phantom configurations by matching the perceived pitch with phantom stimulation to that perceived with monopolar stimulation. Additionally, the effects of electrode location, type of electrode array, and stimulus level on the perceived pitch were investigated. DESIGN: Fifteen adult advanced bionics CI users participated in this study, which included four experiments to eventually measure the shifts in place of excitation with five different phantom configurations. The proportions of current delivered to the compensating electrode, expressed as σ, were 0.5, 0.6, 0.7, and 0.8 for the symmetrical biphasic pulses (SBC0.5, SBC0.6, SBC0.7, and SBC0.8) and 0.75 for the pseudomonophasic pulse shape (PSA0.75). A pitch discrimination experiment was first completed to determine which basal and apical electrode contacts should be used for the subsequent experiments. An extensive loudness balancing experiment followed where both the threshold level (T-level) and most comfortable level (M-level) were determined to enable testing at multiple levels of the dynamic range. A pitch matching experiment was then performed to estimate the shift in place of excitation at the chosen electrode contacts. These rough shifts were then used in the subsequent experiment, where the shifts in place of excitation were determined more accurately. RESULTS: Reliable data were obtained from 20 electrode contacts. The average shifts were 0.39, 0.53, 0.64, 0.76, and 0.53 electrode contacts toward the apex for SBC0.5, SBC0.6, SBC0.7, SBC0.8, and PSA0.75, respectively. When only the best configurations per electrode contact were included, the average shift in place of excitation was 0.92 electrode contacts (range: 0.25 to 2.0). While PSA0.75 leads to equal results as the SBC configurations in the apex, it did not result in a significant shift at the base. The shift in place of excitation was significantly larger at the apex and with lateral wall electrode contacts. The stimulus level did not affect the shift. CONCLUSIONS: Phantom stimulation results in significant shifts in place of excitation, especially at the apical part of the electrode array. The phantom configuration that leads to the largest shift in place of excitation differs between subjects. Therefore, the settings of the phantom electrode should be individualized so that the phantom stimulation is optimized for each CI user. The real added value to the sound quality needs to be established in a take-home trial.

Prediction of aspiration in dysphagia using logistic regression: oral intake and self-evaluation.

OBJECTIVES: Oropharyngeal dysphagia (OD) has a major influence on health in general and health-related quality of life (HR-QoL) in particular. The gold standard assessments for OD, especially for aspiration in OD, are fiberoptic endoscopic evaluation of swallowing (FEES) and videofluoroscopy (VFSS), but not all patients have access to such procedures. Therefore, the current study built a prediction model to forecast aspiration in patients with OD on the basis of common self-evaluation questionnaires and oral intake status. METHODS: A consecutive series of 111 patients with confirmed diagnosis of OD was measured according to a standardised protocol using the following tools: the Swallowing Quality of Life Questionnaire (SWAL-QOL), the Dysphagia Handicap Index (DHI), two self-report visual analogue scales which measure the Severity and the Impairment of the swallowing problem on everyday social life as experienced by the patient, the Eating Assessment Tool 10 (EAT-10), the Functional Oral Intake Scale (FOIS) and subsequently FEES (the gold standard). Penalised logistic regression was carried out to predict aspiration. The performance of the resulting models was evaluated by constructing receiver operating characteristics (ROC) curves and computing areas under the curve (AUC). RESULTS: The final model showed an AUC of 0.92, indicating excellent performance. CONCLUSION: This study shows that it may be possible to accurately predict aspiration in oropharyngeal dysphagia by a non-invasive and non-instrumental assessment protocol including oral intake status and self-report questionnaires on functional health status and HR-QoL.

Influence of batch effect correction methods on drug induced differential gene expression profiles.

BACKGROUND: Batch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signature-based drug repositioning. Herein, we conducted differential analyses on the Connectivity Map (CMAP) database using several batch effect correction methods to evaluate the influence of batch effect correction methods on computational drug repositioning using microarray data and compare several batch effect correction methods. RESULTS: Differences in average signature size were observed with different methods applied. The gene signatures identified by the Latent Effect Adjustment after Primary Projection (LEAPP) method and the methods fitted with Linear Models for Microarray Data (limma) software demonstrated little agreement. The external validity of the gene signatures was evaluated by connectivity mapping between the CMAP database and the Library of Integrated Network-based Cellular Signatures (LINCS) database. The results of connectivity mapping indicate that the genes identified were not reliable for drugs with total sample size (drug + control samples) smaller than 40, irrespective of the batch effect correction method applied. With total sample size larger than 40, the methods correcting for batch effects produced significantly better results than the method with no batch effect correction. In a simulation study, the power was generally low for simulated data with sample size smaller than 40. We observed best performance when using the limma method correcting for two principal components. CONCLUSION: Batch effect correction methods strongly impact differential gene expression analysis when the sample size is large enough to contain sufficient information and thus the downstream drug repositioning. We recommend including two or three principal components as covariates in fitting models with limma when sample size is sufficient (larger than 40 drug and controls combined).

Powerful testing via hierarchical linkage disequilibrium in haplotype association studies.

Marginal tests based on individual SNPs are routinely used in genetic association studies. Studies have shown that haplotype-based methods may provide more power in disease mapping than methods based on single markers when, for example, multiple disease-susceptibility variants occur within the same gene. A limitation of haplotype-based methods is that the number of parameters increases exponentially with the number of SNPs, inducing a commensurate increase in the degrees of freedom and weakening the power to detect associations. To address this limitation, we introduce a hierarchical linkage disequilibrium model for disease mapping, based on a reparametrization of the multinomial haplotype distribution, where every parameter corresponds to the cumulant of each possible subset of a set of loci. This hierarchy present in the parameters enables us to employ flexible testing strategies over a range of parameter sets: from standard single SNP analyses through the full haplotype distribution tests, reducing degrees of freedom and increasing the power to detect associations. We show via extensive simulations that our approach maintains the type I error at nominal level and has increased power under many realistic scenarios, as compared to single SNP and standard haplotype-based studies. To evaluate the performance of our proposed methodology in real data, we analyze genome-wide data from the Wellcome Trust Case-Control Consortium.

Evaluation of KDR rs34231037 as a predictor of sunitinib efficacy in patients with metastatic renal cell carcinoma.

The identification of biomarkers able to predict clinical benefit from vascular endothelial growth factor receptor (VEGFR) tyrosine kinase inhibitors is urgently needed. Recently, Maitland and colleagues described an association between KDR-rs34231037 and soluble VEGFR2 levels as well as pazopanib pharmacodynamics. We investigated in a well-characterized series of metastatic clear cell renal cell carcinoma patients whether rs34231037 could influence sunitinib response. Clinical data and DNA were available from an international series of 276 patients. KDR-rs34231037 association with sunitinib response, clinical benefit, and progression-free survival was analyzed using logistic and Cox regression analyses. We found that G-allele carriers were over-represented among patients with clinical benefit during sunitinib treatment compared with those refractory to the treatment (odds ratio: 3.78; 95% confidence interval: 1.02-14.06; P=0.047, multivariable analysis). In conclusion, rs34231037 variant carriers seemed to have better sunitinib response than wild-type patients. Moreover, the association with tumor size reduction suggests that this single nucleotide polymorphism might also identify patients with successful tumor downsizing under anti-VEGFR therapy.