In search of Pinkel's children: unravelling the biological heterogeneity of childhood acute lymphoblastic leukaemia by genotype and treatment molecular response

BACKGROUND

Acute lymphoblastic leukaemia (ALL), the commonest childhood malignancy has seen remarkable progress since the 1960s with cure rates now approaching 85%. To achieve this patients undergo intensive treatment that usually takes 2.5-3.5 years involving on average 15 different chemotherapeutic drugs. In 1971, Donald Pinkel reported Total Therapy-Protocol V that used 5 drugs and cranial radiation therapy over a similar time period. Today, one half of these patients (Pinkel's children) remain alive and free of leukaemia.

AIM

The aim of this study was to evaluate the impact post-induction minimal residual disease (MRD) levels had on survival and its relationship with the more established clinical and biological prognostic predictors of outcome in the hope of identifying a subgroup of patients that are at very low risk of failure.

METHODS

A retrospective review of 250 Irish children with ALL was carried out. MRD status after 28 days of induction chemotherapy and other known predictors of outcome were correlated with 5 year event-free survival (EFS).

RESULTS

MRD status was the strongest predictor of outcome with 5 year EFS rates greater that 90% seen in those patients with low-risk MRD and this was associated with TEL/AML1 rearrangement, high hyperdiploidy (HH) karyotype and female gender.

CONCLUSION

Both MRD and karyotype are powerful determinants of outcome in childhood ALL. Therefore, it is reasonable to conclude that the majority of children cured by Pinkel et al. in the late 1960s were most likely composed of low-risk MRD, TEL/AML1 and HH patients.

Managing the Impact of Illness: The Experiences of Men with Prostate Cancer and their Spouses

This qualitative study explored issues of support and coping for couples where the man had been diagnosed with prostate cancer. Thirty-four men with prostate cancer and their spouses were interviewed separately at three points in time: prior to surgery; 8 to 10 weeks post-surgery; and 11 to 13 months post-surgery. The core category for the couples' experience with diagnosis and treatment for prostate cancer was Managing the Impact of Illness. Five major domains emerged, including: dealing with the practicalities; stopping illness from interfering with everyday life; keeping relationships working; managing feelings; and making sense of it all. While it was clearly important for couples to manage illness and to reduce its potential intrusion into everyday life, this strategy had psychological costs as well as benefits. Men struggled to stay in control of their emotions and their lives, typically vacillating between the pulls of fierce self-reliance and fearful neediness. Women were constrained from employing their usual strategies of coping and were distressed by the complicated requirements of being supportive while also honoring their partners' need for self-reliance.

Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies

A revision of an established 34 SNP forensic ancestry test has been made by swapping the under-performing rs727811 component SNP with the highly informative rs3827760 that shows a near-fixed East Asian specific allele. We collated SNP variability data for the revised SNP set in 66 reference populations from 1000 Genomes and HGDP-CEPH panels and used this as reference data to analyse four U.S. populations showing a range of admixture patterns. The U.S. Hispanics sample in particular displayed heterogeneous values of co-ancestry between European, Native American and African contributors, likely to reflect in part, the way this disparate group is defined using cultural as well as population genetic parameters. The genotyping of over 700 U.S. population samples also provided the opportunity to thoroughly gauge peak mobility variation and peak height ratios observed from routine use of the single base extension chemistry of the 34-plex test. Finally, the genotyping of the widely used DNA profiling Standard Reference Material samples plus other control DNAs completes the audit of the 34-plex assay to allow forensic practitioners to apply this test more readily in their own laboratories.

Craniofacial variations in the tricho-dento-osseous syndrome

Tricho-dento-osseous (TDO) syndrome is an autosomal dominant trait characterized by curly kinky hair at birth, enamel hypoplasia, taurodontism, thickening of cortical bones and variable expression of craniofacial morphology. Genetic studies have identified a 4-bp deletion in the DLX3 gene that is associated with TDO; however, phenotypic characterization and classification of TDO remains unclear in the literature. This study compares the craniofacial variations between 53 TDO-affected subjects and 34 unaffected family members. Standardized cephalograms were obtained and digitized. Cephalometric measurements were analyzed using a general linear model with family as a random effect. Numerous craniofacial measurements from both groups showed marked variability. TDO-affected subjects showed a Class III skeletal pattern (smaller SNA and ANB angles), longer mandibular corpus length (GoGn) and shorter ramus height (p < 0.05).

Further development of forensic eye color predictive tests

In forensic analysis predictive tests for external visible characteristics (or EVCs), including inference of iris color, represent a potentially useful tool to guide criminal investigations. Two recent studies, both focused on forensic testing, have analyzed single nucleotide polymorphism (SNP) genotypes underlying common eye color variation (Mengel-From et al., Forensic Sci. Int. Genet. 4:323 and Walsh et al., Forensic Sci. Int. Genet. 5:170). Each study arrived at different recommendations for eye color predictive tests aiming to type the most closely associated SNPs, although both confirmed rs12913832 in HERC2 as the key predictor, widely recognized as the most strongly associated marker with blue and brown iris colors. Differences between these two studies in identification of other eye color predictors may partly arise from varying approaches to assigning phenotypes, notably those not unequivocally blue or dark brown and therefore occupying an intermediate iris color continuum. We have developed two single base extension assays typing 37 SNPs in pigmentation-associated genes to study SNP-genotype based prediction of eye, skin, and hair color variation. These assays were used to test the performance of different sets of eye color predictors in 416 subjects from six populations of north and south Europe. The presence of a complex and continuous range of intermediate phenotypes distinct from blue and brown eye colors was confirmed by establishing eye color populations compared to genetic clusters defined using Structure software. Our study explored the effect of an expanded SNP combination beyond six markers has on the ability to predict eye color in a forensic test without extending the SNP assay excessively - thus maintaining a balance between the test's predictive value and an ability to reliably type challenging DNA with a multiplex of manageable size. Our evaluation used AUC analysis (area under the receiver operating characteristic curves) and naïve Bayesian likelihood-based classification approaches. To provide flexibility in SNP-based eye color predictive tests in forensic applications we modified an online Bayesian classifier, originally developed for genetic ancestry analysis, to provide a straightforward system to assign eye color likelihoods from a SNP profile combining additional informative markers from the predictors analyzed by our study plus those of Walsh and Mengel-From. Two advantages of the online classifier is the ability to submit incomplete SNP profiles, a common occurrence when typing challenging DNA, and the ability to handle physically linked SNPs showing independent effect, by allowing the user to input frequencies from SNP pairs or larger combinations. This system was used to include the submission of frequency data for the SNP pair rs12913832 and rs1129038: indicated by our study to be the two SNPs most closely associated to eye color.

Infection prevention practice: how does experience affect knowledge and application?

The purpose of this study was to evaluate nurses’ knowledge of infection prevention procedures, the degree to which they were applied correctly, and whether length of service affected either knowledge or application. Nurses with over five years of experience had significantly increased understanding of infection prevention ( p=0.009) and significantly increased application of knowledge to practice ( p=0.001), compared to nurses with five years or less experience. In particular, understanding of hand hygiene and use of personal protective equipment (PPE) was poor although application was compliant, while knowledge of care of patients with meticillin resistant Staphylococcus aureus (MRSA) and Clostridium difficile was poor, which was reflected by substandard application of knowledge to practice. The results of this study suggest that focusing infection prevention education around patients with specific infections, such as MRSA and C. difficile, rather than on individual standard precautions may more effectively increase knowledge and therefore application of infection prevention practices.

Non-invasive therapy for altered facial sensation following orthognathic surgery: an exploratory randomized clinical trial of intranasal vitamin B12 spray

AIM

The aim of the study was to obtain pilot data on the putative effects of intranasal spray Vitamin B12 in lessening the impairment from orthognathic surgery on large and small diameter nerve fiber functions.

METHODS

Thirty-five subjects scheduled for a mandibular osteotomy were enrolled in an open-label two-group parallel stratified-block randomized clinical trial: Intranasal Vitamin B12 Spray (B12), with weekly doses self-administered two weeks before until 6 months after surgery, or no intranasal spray. All subjects received sensory retraining exercises. Large fiber tactile (contact detection) and small fiber thermal (warm, cool, heat discomfort, and cold discomfort) thresholds were obtained before and at 1, 3, and 6 months after surgery. For each, the mean maximum impairment was estimated for group and visit, controlling for age and type of surgery.

RESULTS

The demographics and pre-surgery threshold values of the two groups did not differ (P>0.16). At and 6 months after surgery, serum B12 levels were substantially higher in the B12 group (P<0.01). At one month post, average impairment for every threshold measure was less for the B12 group. From 1 to 3 months, the differences between the two groups decreased for the tactile measures but stayed the same (cool and warm perception) or increased (cold and heat discomfort perception) for the thermal measures. At 6 months, the B12 group remained less impaired for the thermal measures.

CONCLUSION

This pilot RCT indicates that the effects of intranasal Vitamin B12 spray, initiated prior to surgery, on sensory function are sufficiently promising to justify progression to a Phase III RCT.

Strange beta: an assistance system for indoor rock climbing route setting

This paper applies the mathematics of chaos to the task of designing indoor rock-climbing routes. Chaotic variation has been used to great advantage on music and dance, but the challenges here are quite different, beginning with the representation. We present a formalized system for transcribing rock climbing problems and then describe a variation generator that is designed to support human route-setters in designing new and interesting climbing problems. This variation generator, termed strange beta, uses chaos to introduce novelty. We validated this approach with a large blinded study in a commercial climbing gym, in cooperation with experienced climbers and expert route setters. The results show that strange beta can help a human setter produce routes that are at least as good as, and in some cases better than, those produced in the traditional manner.

Vapour phase: a potential future use for essential oils as antimicrobials?

Essential oil (EO) vapours have been known for their antimicrobial properties since the 4th century B.C.; however, it was not until the early 1960s that research into the potential of these volatile oils was explored. More recently, the use of EOs such as tea tree, bergamot, lavender and eucalyptus in vapour form has been shown to have antimicrobial effects against both bacteria and fungi, with range of methods being developed for dispersal and efficacy testing. To date, many applications for EO vapours as antimicrobials have been identified including in the food and clinical arenas.

Application of Autosomal SNPs and Indels in Forensic Analysis

The potential applications of short binary markers to forensic analysis are reviewed. Short binary markers are the most common human genomic variation and include single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (Indels). This review outlines their use and performance in typing highly degraded DNA - the original rationale for developing SNPs for forensic analysis - as well as their ability to infer the ancestry or likely pigmentation characteristics of an individual not present on a national DNA database, thus potentially providing investigative leads. Throughout the review, reference is made to short Indels as a new and potentially powerful alternative to SNPs for enhancing short tandem repeat (STR) results by using a simple amplification to capillary electrophoresis (PCR-to-CE) technique that retains the direct relationship between input DNA and signal strength, offering much improved mixture-detection capabilities while retaining the favorable characteristics of short amplicon PCR.

Saving Lives audits: do they improve infection prevention and control practice?

Aretrospective audit evaluation was conducted to determine whether the introduction of two clinical skills trainers for four months in a district general hospital improved compliance with infection prevention and control practices. Saving Lives (Department of Health, 2010) peripheral venous cannula and urinary catheter high impact intervention audit data were analysed for six months before, four months during and six months after the clinical skills training was implemented for six control wards and seven intervention wards. Findings showed that although the control wards did not improve compliance significantly over the study period, the intervention wards improved compliance with the high impact intervention care bundles studied and that this practice was sustained for six months after the clinical skills training. The findings suggest that education is required to improve clinical skills surrounding cannulation and catheterisation, which can then be sustained by Saving Lives audits to reduce the risk of infection to patients.

A new SNP assay for identification of highly degraded human DNA

There is growing evidence that the histone-DNA complexes found in nucleosomes offer protection from DNA degradation processes, including apoptotic events in addition to bacterial and environmental degradation. We sought to locate human nucleosome regions and build a catalogue of SNPs sited near the middle of these genomic segments that could be combined into a single PCR multiplex specifically for use with extremely degraded human genomic DNA samples. Using recently optimized bio-informatics tools for the reliable identification of nucleosome sites based on sequence motifs and their positions relative to known promoters, 1395 candidate loci were collected to construct an 18-plex single base extension assay. Genotyping performance of the nucleosome SNPs was tested using artificially degraded DNA and 24 casework samples where the likely state of degradation of DNA was established by comparison to profile completeness in four other forensic assays: a standard 15-plex STR identification test, a miniaturized STR multiplex and two autosomal SNP multiplexes. The nucleosome SNP assay gave genotyping success rates 6% higher than the best existing forensic SNP assay: the SNPforID Auto-2 29-plex and significantly higher than the mini-STR assay. The nucleosome SNPs we located and combined therefore provide a new type of marker set that can be used to supplement existing approaches when the analysed DNA is likely to be extremely degraded and may fail to give sufficient STR genotypes for a reliable identification.

The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data

Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses.

A study of East Timor variability using the SNPforID 52-plex SNP panel

A set of 52 autosomal single nucleotide polymorphism (SNP) loci was analyzed in 46 unrelated individuals from the East Timor population using the forensic assay previously described by Sanchez et al. (2006) [J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe Court, PM. Schneider, A. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713-1724]. Allele frequencies are presented for the 52 SNPs with all loci in Hardy-Weinberg equilibrium for the study population. Comparison with African, European, East Asian and Oceanian populations of the CEPH human genome diversity panel (CEPH-HGDP) revealed significant differences in allele frequency distributions between East Timor and each of the above population groups. Statistical parameters measuring forensic informativeness were also calculated and the values obtained reached comparable levels to those previously described for the other global population groups. This is the first study of variability in these SNPs in an Oceanian population outside of the CEPH-HGDP.

Randomised controlled trial of thermostatic mixer valves in reducing bath hot tap water temperature in families with young children in social housing

OBJECTIVES

To assess the effectiveness of thermostatic mixing valves (TMVs) in reducing bath hot tap water temperature, assess acceptability of TMVs to families and impact on bath time safety practices.

DESIGN

Pragmatic parallel arm randomised controlled trial.

SETTING

A social housing organisation in Glasgow, Scotland, UK.

PARTICIPANTS

124 families with at least one child under 5 years.

INTERVENTION

A TMV fitted by a qualified plumber and educational leaflets before and at the time of TMV fitting.

MAIN OUTCOME MEASURES

Bath hot tap water temperature at 3-month and 12-month post-intervention or randomisation, acceptability, problems with TMVs and bath time safety practices.

RESULTS

Intervention arm families had a significantly lower bath hot water temperature at 3-month and 12-month follow-up than families in the control arm (3 months: intervention arm median 45.0°C, control arm median 56.0°C, difference between medians, -11.0, 95% CI -14.3 to -7.7); 12 months: intervention arm median 46.0°C, control arm median 55.0°C, difference between medians -9.0, 95% CI -11.8 to -6.2) They were significantly more likely to be happy or very happy with their bath hot water temperature (RR 1.43, 95% CI 1.05 to 1.93), significantly less likely to report the temperature as being too hot (RR 0.33, 95% CI 0.16 to 0.68) and significantly less likely to report checking the temperature of every bath (RR 0.84, 95% CI 0.73 to 0.97). Seven (15%) intervention arm families reported problems with their TMV.

CONCLUSIONS

TMVs and accompanying educational leaflets are effective at reducing bath hot tap water temperatures in the short and longer term and are acceptable to families. Housing providers should consider fitting TMVs in their properties and legislators should consider mandating their use in refurbishments as well as in new builds.

Soft tissue response to mandibular advancement using 3D CBCT scanning

This prospective longitudinal study assessed the 3D soft tissue changes following mandibular advancement surgery. Cranial base registration was performed for superimposition of virtual models built from cone beam computed tomography (CBCT) volumes. Displacements at the soft and hard tissue chin (n = 20), lower incisors and lower lip (n = 21) were computed for presurgery to splint removal (4-6-week surgical outcome), presurgery to 1 year postsurgery (1-year surgical outcome), and splint removal to 1 year postsurgery (postsurgical adaptation). Qualitative evaluations of color maps illustrated the surgical changes and postsurgical adaptations, but only the lower lip showed statistically significant postsurgical adaptations. Soft and hard tissue chin changes were significantly correlated for each of the intervals evaluated: presurgery to splint removal (r = 0.92), presurgery to 1 year postsurgery (r = 0.86), and splint removal to 1 year postsurgery (r = 0.77). A statistically significant correlation between lower incisor and lower lip was found only between presurgery and 1 year postsurgery (r = 0.55). At 1 year after surgery, 31% of the lower lip changes were explained by changes in the lower incisor position while 73% of the soft tissue chin changes were explained by the hard chin. This study suggests that 3D soft tissue response to mandibular advancement surgery is markedly variable.

Hypnotic modulation of resting state fMRI default mode and extrinsic network connectivity

Resting state fMRI (functional magnetic resonance imaging) acquisitions are characterized by low-frequency spontaneous activity in a default mode network (encompassing medial brain areas and linked to self-related processes) and an anticorrelated "extrinsic" system (encompassing lateral frontoparietal areas and modulated via external sensory stimulation). In order to better determine the functional contribution of these networks to conscious awareness, we here sought to transiently modulate their relationship by means of hypnosis. We used independent component analysis (ICA) on resting state fMRI acquisitions during normal wakefulness, under hypnotic state, and during a control condition of autobiographical mental imagery. As compared to mental imagery, hypnosis-induced modulation of resting state fMRI networks resulted in a reduced "extrinsic" lateral frontoparietal cortical connectivity, possibly reflecting a decreased sensory awareness. The default mode network showed an increased connectivity in bilateral angular and middle frontal gyri, whereas its posterior midline and parahippocampal structures decreased their connectivity during hypnosis, supposedly related to an altered "self" awareness and posthypnotic amnesia. In our view, fMRI resting state studies of physiological (e.g., sleep or hypnosis), pharmacological (e.g., sedation or anesthesia), and pathological modulation (e.g., coma or related states) of "intrinsic" default mode and anticorrelated "extrinsic" sensory networks, and their interaction with other cerebral networks, will further improve our understanding of the neural correlates of subjective awareness.

Regression models for patient-reported measures having ordered categories recorded on multiple occasions

OBJECTIVES

The article reviews proportional and partial proportional odds regression for ordered categorical outcomes, such as patient-reported measures, that are frequently used in clinical research in dentistry.

METHODS

The proportional odds regression model for ordinal data is a generalization of ordinary logistic regression for dichotomous responses. When the proportional odds assumption holds for some but not all of the covariates, the lesser known partial proportional odds model is shown to provide a useful extension.

RESULTS

The ordinal data models are illustrated for the analysis of repeated ordinal outcomes to determine whether the burden associated with sensory alteration following a bilateral sagittal split osteotomy procedure differed for those patients who were given opening exercises only following surgery and those who received sensory retraining exercises in conjunction with standard opening exercises.

CONCLUSIONS

Proportional and partial proportional odds models are broadly applicable to the analysis of cross-sectional and longitudinal ordinal data in dental research.

Inferior alveolar nerve injury following orthognathic surgery: a review of assessment issues

The sensory branches of the trigeminal nerve encode information about facial expressions, speaking and chewing movements, and stimuli that come into contact with the orofacial tissues. Whatever the cause, damage to the inferior alveolar nerve negatively affects the quality of facial sensibility as well as the patient's ability to translate patterns of altered nerve activity into functionally meaningful motor behaviours. There is no generally accepted, standard method of estimating sensory disturbances in the distribution of the inferior alveolar nerve following injury. Assessment of sensory alterations can be conducted using three types of measures: (i) objective electrophysiological measures of nerve conduction, (ii) sensory testing (stimulus) measures and (iii) patient report. Each type of measure with advantages and disadvantages for use are reviewed.

Management of a complex wound in a person with spinal cord injury and mental illness

This paper highlights the important nexus between physical and mental health by examining a case concerning a patient with a lower spinal cord injury and mental illness who subsequently developed two pressure ulcers. It examines how clinicians can benefit from looking beyond typical assumptions when caring for an individual with complex needs in the community setting. In such circumstances, the need for a holistic and collaborative approach to wound care is vital. This involves taking into account the individual's mental health care needs, which can be overlooked in the first instance. Recommendations for clinical practice centre on involving the patient in his or her dietary, psychological and physical care, thereby helping to build resilience to any mental health problems and promoting a positive physical recovery.

Sensory retraining: burden in daily life related to altered sensation after orthognathic surgery, a randomized clinical trial

OBJECTIVE

Assess the long-term effect of sensory retraining exercises, age, gender, type of surgery, and pre-surgical psychological distress on patients' perception of the interference related to altered sensation 2 years after orthognathic surgery.

SETTING AND SAMPLE POPULATION

A total of 186 subjects with a developmental dentofacial disharmony were enrolled in a multicenter randomized clinical trial: one center was a community-based practice and the other a university-based center.

METHODS AND MATERIALS

Subjects were randomly allocated to two groups: standard of care mouth opening exercises after BSSO or a progressive series of sensory retraining facial exercises in addition to the opening exercises. At 1, 3, 6, 12, and 24 months after surgery, subjects scored unusual feelings on the face, numbness, and loss of lip sensitivity from 'no problem (1)' to 'serious problem (7)'. A marginal proportional odds model was fit for each of the ordinal outcomes.

RESULTS

Up to 2 years after surgery, the opening exercise only group had a higher likelihood of reporting interference in daily activities related to numbness and loss of lip sensitivity than the sensory retraining exercise group. The difference between the two groups was relatively constant. Older subjects and those with elevated psychological distress before surgery reported higher burdens related to unusual facial feelings, numbness, and loss of lip sensitivity (p < 0.02).

CONCLUSION

The positive effect of sensory retraining facial exercises observed after surgery is maintained over time. Clinicians should consider the patient's age and psychological well-being prior to providing pre-surgical counseling regarding the impact on daily life of persistent altered sensation following a mandibular osteotomy.