The genetics of skin, hair, and eye color variation and its relevance to forensic pigmentation predictive tests

This review examines the potential application of single nucleotide polymorphism (SNP)-based predictive tests for skin, hair, and eye color to forensic analysis in support of police investigations lacking DNA database matches or eyewitness testimony. Brief descriptions of the biology of melanogenesis and the main genes involved are presented in order to understand the basis of common pigmentation variation in humans. We outline the most recently developed forensically sensitive multiplex tests that can be applied to investigative analyses. The review also describes the biology of the SNPs with the closest associations to, and therefore the best predictors for, common variation in eye, hair, and skin pigmentation. Because pigmentation pathways are complex in their patterns, many of the better-studied human albinism traits provide insight into how pigmentation SNPs interact, control, or modify gene expression and show varying degrees of association with the key genes identified to date. These aspects of SNP action are discussed in an overview of each of the functional groups of pigmentation genes.

Calculated globulin (CG) as a screening test for antibody deficiency

Calculated globulin (total protein - albumin) is usually tested as part of a liver function test profile in both primary and secondary care and determines the serum globulin concentration, of which immunoglobulins are a major component. The main use hitherto of calculated globulin is to detect paraproteins when the level is high. This study investigated the potential to use low levels of calculated globulin to detect antibody deficiency. Serum samples with calculated globulin cut-off < 18 g/l based on results of a pilot study were collected from nine hospitals in Wales over a 12-month period. Anonymized request information was obtained and the samples tested for immunoglobulin levels, serum electrophoresis and, if appropriate, immunofixation. A method comparison for albumin measurement using bromocresol green and bromocresol purple was undertaken. Eighty-nine per cent (737 of 826) samples had an immunoglobulin (Ig)G level of < 6 g/l using the bromocresol green methodology with a cut-off of < 18 g/l, and 56% (459) had an IgG of < 4 g/l. Patients with both secondary and primary antibody deficiency were discovered and serum electrophoresis and immunofixation showed that 1·2% (10) had previously undetected small paraproteins associated with immune-paresis. Using bromocresol purple, 74% of samples had an IgG of < 6 g/l using a cut-off of < 23 g/l. Screening using calculated globulin with defined cut-off values detects both primary and secondary antibody deficiency and new paraproteins associated with immune-paresis. It is cheap, widely available and under-utilized. Antibody-deficient patients have been discovered using information from calculated globulin values, shortening diagnostic delay and time to treatment with immunoglobulin replacement therapy.

A SNaPshot of next generation sequencing for forensic SNP analysis

Forensic phenotyping can provide useful intelligence regarding the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of an evidentiary sample. Currently, single nucleotide polymorphism (SNP) based inference of BGA and EVCs is performed most commonly using SNaPshot(®), a single base extension (SBE) assay. However, a single SNaPshot multiplex PCR is limited to 30-40 SNPs. Next generation sequencing (NGS) offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. The PCR multiplexes from five SNaPshot assays (SNPforID 52plex, SNPforID 34plex, Eurasiaplex, IrisPlex and an unpublished BGA assay) were applied to three different DNA template amounts (0.1, 0.2 and 0.3 ng) in three samples (9947A and 007 control DNAs and a male donor). The pooled PCR amplicons containing 136 unique SNPs were sequenced using Life Technologies' Ion Torrent™ PGM system. Approximately 72 Mb of sequence was generated from two 10 Mb Ion 314™ v1 chips. Accurate genotypes were readily obtained from all three template amounts. Of a total of 408 genotypes, 395 (97%) were fully concordant with SNaPshot across all three template amounts. Of those genotypes discordant with SNaPshot, six Ion Torrent sequences (1.5%) were fully concordant with Sanger sequencing across the three template amounts. Seven SNPs (1.7%) were either discordant between template amounts or discordant with Sanger sequencing. Sequence coverage observed in the negative control, and, allele coverage variation for heterozygous genotypes highlights the need to establish a threshold for background levels of sequence output and heterozygous balance. This preliminary study of the Ion Torrent PGM system has demonstrated considerable potential for use in forensic DNA analyses as a low to medium throughput NGS platform using established SNaPshot assays.

Regression analysis of correlated ordinal data using orthogonalized residuals

Semi-parametric regression models for the joint estimation of marginal mean and within-cluster pairwise association parameters are used in a variety of settings for population-averaged modeling of multivariate categorical outcomes. Recently, a formulation of alternating logistic regressions based on orthogonalized, marginal residuals has been introduced for correlated binary data. Unlike the original procedure based on conditional residuals, its covariance estimator is invariant to the ordering of observations within clusters. In this article, the orthogonalized residuals method is extended to model correlated ordinal data with a global odds ratio, and shown in a simulation study to be more efficient and less biased with regards to estimating within-cluster association parameters than an existing extension to ordinal data of alternating logistic regressions based on conditional residuals. Orthogonalized residuals are used to estimate a model for three correlated ordinal outcomes measured repeatedly in a longitudinal clinical trial of an intervention to improve recovery of patients' perception of altered sensation following jaw surgery.

A high-dose preparation of lactobacilli and bifidobacteria in the prevention of antibiotic-associated and Clostridium difficile diarrhoea in older people admitted to hospital: a multicentre, randomised, double-blind, placebo-controlled, parallel arm trial (PLACIDE)

BACKGROUND

Antibiotic-associated diarrhoea (AAD) occurs most commonly in older people admitted to hospital and within 12 weeks of exposure to broad-spectrum antibiotics. Although usually a mild and self-limiting illness, the 15-39% of cases caused by Clostridium difficile infection [C. difficile diarrhoea (CDD)] may result in severe diarrhoea and death. Previous research has shown that probiotics, live microbial organisms that, when administered in adequate numbers, are beneficial to health, may be effective in preventing AAD and CDD.

OBJECTIVES

To determine the clinical effectiveness and cost-effectiveness of a high-dose, multistrain probiotic in the prevention of AAD and CDD in older people admitted to hospital.

DESIGN

A multicentre, randomised, double-blind, placebo-controlled, parallel-arm trial.

SETTING

Medical, surgical and elderly care inpatient wards in five NHS hospitals in the UK.

PARTICIPANTS

Eligible patients were aged ≥ 65 years, were exposed to one or more oral or parenteral antibiotics and were without pre-existing diarrhoeal disorders, recent CDD or at risk of probiotic adverse effects. Out of 17,420 patients screened, 2981 (17.1%) were recruited. Participants were allocated sequentially according to a computer-generated random allocation sequence; 1493 (50.1%) were allocated to the probiotic and 1488 (49.9%) to the placebo arm.

INTERVENTIONS

Vegetarian capsules containing two strains of lactobacilli and two strains of bifidobacteria (a total of 6 × 10(10) organisms per day) were taken daily for 21 days. The placebo was inert maltodextrin powder in identical capsules.

MAIN OUTCOME MEASURES

The occurrence of AAD within 8 weeks and CDD within 12 weeks of recruitment was determined by participant follow-up and checking hospital laboratory records by research nurses who were blind to arm allocation.

RESULTS

Analysis based on the treatment allocated included 2941 (98.7%) participants. Potential risk factors for AAD at baseline were similar in the two study arms. Frequency of AAD (including CDD) was similar in the probiotic (159/1470, 10.8%) and placebo arms [153/1471, 10.4%; relative risk (RR) 1.04; 95% confidence interval (CI) 0.84 to 1.28; p = 0.71]. CDD was an uncommon cause of AAD and occurred in 12/1470 (0.8%) participants in the probiotic and 17/1471 (1.2%) in the placebo arm (RR 0.71; 95% CI 0.34 to 1.47; p = 0.35). Duration and severity of diarrhoea, common gastrointestinal symptoms, serious adverse events and quality of life measures were also similar in the two arms. Total health-care costs per patient did not differ significantly between the probiotic (£8020; 95% CI £7620 to £8420) and placebo (£8010; 95% CI £7600 to £8420) arms.

CONCLUSION

We found no evidence that probiotic administration was effective in preventing AAD. Although there was a trend towards reduced CDD in the probiotic arm, on balance, the administration of this probiotic seems unlikely to benefit older patients exposed to antibiotics. A better understanding of the pathogenesis of AAD and CDD and the strain-specific effects of probiotics is needed before further clinical trials of specific microbial preparations are undertaken. Evaluation of the effectiveness of other probiotics will be difficult where other measures, such as antibiotic stewardship, have reduced CDD rates.

TRIAL REGISTRATION

This trial is registered as ISRCTN70017204.

FUNDING

This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 17, No. 57. See the NIHR Journals Library website for further project information.

Nurses' experiences providing palliative care to individuals living in rural communities: aspects of the physical residential setting

INTRODUCTION

Efforts are needed to improve palliative care in rural communities, given the unique characteristics and inherent challenges with respect to working within the physical aspects of residential settings. Nurses who work in rural communities play a key role in the delivery of palliative care services. Hence, the purpose of this study was to explore nurses' experiences of providing palliative care in rural communities, with a particular focus on the impact of the physical residential setting.

METHODS

This study was grounded in a qualitative approach utilizing an exploratory descriptive design. Individual telephone interviews were conducted with 21 community nurses. Data were analyzed by thematic content analysis.

RESULTS

Nurses described the characteristics of working in a rural community and how it influences their perception of their role, highlighting the strong sense of community that exists but how system changes over the past decade have changed the way they provide care. They also described the key role that they play, which was often termed a 'jack of all trades', but focused on providing emotional, physical, and spiritual care while trying to manage many challenges related to transitioning and working with other healthcare providers. Finally, nurses described how the challenges of working within the physical constraints of a rural residential setting impeded their care provision to clients who are dying in the community, specifically related to the long distances that they travel while dealing with bad weather.

CONCLUSIONS

These study findings contribute to our understanding of the experiences of nurses working in rural communities in terms of the provision of palliative care and the influence of the physical residential setting that surrounds them. These findings are important since nurses play a major role in caring for community-dwelling clients who are dying, but they are confronted with many obstacles. As such, these results may help inform future decisions about how to best improve access to important services and ways to support them while providing palliative care to rural individuals.

The effects of lip revision surgery on nasolabial esthetics in patients with cleft lip

OBJECTIVES

1) To determine the concordance among surgeons on subjective assessments of nasolabial esthetics in children with repaired cleft lip; and 2) to evaluate longitudinal changes in nasolabial esthetics in relation to cleft lip revision surgery.

SETTING AND SAMPLE POPULATION

School of Dentistry at University of North Carolina, Chapel Hill. Children with repaired unilateral cleft lip: 32 had lip revision surgery and 27 did not have surgery.

MATERIALS AND METHODS

Retrospective observational study from a non-randomized clinical trial. Ratings of nasolabial esthetics performed by six surgeons using the Asher-McDade scale at baseline and 12-month follow-up.

RESULTS

Concordance among surgeons ranged from poor to acceptable. Nasolabial ratings at follow-up were better in the Revision group than in the Non-Revision group, although differences were small. The most prevalent change in the Revision Group was improvement in one or more units on the scale, while 'no change' was most prevalent in the Non-Revision group. Participants in the Revision group were more likely to receive a 'no' in relation to the need for lip or nose revision at the follow-up visit.

CONCLUSION

There were mild esthetic improvements observed in relation to lip revision surgery, which should be interpreted with caution given the subjectivity of the rating method used.

Are bioresorbable polylactate devices comparable to titanium devices for stabilizing Le Fort I advancement?

The purpose of this study was to evaluate whether skeletal and dental outcomes following Le Fort I surgery differed when stabilization was performed with polylactate bioresorbable devices or titanium devices. Fifty-seven patients with preoperative records and at least 1 year postoperative records were identified and grouped according to the stabilization method. All cephalometric X-rays were traced and digitized by a single operator. Analysis of covariance was used to compare the postsurgical change between the two stabilization methods. Twenty-seven patients received bioresorbable devices (group R), while 30 received titanium devices (group M). There were no statistically significant differences between the two groups with respect to gender, race/ethnicity, age, or dental and skeletal movements during surgery. Subtle postsurgical differences were noted, but were not statistically significant. Stabilization of Le Fort I advancement with polylactate bioresorbable and titanium devices produced similar clinical outcomes at 1 year following surgery.

PRoNTo: pattern recognition for neuroimaging toolbox

In the past years, mass univariate statistical analyses of neuroimaging data have been complemented by the use of multivariate pattern analyses, especially based on machine learning models. While these allow an increased sensitivity for the detection of spatially distributed effects compared to univariate techniques, they lack an established and accessible software framework. The goal of this work was to build a toolbox comprising all the necessary functionalities for multivariate analyses of neuroimaging data, based on machine learning models. The “Pattern Recognition for Neuroimaging Toolbox” (PRoNTo) is open-source, cross-platform, MATLAB-based and SPM compatible, therefore being suitable for both cognitive and clinical neuroscience research. In addition, it is designed to facilitate novel contributions from developers, aiming to improve the interaction between the neuroimaging and machine learning communities. Here, we introduce PRoNTo by presenting examples of possible research questions that can be addressed with the machine learning framework implemented in PRoNTo, and cannot be easily investigated with mass univariate statistical analysis.

A UK national audit of hereditary and acquired angioedema

Hereditary angioedema (HAE) and acquired angioedema (AAE) are rare life-threatening conditions caused by deficiency of C1 inhibitor (C1INH). Both are characterized by recurrent unpredictable episodes of mucosal swelling involving three main areas: the skin, gastrointestinal tract and larynx. Swelling in the gastrointestinal tract results in abdominal pain and vomiting, while swelling in the larynx may be fatal. There are limited UK data on these patients to help improve practice and understand more clearly the burden of disease. An audit tool was designed, informed by the published UK consensus document and clinical practice, and sent to clinicians involved in the care of HAE patients through a number of national organizations. Data sets on 376 patients were received from 14 centres in England, Scotland and Wales. There were 55 deaths from HAE in 33 families, emphasizing the potentially lethal nature of this disease. These data also show that there is a significant diagnostic delay of on average 10 years for type I HAE, 18 years for type II HAE and 5 years for AAE. For HAE the average annual frequency of swellings per patient affecting the periphery was eight, abdomen 5 and airway 0·5, with wide individual variation. The impact on quality of life was rated as moderate or severe by 37% of adult patients. The audit has helped to define the burden of disease in the UK and has aided planning new treatments for UK patients.

Abstract P4-05-16: Quality metric study of real-time targeted massive parallel sequencing (MPS) (ampliseq comprehensive cancer panel (CCP)) and bioinformatics in early breast cancer (EBC) using life technologies ion proton system

We undertook a prospective quality assurance and metric study in 26 women with early breast cancer (EBC) in order to identify issues that may interfere with real-time integration of massive parallel sequencing (MPS) with clinical and pathology parameters for clinical decision making.

Pre-operatively, patients underwent formal informed consent process with the aid of bespoke multimedia (iPad) technology to educate patients on a) the logistical aims of the trial b) somatic and hereditary genomics c) privacy and off target (non-cancer) issues.

On Day 1, seven patients (27%) underwent WLE & SNB, 17 (65%) WLE & AXLND, 2 (7%) Mastectomy & SNB.

Samples (tumour and normal) were collected fresh into Qiagen PaxGene Tissue Container preserving both morphology and biomolecules of the sample with lysis of tissues overnight.

Day 2&3; DNA extraction was performed using the Qiagen DSP kit over 1 hour.

DNA MPS CCP was performed on Life technologies Proton P1 chip using in-house modification of manufacturers protocol. The average time taken to run CCP includes 2 days library preparation; 4 hour sequencing run, 8 hours primary analysis for generating read alignments and sequencing files. The Ampliseq protocol required modifications with respect to template input amount and cycling parameters in order to increase the fidelity of library preparation. Limitations in sequencing depth and read qualities with the current technologies lend themselves to approximately 5-6 samples/sequencing run/day if 500x read depth per amplicon is desired.

Days 4-6 manually curated bioinformatics against publicly available mutation databases (e.g. COSMIC, ENSEMBL etc.)

Day 7 communication of results

Molecular Pathology results

The median age was 57, (32-84), 18 (72%) were postmenopausal. Histopathology invasive ductal 22 (84%), invasive lobular 2 (8%) metaplastic 2 (8%).

TNM Staging: T1b 5 (19%), T1c 9 (35%) T2 12 (46%); N0 23 (88%), N1mi 1 (4%), N1a 1 (4%), N2a 1 (4%).

Hormone receptors antibodies: ER (Roche SP1) Strong 20 (77%), Moderate 1 (4%), Weak 1 (4%), Negative 4 (15%); PR (Roche 1E2) Strong 11 (42%), Moderate 10 (38%), Weak 0 (0%), Negative 5 (19%); HER2 IHC (Ventana 4B5) Strong 1 (4%), Moderate 6 (23%), Weak 6 (23%), Negative 13 (50%); HER2 SISH (Ventana inform single probe); 1 SISH positive (mean copy number 29.6); 4 patients (15%) triple negative.

Molecular aberrations identified included oncogenes TP53 2 (8%), PIK3CA 12 (46%) HRAS 2 (8%), AKT1 1 (4%); tumour suppressor genes MLL3 2 (8%), MSH6 1 (4%), ARID1A 1 (4%), and in the germline in tumour suppressor genes EPHB6 1 (4%) and LTK 1 (4%).

Significant technical and bioinformatic challenges were encountered during the development of this metric study including Ampliseq protocol modification and parameter tuning for variant calling algorithm.

In summary, many challenges face the clinical laboratory developing high throughput MPS using desktop MPS. To date this is the first publication of the new Ion Proton P1 chips in development for real-time clinical decision making. Copy-number variation (CNV), RNA-Seq, Methyl-Seq data will be available for presentation at San Antonio.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-05-16.

RNA/DNA co-analysis from human menstrual blood and vaginal secretion stains: results of a fourth and fifth collaborative EDNAP exercise

The European DNA Profiling Group (EDNAP) organized a fourth and fifth collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling. The task was to identify dried menstrual blood and vaginal secretion stains using specific RNA biomarkers, and additionally test 3 housekeeping genes for their suitability as reference genes. Six menstrual blood and six vaginal secretion stains, two dilution series (1/4-1/64 pieces of a menstrual blood/vaginal swab) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 24 participating laboratories, using RNA extraction or RNA/DNA co-extraction methods. Two novel menstrual blood mRNA multiplexes were used: MMP triplex (MMP7, MMP10, MMP11) and MB triplex (MSX1, LEFTY2, SFRP4) in conjunction with a housekeeping gene triplex (B2M, UBC, UCE). Two novel mRNA multiplexes and a HBD1 singleplex were used for the identification of vaginal secretion: Vag triplex (MYOZ1, CYP2B7P1 and MUC4) and a Lactobacillus-specific Lacto triplex (Ljen, Lcris, Lgas). The laboratories used different chemistries and instrumentation and all were able to successfully isolate and detect mRNA in dried stains. The simultaneous extraction of RNA and DNA allowed for positive identification of the tissue/fluid source of origin by mRNA profiling as well as a simultaneous identification of the body fluid donor by STR profiling, also from old and compromised casework samples. The results of this and the previous collaborative RNA exercises support RNA profiling as a reliable body fluid identification method that can easily be combined with current STR typing technology.

Effectiveness and cost-effectiveness of a universal parenting skills programme in deprived communities: multicentre randomised controlled trial

OBJECTIVE

To evaluate the effectiveness and cost utility of a universally provided early years parenting programme.

DESIGN

Multicentre randomised controlled trial with cost-effectiveness analysis.

SETTING

Early years centres in four deprived areas of South Wales.

PARTICIPANTS

Families with children aged between 2 and 4 years. 286 families were recruited and randomly allocated to the intervention or waiting list control.

INTERVENTION

The Family Links Nurturing Programme (FLNP), a 10-week course with weekly 2 h facilitated group sessions.

MAIN OUTCOME MEASURES

Negative and supportive parenting, child and parental well-being and costs assessed before the intervention, following the course (3 months) and at 9 months using standardised measures.

RESULTS

There were no significant differences in primary or secondary outcomes between trial arms at 3 or 9 months. With '+' indicating improvement, difference in change in negative parenting score at 9 months was +0.90 (95%CI -1.90 to 3.69); in supportive parenting, +0.17 (95%CI -0.61 to 0.94); and 12 of the 17 secondary outcomes showed a non-significant positive effect in the FLNP arm. Based on changes in parental well-being (SF-12), the cost per quality-adjusted life year (QALY) gained was estimated to be £34 913 (range 21 485-46 578) over 5 years and £18 954 (range 11 664-25 287) over 10 years. Probability of cost per QALY gained below £30 000 was 47% at 5 years and 57% at 10 years. Attendance was low: 34% of intervention families attended no sessions (n=48); only 47% completed the course (n=68). Also, 19% of control families attended a parenting programme before 9-month follow-up.

CONCLUSIONS

Our trial has not found evidence of clinical or cost utility for the FLNP in a universal setting. However, low levels of exposure and contamination mean that uncertainty remains.

TRIAL REGISTRATION

The trial is registered with Current Controlled Trials ISRCTN13919732.

A decision impact, decision conflict and economic assessment of routine Oncotype DX testing of 146 women with node-negative or pNImi, ER-positive breast cancer in the U.K

Background:

Tumour gene expression analysis is useful in predicting adjuvant chemotherapy benefit in early breast cancer patients. This study aims to examine the implications of routine Oncotype DX testing in the UK.

Methods:

Women with oestrogen receptor positive (ER+), pNO or pN1mi breast cancer were assessed for adjuvant chemotherapy and subsequently offered Oncotype DX testing, with changes in chemotherapy decisions recorded. A subset of patients completed questionnaires about their uncertainties regarding chemotherapy decisions pre- and post-testing. All patients were asked to complete a diary of medical interactions over the next 6 months, from which economic data were extracted to model the cost-effectiveness of testing.

Results:

Oncotype DX testing resulted in changes in chemotherapy decisions in 38 of 142 (26.8%) women, with 26 of 57 (45.6%) spared chemotherapy and 12 of 85 (14.1%) requiring chemotherapy when not initially recommended (9.9% reduction overall). Decision conflict analysis showed that Oncotype DX testing increased patients' confidence in treatment decision making. Economic analysis showed that routine Oncotype DX testing costs £6232 per quality-adjusted life year gained.

Conclusion:

Oncotype DX decreased chemotherapy use and increased confidence in treatment decision making in patients with ER+ early-stage breast cancer. Based on these findings, Oncotype DX is cost-effective in the UK setting.