Aligned or misaligned: Are public funding models for speech-language pathology reflecting recommended evidence? An exploratory survey of Australian speech-language pathologists

Government subsidised funding arrangements serve as an essential medium for families to access private speech-language pathology (SLP) services in Australia. This study aimed to investigate whether, from a provider perspective, contemporary public funding models (PFMs) align with best-available scientific evidence for management of children and young persons with swallowing and communication disorders within Australian private-practice settings. This exploratory study was distributed to paediatric speech-language pathologists throughout Australia via an online survey. A total of 121 valid surveys were completed by Australian speech-language pathologists with divergent career experiences. In comparing three familiar PFMs using mixed effects logistic regression models to estimate odds ratios, results indicated that perceived congruence with recommended scientific evidence for SLP management varied across PFMs: the odds of failing to align with scientific evidence was 4.92 times higher for Medicare's Chronic Disease Management Plan (MBS_CDMP) than for the National Disability Insurance Scheme; and 7.40 times higher in comparison to Medicare's Helping Children with Autism initiative. This study is the first to report on (in)congruence between PFMs that provide access to independent Australian SLP services for children and young persons and best available scientific evidence to inform clinical practice. Participants identified that: (a) four out of seven contemporary PFMs were unfamiliar to speech-language pathologists; and (b) MBS_CDMP initiative failed to align with the evidence-base for best scientific SLP management.

Magnetically Detected Protein Binding Using Spin-Labeled Slow Off-Rate Modified Aptamers

Recent developments in aptamer chemistry open up opportunities for new tools for protein biosensing. In this work, we present an approach to use immobilized slow off-rate modified aptamers (SOMAmers) site-specifically labeled with a nitroxide radical via azide-alkyne click chemistry as a means for detecting protein binding. Protein binding induces a change in rotational mobility of the spin label, which is detected via solution-state electron paramagnetic resonance (EPR) spectroscopy. We demonstrate the workflow and test the protocol using the SOMAmer SL5 and its protein target, platelet-derived growth factor B (PDGF-BB). In a complete site scan of the nitroxide over the SOMAmer, we determine the rotational mobility of the spin label in the absence and presence of target protein. Several sites with sufficiently tight affinity and large rotational mobility change upon protein binding are identified. We then model a system where the spin-labeled SOMAmer assay is combined with fluorescence detection via diamond nitrogen-vacancy (NV) center relaxometry. The NV center spin-lattice relaxation time is modulated by the rotational mobility of a proximal spin label and thus responsive to SOMAmer-protein binding. The spin label-mediated assay provides a general approach for transducing protein binding events into magnetically detectable signals.

POS0656 FRAILTY AND RISK OF ADVERSE OUTCOMES IN BIOLOGIC OR TARGETED-SYNTHETIC DMARD TREATED PATIENTS WITH RHEUMATOID ARTHRITIS

Background

Recently, it has been recognized that frailty and pre-frailty are common in patients with rheumatoid arthritis (RA) [1]. Whether frailty status portends an increased risk of adverse outcomes in patients with RA on biologic or targeted synthetic disease modifying anti-rheumatic drugs (b- or tsDMARDs) remains unknown.

Objectives

To evaluate the association between frailty and adverse outcomes in patients with RA exposed to b- or tsDMARDs.

Methods

Using the IBM/Watson MarketScan Commercial Claims and Encounters Databases, we identified all patients with RA who filled new prescriptions (or received infusions) for TNFα antagonists (TNFi), non-TNFi biologics (rituximab, abatacept, tocilizumab) or Janus Kinase inhibitors (JAKi) between 2008-2019. We used a 1-year lookback period without the use of these drugs to identify new users. The date of the first prescription within these three drug categories was the index date. Patients’ frailty risk score was calculated using the Claims-Based Frailty Index (CFI) [2], which estimates a deficit-accumulation frailty index using International Classification of Diseases codes, Current Procedural Terminology codes, and Healthcare Common Procedure Coding System codes in administrative claims data in the 1-year baseline period. The index ranges from 0 (not at all frail) to 1 (severely frail). The primary outcome was time to serious infections (those requiring hospitalization); secondary outcomes: any infection (outpatient or inpatient encounters) and all-cause hospitalizations.

Patients were followed until 1) outcome occurrence; 2) disenrollment; 3) >90 days elapsed (or >180 days for rituximab) without further fills of the first drug categories; 4) they filled/received infusions of b-/tsDMARDs from a different drug category; or 5) 2 years after index. Cox proportional hazards adjusting for demographics, calendar year, serious and/or opportunistic infections in the 12-months prior to index were used to estimate the adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for each outcome. In separate model, we additionally adjusted for comorbidity burden, and health care utilization (HCU).

Results

A total of 62,246 patients with RA met our inclusion criteria of whom 50,910 (82%) started TNFi as their first biologic, 9525 (15%) non-TNFi biologics, and 1811 (3%) JAKi. Among these, 3928 (6%) were considered frail. In multivariable analyses, frail patients had higher risk of serious infections compared to non-frail patients (aHR 2.37, 95% CI 2.05-2.74) which decreased to aHR 1.34, 95% CI 1.13-1.58 (Table 1) after adjusting for comorbidity burden and the HCU. Similarly, frailty was associated with increased risk of any infection (aHR 1.18, 95% CI 1.11-1.25), and all-cause hospitalizations (aHR 1.34, 95% CI 1.21-1.49) relative to non-frail individuals.

Table 1.

Multivariable models evaluating the association between frailty status and inpatient infections as the outcome

Variable#Hazard Ratio (95% Confidence Interval)@Hazard Ratio (95% Confidence Interval)Frail2.37 (2.05, 2.74)1.34 (1.13, 1.58)

#Model adjusts for age, sex, major infection requiring inpatient admission in 12 months prior, concomitant baseline drugs such as csDMARDs, glucocorticoids, NSAIDs and opioids

@Model additionally adjusts for Chalrson comorbidy score and healthcare utilization

Conclusion

Frailty is an important predictor for the risk of adverse outcomes among patients with RA treated with b- or tsDMARDs. Our findings underscore the need for considering this parameter in patient evaluations (even among younger patients) in the clinic.

References

[1]Salaffi F et al: Prevalence of frailty and its associated factors in patients with rheumatoid arthritis: a cross-sectional analysis. Clin Rheumatol 2019

[2]Kim DH et al. Validation of a Claims-Based Frailty Index Against Physical Performance and Adverse Health Outcomes in the Health and Retirement Study. J Gerontol A Biol Sci Med Sci 2019

Acknowledgements

I have no acknowledgements to declare.

Disclosure of Interests

None declared

Abstract P5-09-06: Underdiagnosis of HBOC in breast cancer patients: Are genetic testing guidelines a tool or an obstacle?

Background: Pathogenic genetic variants are estimated to occur in 10-15% of all breast cancer patients, with BRCA 1/2 accounting for 40-50% of pathogenic/likely pathogenic (P/LP) variants. However, it is estimated that <30% of breast cancer patients harboring a BRCA 1/2 variant have been identified, with the percentage being much less for ˜20 other breast cancer associated genes. Reasons for this are multifactorial and include complicated and restrictive testing guidelines developed at a time when the cost of testing was high and guidelines for management were limited. Today, cost has plummeted and there are definitive management guidelines for a broader range of genes. We created a community based Registry to determine the incidence of P/LP variants in breast cancer patients who meet and who do not meet the NCCN 2017 genetic testing criteria.

Methods: An IRB-approved multicenter prospective registry was initiated with 20 community and academic sites experienced incancer genetic testing and counseling.

Eligibility criteria included patients with a breast cancer diagnosis who had not been previously tested. Consecutive patients aged 18-90 were consented and underwent an 80 gene panel test (Invitae –Multi-Cancer Panel). The non-inferiority study was powered to detect a difference in P/LP variant rate of 4 percentage points with statistical significance (p<0.05, Fisher's exact test).

HIPAA compliant electronic case report forms collected information on patient diagnosis, test results, and physician recommendations made after test results were received.

Results: Over 1000 patients were enrolled and data from 910 subjects analyzed to date. 50.4% met NCCN criteria and 49.5% did not. Median age for the enrolled patients is 60.5 and ranged from 22-93. 56.0% of patients were recently diagnosed with breast cancer. 10.9% of patients had a history of a prior non breast cancer. Overall, 8.9% of patients had a pathogenicvariant. 9.6% of patients who met NCCN criteria with test results had a P/LP variant. 8.2% of patients who did not meet criteria had a P/LP variant. The difference of positive cases among the two groups is not statistically significant (P = 0.49)

4.9% of patients had pathogenic variants if only an 11 gene standard breast cancer panel was considered.

The spectrum of mutated genes varied between the two groups, with some overlap.

Conclusions:

There was no statistically significant difference in the number of pathogenic/likely pathogenic variants between those patients who met and those who did not meet NCCN guidelines. Expanded panel testing yields more medically actionable P/LP variants than testing BRCA 1/2 alone or breast cancer panels with 11 genes. This study demonstrates that there will be a significant number of patients with P/LP variants are missed if NCCN guidelines are required for genetic testing. Current NCCN guidelines for the genetic testing of breast cancer patients are an obstacle to identifying patients with P/LP variants and should be removed.

Universal BC Genetic Testing RegistryNCCN Criteria (910 patients analyzed)#/% who have P/LP variants#/% who do not have P/LP variantsPatients who meet guidelines44/459 (9.6%)415/459 (90.4%)Patients who do not meet guidelines37/451 (8.2%)414/451 (91.8%)

Citation Format: Beitsch P, Whitworth P, Baron P, Rosen B, Compagnoni G, Simmons R, Smith LA, Holmes D, Brown E, Gold L, Clark P, Coomer C, Grady I, Barbosa K, Riley L, Kinney M, Lyons S, MacDonald H, Kahn S, Ruiz A, Patel R, Curcio L, Esplin E, Yang S. Underdiagnosis of HBOC in breast cancer patients: Are genetic testing guidelines a tool or an obstacle? [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-09-06.

Abstract P5-09-03: Expanded panel testing superior to BRCA1/2 and breast cancer panel in patients with breast cancer

Background: The testing of hereditary breast and ovarian cancer (HBOC) patients for BRCA1/2 only was established years ago to identify patients with clinically actionable variants and limit the economic burden. However, the cost of genetic testing has plummeted, and the number of breast cancer-risk genes with management guidelines has expanded. We created a community-based registry to test all breast cancer patients. A primary objective of this registry included accruing and comparing patients who did and did not meet NCCN guidelines and determining if providing all breast cancer patients with comprehensive multi-gene panel testing yields additional clinical value than testing BRCA1/2 alone.

Methods: An IRB-approved multicenter prospective registry was initiated with 20 community-based and academic breast sites, selected to insure geographic and ethnic diversity. Consecutive patients ages 18-90 with current or prior breast cancer were offered testing with an 80-gene panel (Invitae, San Francisco, CA). HIPAA-compliant case report forms collected patient diagnosis, test results, and physician recommendations made after test results.

Results: Over 1,000 patients were enrolled and data on 911 have been analyzed to date. Median age of patients is 60.5 (range 22 to 93). 56.0% were recently diagnosed with breast cancer. Of these patients, 50.54% met NCCN criteria, and 49.5% did not. 10.9% had history of a prior non-breast cancer. The pathogenic/likely pathogenic (P/LP) variant rate for patients on a comprehensive 80-gene panel was 8.9%. When restricted to a guidelines-based 11-gene breast cancer panel (BRCA1/2, ATM, CDH1, CHEK2, NBN, NF1, PTEN, STK11, TP53, PALB2), 4.9% had P/LP variants; when limited to BRCA1/2, 1.6% had P/LP variants. Of all patients with P/LP findings, 93% had variants in cancer-risk genes with established management recommendations (Table 1) and 80% had germline variants conferring eligibility for precision medicine-based cancer treatments, such as PARP inhibitors, through actively enrolling clinical trials.

Conclusions: This study demonstrates that comprehensive panel testing of breast cancer patients provides a higher yield of clinically actionable P/LP variants than BRCA1/2 testing alone. Limited panels may miss clinically relevant P/LP variants, leaving risk for preventable cancers undiscovered and unnecessarily restricting patients' treatment options. These results also suggest that variants in tumor suppressor genes, not previously thought related to breast cancer, may contribute to its etiology. A comprehensive panel strategy reveals untapped clinical utility and can impact breast cancer patient care by informing implementation of precision medicine treatment interventions and guiding long-term medical management and surveillance for patients and their family members.

 PatientsVariantsWith breast cancer management guidelines (including variants ATM*, BRCA1*, BRCA2*, CHEK2*, NBN*, NF1, PALB2*, TP53*)45 (56%)46 (55%)With cancer guidelines and clinical management implications (including variants BARD1*, FH, MITF, MSH6*, MUTYH*, PTCH1, RAD50*, RAD51C*, RAD51D*, RB1, RET, VHL)31 (38%)33 (39%)Evidence of actionability accruing (including variants BLM, DIS3L2, RECQL4)5 (6%)5 (6%)Totals8184*P/LP variants in these genes confer potential clinical trial eligibility, e.g. NCT02401347.

Citation Format: Beitsch P, Whitworth P, Baron P, Rosen B, Compagnoni G, Simmons R, Smith LA, Holmes D, Brown E, Gold L, Clark P, Coomer C, Grady I, Barbosa K, Riley L, Kinney M, Lyons S, MacDonald H, Kahn S, Ruiz A, Patel R, Curcio L, Esplin E, Yang S, Michalski S. Expanded panel testing superior to BRCA1/2 and breast cancer panel in patients with breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-09-03.

High prevalence of slight and mild hearing loss across mid-life: a cross-sectional national Australian study

OBJECTIVES

Although presbycusis typically becomes symptomatic only in older age, slight and mild hearing loss may be detectable well before this. We studied current prevalence and characteristics of hearing loss in Australian mid-life adults.

STUDY DESIGN

This was a population-derived national cross-sectional study nested within the Longitudinal Study of Australian Children.

METHODS

A total of 1485 parents/guardians (87.3% female) aged 30-59 years underwent air-conduction audiometry. Hearing loss was defined in three ways to maximize cross-study comparability: high Fletcher index (mean of 1, 2 and 4 kHz; primary outcome relevant to speech perception), lower frequency (mean of 1 and 2 kHz) and higher frequency (mean of 4 and 8 kHz). Multivariable logistic regression examined how losses vary by age, sex and neighbourhood disadvantage.

RESULTS

On high Fletcher index, 27.3% had bilateral and 23.8% unilateral thresholds >15 dB hearing level (HL) (slight or worse), and 4.9% had bilateral and 6.3% unilateral thresholds >25 dB HL (mild or worse). Bilateral higher frequency losses were more common than lower frequency losses for thresholds >15 dB HL (30.9% vs. 26.4%) and >25 dB HL (11.0% vs. 4.6%). Age increased the risk of bilateral speech and higher frequency losses (all P for trend < 0.05), but not lower frequency losses >25 dB HL. Although sex was not associated with speech and lower frequency losses, men were more likely to have bilateral higher frequency losses (e.g. >15 dB HL: odds ratio [OR]: 2.2; 95% confidence interval [CI]: 1.5-3.2, P < 0.001).

CONCLUSIONS

Both slight and mild hearing loss show high and rising prevalence across mid-life. This offers opportunities to prevent progression to reduce the profound later burden of age-related hearing loss.

Does a brief, behavioural intervention, delivered by paediatricians or psychologists improve sleep problems for children with ADHD? Protocol for a cluster-randomised, translational trial

INTRODUCTION

Up to 70% of children with attention-deficit/hyperactivity disorder (ADHD) experience sleep problems. We have demonstrated the efficacy of a brief behavioural intervention for children with ADHD in a large randomised controlled trial (RCT) and now aim to examine whether this intervention is effective in real-life clinical settings when delivered by paediatricians or psychologists. We will also assess the cost-effectiveness of the intervention.

METHODS AND ANALYSIS

Children aged 5-12 years with ADHD (n=320) are being recruited for this translational cluster RCT through paediatrician practices in Victoria and Queensland, Australia. Children are eligible if they meet criteria for ADHD, have a moderate/severe sleep problem and meet American Academy of Sleep Medicine criteria for either chronic insomnia disorder or delayed sleep-wake phase disorder; or are experiencing sleep-related anxiety. Clinicians are randomly allocated at the level of the paediatrician to either receive the sleep training or not. The behavioural intervention comprises 2 consultations covering sleep hygiene and standardised behavioural strategies. The primary outcome is change in the proportion of children with moderate/severe sleep problems from moderate/severe to no/mild by parent report at 3 months postintervention. Secondary outcomes include a range of child (eg, sleep severity, ADHD symptoms, quality of life, behaviour, working memory, executive functioning, learning, academic achievement) and primary caregiver (mental health, parenting, work attendance) measures. Analyses will address clustering at the level of the paediatrician using linear mixed effect models adjusting for potential a priori confounding variables.

ETHICS AND DISSEMINATION

Ethics approval has been granted. Findings will determine whether the benefits of an efficacy trial can be realised more broadly at the population level and will inform the development of clinical guidelines for managing sleep problems in this population. We will seek to publish in leading international paediatric journals, present at major conferences and through established clinician networks.

TRIAL REGISTRATION NUMBER

ISRCTN50834814, Pre-results.

Child oral health in migrant families: A cross-sectional study of caries in 1-4 year old children from migrant backgrounds residing in Melbourne, Australia

Early Childhood Caries (ECC) is the most common, preventable disease of childhood. It can affect children's health and wellbeing and children from migrant families may be at greater risk of developing ECC.

OBJECTIVE

To describe ECC in children from migrant families, and explore possible influences.

BASIC RESEARCH DESIGN

Cross-sectional analysis of caries data collected as baseline data for an oral health promotion study.

PARTICIPANTS

The analysis sample included 630 1-4 year-old children clustered within 481 Iraqi, Lebanese and Pakistani families in Melbourne, Australia.

METHOD

Child participants received a community-based visual dental examination. Parents completed a self-administered questionnaire on demographics, ethnicity, and oral health knowledge, behaviour and attitudes.

MAIN OUTCOME MEASURE

Child caries experience. Bivariate associations between oral health behaviours and ethnicity were tested for significance using chi-square. Multivariate logistic regression analyses were performed to identify associations with ECC, adjusting for demographic variables and accounting for clustering by family.

RESULTS

Overall, 34% of children in the sample experienced caries (both non-cavitated and cavitated). For all caries lesions, parent' length of residence in Australia, consumption of sweet drinks and parental education remained as independent predictors of child caries experience. Adding sugar to drinks was an additional risk factor for cavitation. Ethnicity was associated with some individual oral health behaviours suggesting cultural influences on health, however the relationship was not independent of other predictors.

CONCLUSION

Culturally competent oral health promotion interventions should aim to support migrant families with young children, and focus on reducing sweet drink consumption.

Choosing foods for infants: a qualitative study of the factors that influence mothers

BACKGROUND

Examining the experiences of parents making food choices for infants is important because ultimately this influences what infants eat. Infancy is a critical period when food preferences and eating behaviour begin to develop, shaping dietary patterns, growth and health outcomes. There is limited evidence regarding what or why foods are chosen for infants.

OBJECTIVE

To describe the experiences of mothers making food choices for their infant children.

METHODS

Semi-structured interviews with 32 Australian mothers of infants aged four to 15 months from a range of socioeconomic backgrounds. An inductive thematic analysis through a process of constant comparison was conducted on transcribed interviews.

RESULTS

Mothers described many ideas and circumstances which influenced food choices they made for infants. Themes were developed which encapsulate how the wider environment and individual circumstances combine to result in the food choices made for infants. Beliefs, values, norms and knowledge were a central influence on choices. Cost, quality and availabilities of various foods were also key factors. Related to this, and combined with inherent factors such as perishability and infant acceptability, fresh fruits and vegetables were often singled out as an easy or difficult choice. Influences of time, parents' capacities, social connections and different information sources were clearly apparent. Finally infants' own preferences and how parents helped infants with learning to eat were also key influences on food choices.

CONCLUSIONS

Choosing foods for infants is a complex social practice. An ecological framework depicting the multiple influences on what people eat and sociological theory on food choice regarding the role of 'social structure' and 'human agency' are both applicable to the process of choosing foods for infants. Equity issues may be key regarding the degree to which mothers can choose particular foods for infants (e.g. choosing foods which promote health).

An exploration of the views of Australian mothers on promoting child oral health

BACKGROUND

An important role for parents and caregivers in the prevention of dental caries in children is the early establishment of health promoting behaviours. This study aimed to examine mothers' views on barriers and facilitators to promoting child and family oral health.

METHODS

Semi-structured interviews were undertaken with a purposive sample of mothers (n = 32) of young children. Inductive thematic analysis was conducted.

RESULTS

Parental knowledge and beliefs, past experiences and child behaviour emerged as major influences on children's oral health. Child temperament and parental time pressures were identified as barriers to good oral health with various strategies reported for dealing with uncooperative children at toothbrushing time. Parental oral health knowledge and beliefs emerged as positive influences on child oral health; however, while most mothers were aware of the common causes of dental caries, very few knew of other risk factors such as bedtime feeding. Parents' own oral health experiences were also seen to positively influence child oral health, regardless of whether these were positive or negative experiences.

CONCLUSIONS

Understanding parental oral health beliefs is essential to overcoming barriers and promoting enablers for good child oral health. Improving child oral health also requires consideration of child behaviour, family influences, and increasing awareness of lesser-known influencing factors.

Fit for the Eye: Aptamers in Ocular Disorders

For any new class of therapeutics, there are certain types of indications that represent a natural fit. For nucleic acid ligands in general, and aptamers in particular, the eye has historically been an attractive site for therapeutic intervention. In this review, we recount the discovery and early development of three aptamers designated for use in ophthalmology, one approved (Macugen), and two in late-stage development (Fovista and Zimura). Every one of these molecules was originally intended for other indications. Key improvements in technology, specifically with regard to libraries used for in vitro selection and subsequent chemical optimization of aptamers, have played an important role in allowing the identification of development candidates with suitable properties. The lessons learned from the selection of these molecules are valuable for informing us about the many remaining opportunities for aptamer-based therapeutics in ophthalmology as well as for identifying additional indications for which aptamers as a class of therapeutics have distinct advantages.

Exploring child dental service use among migrant families in metropolitan Melbourne, Australia

BACKGROUND

This study describes and explores factors related to dental service use among migrant children.

METHODS

A cross-sectional analysis of baseline data from Teeth Tales, an exploratory trial implementing a community based child oral health promotion intervention. The sample size and target population was 600 families with 1-4 year old children from Iraqi, Lebanese and Pakistani backgrounds residing in metropolitan Melbourne. Participants were recruited into the study using purposive and snowball sampling techniques.

RESULTS

Most (88%; 550/625) children had never visited the dentist (mean (SD) age 3.06 years (1.11)). In the fully adjusted model the variable most significantly associated with child dental visiting was parent reported 'no reason for child to visit the dentist' (OR = 0.07, p < 0.001). Of those children whose parents reported their child had no reason to visit the dentist, 22% (37/165) experienced dental caries with 8% (13/165) at the level of cavitation.

CONCLUSIONS

Dental service use by migrant preschool children was very low. The relationship between perceived dental need and dental service use is currently not aligned. One in 10 children of select migrant background had visited a dentist, which is in the context of 1 in 3 with dental caries. To improve utilization, health services should consider organizational cultural competence, outreach and increased engagement with the migrant community.

DTC-and-Me: Patient, Provider, Proteins and Regulators

The yet-unrealized potential for more "personalized" Direct-to-Consumer (DTC) tests to fundamentally alter the practice and economics of healthcare is undeniable. However, there are also many challenges to be met, including the herculean task of ensuring that the information provided by such tests is scientifically sound and, ideally, medically actionable. We consider recent events in DTC testing and suggest a "thought experiment" of an approach that could ultimately meet the needs of patients, providers and regulatory authorities.

Community-based healthcare costs for children born low birthweight, preterm and/or small for gestational age: data from the Longitudinal Study of Australian Children

AIM

Children born low birthweight, preterm and/or small for gestational age (SGA) sustain substantially increased costs for hospital-based health care and additional educational support in the first few years of life. This is the first study internationally to investigate costs beyond hospital care, to community-based health care and prescription medicines across early and middle childhood with actual cost data, and to examine these costs according to the severity of perinatal risk.

METHOD

In the prospective Longitudinal Study of Australian Children, we followed two cohorts of children from age of 0 to 5 years (no increased perinatal risk, n = 3973; mild risk, n = 442; and moderate-to-high risk, n = 297), and from age of 4 to 9 years (no increased perinatal risk, n = 3629; mild risk, n = 465; and moderate-to-high risk, n = 361). Children were defined as mild risk if born 32-36 weeks, with birthweight 1500-2499 g, and/or SGA (<5-9th percentile), and moderate-to-high risk if born <32 weeks, birthweight <1500 g and/or extremely SGA (<5th percentile). Federal government expenditure (2011 $AUD) on healthcare attendances and prescription medication from birth to 9 years were calculated via data linkage to the Australian Medicare records.

RESULTS

Mean costs per child were A$362 higher (95% CI $156; 568) from 0 to 5 years and A$306 higher (95% CI $137; 475) from 4 to 9 years, for children with any compared with no increased perinatal risk (P < 0.001). At the population level, an additional A$32m was spent per year for children 0-9 years with any relative to no increased perinatal risk.

CONCLUSIONS

Perinatal risk is a major public health issue conferring considerable additional expense to community-based health care, most marked in the first year of life but persisting up to at least 10 years. Even without additionally considering burden, these findings add to the urgency of identifying effective mechanisms to reduce perinatal risk across its full spectrum.

Carl Woese in Schenectady: the forgotten years

Many of the authors of these short pieces (who were invited to contribute by Robin Gutell) have already written or spoken about Carl Woese since he died at the end of December 2012. My own thoughts were published in PNAS on February 26, 2013. Still saddened by Carl’s death, I re-read what I wrote at that moment. The article was OK, although it was not strong enough for what Carl taught us: he deserved better. I’d like us to admire what Carl did over 50 years (which is a given), and to admire even more the way he did it. While Carl’s accomplishments were huge, his intense dedication to the ideas that consumed him was even more impressive.

Beyond antibodies: new affinity reagents to unlock the proteome

Antibodies have been the workhorse reagents of protein capture and quantification since their 1959 debut in the RIAs developed by Yalow and Berson. However, there are technical challenges to the use of antibodies in highly multiplexed arrays aimed at measuring hundreds or even thousands of proteins at one time. We describe here a recently developed class of synthetic protein-binding reagents (slow off-rate modified aptamer). We discuss the chemical makeup and protein binding specifications of slow off-rate modified aptamer reagents, compare them to traditional aptamers and antibodies, briefly describe the novel proteomic assay that takes advantage of their unique properties, and provide several examples of their multiple applications to biomarker discovery and validation across a range of biomedical science questions.

Methodology for the evaluation of the Stephanie Alexander Kitchen Garden program

ISSUES ADDRESSED

Community and school cooking and gardening programs have recently increased internationally. However, despite promising indications, there is limited evidence of their effectiveness. This paper presents the evaluation framework and methods negotiated and developed to meet the information needs of all stakeholders for the Stephanie Alexander Kitchen Garden (SAKG) program, a combined cooking and gardening program implemented in selectively funded primary schools across Australia.

METHODS

The evaluation used multiple aligned theoretical frameworks and models, including a public health ecological approach, principles of effective health promotion and models of experiential learning. The evaluation is a non-randomised comparison of six schools receiving the program (intervention) and six comparison schools (all government-funded primary schools) in urban and rural areas of Victoria, Australia. A mixed-methods approach was used, relying on qualitative measures to understand changes in school cultures and the experiential impacts on children, families, teachers, parents and volunteers, and quantitative measures at baseline and 1 year follow up to provide supporting information regarding patterns of change.

RESULTS

The evaluation study design addressed the limitations of many existing evaluation studies of cooking or garden programs. The multistrand approach to the mixed methodology maintained the rigour of the respective methods and provided an opportunity to explore complexity in the findings. Limited sensitivity of some of the quantitative measures was identified, as well as the potential for bias in the coding of the open-ended questions.

CONCLUSION

The SAKG evaluation methodology will address the need for appropriate evaluation approaches for school-based kitchen garden programs. It demonstrates the feasibility of a meaningful, comprehensive evaluation of school-based programs and also demonstrates the central role qualitative methods can have in a mixed-method evaluation. So what? This paper contributes to debate about appropriate evaluation approaches to meet the information needs of all stakeholders and will support the sharing of measures and potential comparisons between program outcomes for comparable population groups and settings.

Primary healthcare costs associated with sleep problems up to age 7 years: Australian population-based study

OBJECTIVES

In Australian 0-7-year olds with and without sleep problems, to compare (1) type and costs to government of non-hospital healthcare services and prescription medication in each year of age and (2) the cumulative costs according to persistence of the sleep problem.

DESIGN

Cross-sectional and longitudinal data from a longitudinal population study.

SETTING

Data from two cohorts participating in the first two waves of the nationally representative Longitudinal Study of Australian Children.

PARTICIPANTS

Baby cohort at ages 0-1 and 2-3 (n=5107, 4606) and Kindergarten cohort at ages 4-5 and 6-7 (n=4983, 4460).

MEASUREMENTS

Federal Government expenditure on healthcare attendances and prescription medication from birth to 8 years, calculated via linkage to Australian Medicare data, were compared according to parent report of child sleep problems at each of the surveys.

RESULTS

At both waves and in both cohorts, over 92% of children had both sleep and Medicare data. The average additional healthcare costs for children with sleep problems ranged from $141 (age 5) to $43 (age 7), falling to $98 (age 5) to $18 (age 7) per child per annum once family socioeconomic position, child gender, global health and special healthcare needs were taken into account. This equates to an estimated additional $27.5 million (95% CI $9.2 to $46.8 million) cost to the Australian federal government every year for all children aged between 0 and 7 years. In both cohorts, costs were higher for persistent than transient sleep problems.

CONCLUSIONS

Higher healthcare costs were sustained by infants and children with sleep problems. This supports ongoing economic evaluations of early prevention and intervention services for sleep problems considering impacts not only on the child and family but also on the healthcare system.

Taking measure of personalized medicine: the proteome

Good medicine begins, by and large, with measurements. For medicine to become truly personalized, it is critical that the right measurements are made and interpreted. Although genomics holds great promise for deepening our understanding of biology, we believe that a perhaps more critical and transformative measurement for medicine is proteomics, which has lagged behind genomics for largely technological reasons. Proteins uniquely provide a real-time, clinically relevant measure of individual patients. We describe here an entirely new proteomics technology that makes the measure of proteins from biological samples as straightforward as measuring genes, and list some of the applications that have already been performed.

RNA science and its applications-a look toward the future: Albany, NY USA, November 3-4, 2011

On November 3–4, 2010, the Symposium RNA Science and its Applications: A look toward the Future was held at the University at Albany-SUNY in the capital of New York State. Unique to this Symposium’s format were panel discussions following each of the four platform sessions: RNA Technological Innovation: Analysis, Delivery, Nanotechnologies, IT; Infectious and other diseases: The future of small molecule intervention; RNA Discovery and Innovation: Cell and Molecular Biology; and Cancer and Neurological Disease: The future of small RNAs as therapeutics and tools of investigation. The meeting was organized by Thomas Begley, Marlene Belfort, Daniele Fabris, Melinda Larsen, Pan T.X. Li, Albert Millis, Li Niu, David Shub, and Carla Theimer of The RNA Institute at University at Albany-SUNY, Paul F. Agris, Director, and Jennifer S. Montimurro, Program Manager.

Effects of continuity of care by a primary midwife (caseload midwifery) on caesarean section rates in women of low obstetric risk: the COSMOS randomised controlled trial

OBJECTIVE

To determine whether primary midwife care (caseload midwifery) decreases the caesarean section rate compared with standard maternity care.

DESIGN

Randomised controlled trial.

SETTING

Tertiary-care women's hospital in Melbourne, Australia.

POPULATION

A total of 2314 low-risk pregnant women.

METHODS

Women randomised to caseload received antenatal, intrapartum and postpartum care from a primary midwife with some care by 'back-up' midwives. Women randomised to standard care received either midwifery or obstetric-trainee care with varying levels of continuity, or community-based general practitioner care.

MAIN OUTCOME MEASURES

PRIMARY OUTCOME

caesarean birth. Secondary outcomes included instrumental vaginal births, analgesia, perineal trauma, induction of labour, infant admission to special/neonatal intensive care, gestational age, Apgar scores and birthweight.

RESULTS

In total 2314 women were randomised-1156 to caseload and 1158 to standard care. Women allocated to caseload were less likely to have a caesarean section (19.4% versus 24.9%; risk ratio [RR] 0.78; 95% CI 0.67-0.91; P = 0.001); more likely to have a spontaneous vaginal birth (63.0% versus 55.7%; RR 1.13; 95% CI 1.06-1.21; P < 0.001); less likely to have epidural analgesia (30.5% versus 34.6%; RR 0.88; 95% CI 0.79-0.996; P = 0.04) and less likely to have an episiotomy (23.1% versus 29.4%; RR 0.79; 95% CI 0.67-0.92; P = 0.003). Infants of women allocated to caseload were less likely to be admitted to special or neonatal intensive care (4.0% versus 6.4%; RR 0.63; 95% CI 0.44-0.90; P = 0.01). No infant outcomes favoured standard care.

CONCLUSION

In settings with a relatively high baseline caesarean section rate, caseload midwifery for women at low obstetric risk in early pregnancy shows promise for reducing caesarean births.

Life's simple measures: unlocking the proteome

Using modified nucleotides and selecting for slow off-rates in the SELEX procedure, we have evolved a special class of aptamers, called SOMAmers (slow off-rate modified aptamers), which bind tightly and specifically to proteins in body fluids. We use these in a novel assay that yields 1:1 complexes of the SOMAmers with their cognate proteins in body fluids. Measuring the SOMAmer concentrations of the resultant complexes reflects the concentration of the proteins in the fluids. This is simply done by hybridization to complementary sequences on solid supports, but it can also be done by any other DNA quantification technology (including NexGen sequencing). We use measurements of over 1000 proteins in under 100 μL of serum or plasma to answer important medical questions, two of which are reviewed here. A number of bioinformatics methods have guided our discoveries, including principal component analysis. We use various methods to evaluate sample handling procedures in our clinical samples and can identify many parameters that corrupt proteomics analysis.

Protein signature of lung cancer tissues

Lung cancer remains the most common cause of cancer-related mortality. We applied a highly multiplexed proteomic technology (SOMAscan) to compare protein expression signatures of non small-cell lung cancer (NSCLC) tissues with healthy adjacent and distant tissues from surgical resections. In this first report of SOMAscan applied to tissues, we highlight 36 proteins that exhibit the largest expression differences between matched tumor and non-tumor tissues. The concentrations of twenty proteins increased and sixteen decreased in tumor tissue, thirteen of which are novel for NSCLC. NSCLC tissue biomarkers identified here overlap with a core set identified in a large serum-based NSCLC study with SOMAscan. We show that large-scale comparative analysis of protein expression can be used to develop novel histochemical probes. As expected, relative differences in protein expression are greater in tissues than in serum. The combined results from tissue and serum present the most extensive view to date of the complex changes in NSCLC protein expression and provide important implications for diagnosis and treatment.

Aptamers and the RNA world, past and present

Aptamers and the SELEX process were discovered over two decades ago. These discoveries have spawned a productive academic and commercial industry. The collective results provide insights into biology, past and present, through an in vitro evolutionary exploration of the nature of nucleic acids and their potential roles in ancient life. Aptamers have helped usher in an RNA renaissance. Here we explore some of the evolution of the aptamer field and the insights it has provided for conceptualizing an RNA world, from its nascence to our current endeavor employing aptamers in human proteomics to discover biomarkers of health and disease.

Advances in human proteomics at high scale with the SOMAscan proteomics platform

In 1997, while still working at NeXstar Pharmaceuticals, several of us made a proteomic bet. We thought then, and continue to think, that proteomics offers a chance to identify disease-specific biomarkers and improve healthcare. However, interrogating proteins turned out to be a much harder problem than interrogating nucleic acids. Consequently, the 'omics' revolution has been fueled largely by genomics. High-scale proteomics promises to transform medicine with personalized diagnostics, prevention, and treatment. We have now reached into the human proteome to quantify more than 1000 proteins in any human matrix - serum, plasma, CSF, BAL, and also tissue extracts - with our new SOMAmer-based proteomics platform. The surprising and pleasant news is that we have made unbiased protein biomarker discovery a routine and fast exercise. The downstream implications of the platform are substantial.

High-content affinity-based proteomics: unlocking protein biomarker discovery

Single protein biomarkers measured with antibody-based affinity assays are the basis of molecular diagnostics in clinical practice today. There is great hope in discovering new protein biomarkers and combinations of protein biomarkers for advancing medicine through monitoring health, diagnosing disease, guiding treatment, and developing new therapeutics. The goal of high-content proteomics is to unlock protein biomarker discovery by measuring many (thousands) or all (∼23,000) proteins in the human proteome in an unbiased, data-driven approach. High-content proteomics has proven technically difficult due to the diversity of proteins, the complexity of relevant biological samples, such as blood and tissue, and large concentration ranges (in the order of 10(12) in blood). Mass spectrometry and affinity methods based on antibodies have dominated approaches to high-content proteomics. For technical reasons, neither has achieved adequate simultaneous performance and high-content. Here we review antibody-based protein measurement, multiplexed antibody-based protein measurement, and limitations of antibodies for high-content proteomics due to their inherent cross-reactivity. Finally, we review a new affinity-based proteomic technology developed from the ground up to solve the problem of high content with high sensitivity and specificity. Based on a new generation of slow off-rate modified aptamers (SOMAmers), this technology is unlocking biomarker discovery.

Unlocking biomarker discovery: large scale application of aptamer proteomic technology for early detection of lung cancer

Background

Lung cancer is the leading cause of cancer deaths worldwide. New diagnostics are needed to detect early stage lung cancer because it may be cured with surgery. However, most cases are diagnosed too late for curative surgery. Here we present a comprehensive clinical biomarker study of lung cancer and the first large-scale clinical application of a new aptamer-based proteomic technology to discover blood protein biomarkers in disease.

Methodology/Principal Findings

We conducted a multi-center case-control study in archived serum samples from 1,326 subjects from four independent studies of non-small cell lung cancer (NSCLC) in long-term tobacco-exposed populations. Sera were collected and processed under uniform protocols. Case sera were collected from 291 patients within 8 weeks of the first biopsy-proven lung cancer and prior to tumor removal by surgery. Control sera were collected from 1,035 asymptomatic study participants with ≥10 pack-years of cigarette smoking. We measured 813 proteins in each sample with a new aptamer-based proteomic technology, identified 44 candidate biomarkers, and developed a 12-protein panel (cadherin-1, CD30 ligand, endostatin, HSP90α, LRIG3, MIP-4, pleiotrophin, PRKCI, RGM-C, SCF-sR, sL-selectin, and YES) that discriminates NSCLC from controls with 91% sensitivity and 84% specificity in cross-validated training and 89% sensitivity and 83% specificity in a separate verification set, with similar performance for early and late stage NSCLC.

Conclusions/Significance

This study is a significant advance in clinical proteomics in an area of high unmet clinical need. Our analysis exceeds the breadth and dynamic range of proteome interrogated of previously published clinical studies of broad serum proteome profiling platforms including mass spectrometry, antibody arrays, and autoantibody arrays. The sensitivity and specificity of our 12-biomarker panel improves upon published protein and gene expression panels. Separate verification of classifier performance provides evidence against over-fitting and is encouraging for the next development phase, independent validation. This careful study provides a solid foundation to develop tests sorely needed to identify early stage lung cancer.

Aptamer-based multiplexed proteomic technology for biomarker discovery

BACKGROUND

The interrogation of proteomes ("proteomics") in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine.

METHODOLOGY/PRINCIPAL FINDINGS

We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma). Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (~100 fM-1 µM), and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states.

CONCLUSIONS/SIGNIFICANCE

We describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.

Aptamer-based multiplexed proteomic technology for biomarker discovery

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.

Automation of the SomaLogic Proteomics Assay: A Platform for Biomarker Discovery

At SomaLogic, we have embarked on an ambitious program of clinical studies using a novel aptamerbased proteomics technology to discover biomarkers and develop new tools to diagnose, understand, and treat human disease. As part of this program, we designed and implemented an automated assay for its highly multiplexed proteomics discovery platform. The performance of the automated assay was validated in a study that compared the automated assay to the specifications of an established manual method. Results showed that the automated method performed to the required specifications, and that the automation system improved the efficiency, productivity, and economics of our biomarker discovery program.

A community standard format for the representation of protein affinity reagents

Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.

Prevalence of multiple sclerosis in Buenos Aires, Argentina using the capture-recapture method

BACKGROUND

Scarce data exist about multiple sclerosis (MS) prevalence in South America. The objective of the study is to determine the prevalence of MS in a high populated area from Argentina (Greater Buenos Aires Metropolitan area) using the capture-recapture methodology.

METHODS

Greater Buenos Aires is the generic denomination that refers to the megalopolis comprised by the autonomous city of Buenos Aires and the surrounding conurbation of the province of Buenos Aires. The study was carried out taking July 1996 as the prevalence month. We used capture-recapture method to estimate the prevalence of MS cross matching registries from four MS Centers.

RESULTS

A total of 803 registries were obtained from the four lists. Log-linear model for capture-recapture method was used to analyze the data. The population of the area based on the 1990 census was 12,594,974; the number of MS cases estimated amongst sources interactions were between 1833 and 2359; the prevalence estimated ranged from 14 to 19.8 cases per 100,000 inhabitants.

CONCLUSIONS

This is the first study to provide epidemiological data on the prevalence of MS in a large population in Argentina (Greater Buenos Aires Metropolitan area). Further epidemiological studies will clarify the true prevalence of MS in South America.

Site of the ischemic penumbra as a predictor of potential for recovery of functions

BACKGROUND AND PURPOSE

Diffusion-perfusion mismatch has been used to estimate salvageable tissue and predict potential for recovery in acute stroke. Location of the salvageable tissue may be as important as volume or percentage in predicting potential for recovery of specific functions. Impaired naming, a common and disabling deficit after left hemisphere stroke, is often associated with tissue dysfunction of left Brodmann area (BA) 37, posterior inferior temporal cortex. We tested the hypothesis that the presence of diffusion-perfusion mismatch within left BA 37 predicts probability and extent of short-term improvement of naming.

METHODS

One hundred five patients with acute left hemisphere ischemic stroke had diffusion-weighted imaging, perfusion-weighted imaging, a test of picture naming, and other language tests at admission and 2 to 4 days later. Linear regression was used to determine whether diffusion-perfusion mismatch in any BA in language cortex, total volume of mismatch, or diffusion or perfusion abnormality predicted degree of improvement in naming by days 3 to 5.

RESULTS

The presence of >20% diffusion-perfusion mismatch in left BA 37 and total volumes of diffusion and perfusion abnormality at day 1 each independently predicted degree of improvement in naming. Mismatch in this area did not predict the degree of improvement in other language tests or the NIH Stroke Scale in this study.

CONCLUSIONS/RELEVANCE

Diffusion-perfusion mismatch in left Brodmann area 37 was strongly associated with acute improvement in naming, independently of volume or percentage of total mismatch or diffusion or perfusion abnormality. These data indicate that mismatch in a particular area is a marker of salvageable tissue and an important predictor of potential for recovery of functions that depend on that area. Location of mismatch before treatment may help to predict potential benefits of reperfusion.

Argentine Patagonia: prevalence and clinical features of multiple sclerosis

There are few studies reporting multiple sclerosis prevalence rates in the Buenos Aires region, Argentina (latitude 34°S) (between 12–18.5/100 000 inhabitants), and no studies have been performed in the larger region between parallels 36° and 55°S. The aim of this study is to determine the prevalence rates and clinical features of multiple sclerosis in residents of the Argentine Patagonia. Four cities from the region were selected for this study, giving a sample population of 417 666 inhabitants (~24% of the total Patagonia population). 1st March 2002 was determined as prevalence day. Patients were ascertained using multiple case-finding methods. The point prevalence rate was 17.2/100 000 (17.2 age-adjusted to the world population). Prevalence rates were higher for women than for men, 22.1 versus 12.2/100 000 inhabitants (21.4 versus 12.7 sex-adjusted to the world population). The study population was mainly of European descent and mestizoes. Clinical features were similar to those reported in other countries. This study shows that Argentine Patagonia is a medium-risk area with no south–north gradient between parallels 55° and 36°S. The Patagonia population shows recent internal migration that makes it difficult to determine whether the exposure to potential risk factors has been long enough to modify the disease incidence.

Theoretical principles of in vitro selection using combinatorial nucleic acid libraries

A new paradigm for drug discovery and biological research has developed from technologies that integrate combinatorial chemistry with rounds of selection and amplification, a technique called in vitro selection or systematic evolution of ligands by exponential enrichment (SELEX). This overview unit discusses nucleic acid libraries that can be used, affinity probability distributions, an equilibrium model for SELEX, and optimal conditions including concentrations and signal-to-noise ratios.

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.

Outcome data from the LEAP (Live, Eat and Play) trial: a randomized controlled trial of a primary care intervention for childhood overweight/mild obesity

OBJECTIVES

To reduce gain in body mass index (BMI) in overweight/mildly obese children in the primary care setting.

DESIGN

Randomized controlled trial (RCT) nested within a baseline cross-sectional BMI survey.

SETTING

Twenty nine general practices, Melbourne, Australia.

PARTICIPANTS

(1) BMI survey: 2112 children visiting their general practitioner (GP) April-December 2002; (2) RCT: individually randomized overweight/mildly obese (BMI z-score <3.0) children aged 5 years 0 months-9 years 11 months (82 intervention, 81 control).

INTERVENTION

Four standard GP consultations over 12 weeks, targeting change in nutrition, physical activity and sedentary behaviour, supported by purpose-designed family materials.

MAIN OUTCOME MEASURES

Primary: BMI at 9 and 15 months post-randomization. Secondary: Parent-reported child nutrition, physical activity and health status; child-reported health status, body satisfaction and appearance/self-worth.

RESULTS

Attrition was 10%. The adjusted mean difference (intervention-control) in BMI was -0.2 kg/m(2) (95% CI: -0.6 to 0.1; P=0.25) at 9 months and -0.0 kg/m(2) (95% CI: -0.5 to 0.5; P=1.00) at 15 months. There was a relative improvement in nutrition scores in the intervention arm at both 9 and 15 months. There was weak evidence of an increase in daily physical activity in the intervention arm. Health status and body image were similar in the trial arms.

CONCLUSIONS

This intervention did not result in a sustained BMI reduction, despite the improvement in parent-reported nutrition. Brief individualized solution-focused approaches may not be an effective approach to childhood overweight. Alternatively, this intervention may not have been intensive enough or the GP training may have been insufficient; however, increasing either would have significant cost and resource implications at a population level.

Photoaptamer arrays applied to multiplexed proteomic analysis

Multiplexed photoaptamer-based arrays that allow for the simultaneous measurement of multiple proteins of interest in serum samples are described. Since photoaptamers covalently bind to their target analytes before fluorescent signal detection, the arrays can be vigorously washed to remove background proteins, providing the potential for superior signal-to-noise ratios and lower limits of quantification in biological matrices. Data are presented here for a 17-plex photoaptamer array exhibiting limits of detection below 10 fM for several analytes including interleukin-16, vascular endothelial growth factor, and endostatin and able to measure proteins in 10% serum samples. The assays are simple, scalable, and reproducible. Affinity of the capture reagent is shown to be directly correlated to the limit of detection for the analyte on the array.

A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment

The targeting of molecular repertoires to complex systems rather than biochemically pure entities is an accessible approach that can identify proteins of biological interest. We have probed antigens presented by a monolayer of tumor cells for their ability to interact with a pool of aptamers. A glioblastoma-derived cell line, U251, was used as the target for systematic evolution of ligands by exponential enrichment by using a single-stranded DNA library. We isolated specifically interacting oligonucleotides, and biochemical strategies were used to identify the protein target for one of the aptamers. Here we characterize the interaction of the DNA aptamer, GBI-10, with tenascin-C, an extracellular protein found in the tumor matrix. Tenascin-C is believed to be involved in both embryogenesis and oncogenesis pathways. Systematic evolution of ligands by exponential enrichment appears to be a successful strategy for the a priori identification of targets of biological interest within complex systems.