Evaluating portable air cleaner effectiveness in residential settings to reduce exposures to biomass smoke resulting from prescribed burns

AIM

Prescribed burning is the most common method employed to reduce fuel loads in flammable landscapes. This practice is designed to reduce the hazard associated with uncontrolled bushfires. Prescribed burns are frequently conducted close to residential areas, and the associated smoke impacts can adversely affect community health. Particulate matter is the predominant pollutant within the smoke and is strongly and consistently linked with adverse health effects. Outdoor smoke readily infiltrates buildings and reduces the quality of indoor air. Portable air cleaners containing high-efficiency particulate air (HEPA) filters are a promising indoor air quality intervention for reducing outdoor smoke exposure.

METHODS

We provided 10 homes from semirural regions of Victoria, Australia, with HEPA cleaners and conducted continuous monitoring of indoor and outdoor fine particulate matter (PM2.5) for 2-4 weeks during prescribed burning periods. We calculated the potential improvements to indoor air quality when operating a HEPA cleaner during a smoke episode. Ventilation measures were conducted to identify points of smoke ingress and housing characteristics that could lead to higher infiltration rates.

RESULTS

Depending on the house, the use of HEPA cleaners resulted in a reduction in indoor PM2.5 concentrations of 30-74%.

CONCLUSIONS

HEPA cleaners have the potential to substantially improve indoor air quality during episodic smoke episodes.

Wood heater smoke and mortality in the Australian Capital Territory: a rapid health impact assessment

OBJECTIVES

To estimate the number of deaths and the cost of deaths attributable to wood heater smoke in the Australian Capital Territory.

STUDY DESIGN

Rapid health impact assessment, based on fine particulate matter (PM2.5 ) data from three outdoor air pollution monitors and published exposure-response functions for natural cause mortality attributed to PM2.5 exposure.

SETTING

Australian Capital Territory (population, 2021: 454 000), 2016-2018, 2021, and 2022 (2019 and 2020 excluded because of the impact of extreme bushfires on air quality).

MAIN OUTCOME MEASURES

Proportion of PM2.5 exposure attributable to wood heaters; numbers of deaths and associated cost of deaths (based on the value of statistical life: $5.3 million) attributable to wood heater smoke.

RESULTS

Wood heater emissions contributed an estimated 1.16-1.73 μg/m3 to the annual mean PM2.5 concentration during the three colder years (2017, 2018, 2021), or 17-25% of annual mean exposure, and 0.72 μg/m3 (15%) or 0.89 μg/m3 (13%) during the two milder years (2016, 2022). Using the most conservative exposure-response function, the estimated annual number of deaths attributable to wood heater smoke was 17-26 during the colder three years and 11-15 deaths during the milder two years. Using the least conservative exposure-response function, an estimated 43-63 deaths per year (colder years) and 26-36 deaths per year (milder years) were attributable to wood heater smoke. The estimated annual equivalent cost of deaths was $57-136 million (most conservative exposure-response function) and $140-333 million (least conservative exposure-response function).

CONCLUSIONS

The estimated annual number of deaths in the ACT attributable to wood heater PM2.5 pollution is similar to that attributed to the extreme smoke of the 2019-20 Black Summer bushfires. The number of wood heaters should be reduced by banning new installations and phasing out existing units in urban and suburban areas.

Five Years of Accurate PM2.5 Measurements Demonstrate the Value of Low-Cost PurpleAir Monitors in Areas Affected by Woodsmoke

Low-cost optical sensors are used in many countries to monitor fine particulate (PM2.5) air pollution, especially in cities and towns with large spatial and temporal variation due to woodsmoke pollution. Previous peer-reviewed research derived calibration equations for PurpleAir (PA) sensors by co-locating PA units at a government regulatory air pollution monitoring site in Armidale, NSW, Australia, a town where woodsmoke is the main source of PM2.5 pollution. The calibrations enabled the PA sensors to provide accurate estimates of PM2.5 that were almost identical to those from the NSW Government reference equipment and allowed the high levels of wintertime PM2.5 pollution and the substantial spatial and temporal variation from wood heaters to be quantified, as well as the estimated costs of premature mortality exceeding $10,000 per wood heater per year. This follow-up study evaluates eight PA sensors co-located at the same government site to check their accuracy over the following four years, using either the original calibrations, the default woodsmoke equation on the PA website for uncalibrated sensors, or the ALT-34 conversion equation (see text). Minimal calibration drift was observed, with year-round correlations, r = 0.98 ± 0.01, and root mean square error (RMSE) = 2.0 μg/m3 for daily average PA PM2.5 vs. reference equipment. The utitilty of the PA sensors without prior calibration at locations affected by woodsmoke was also demonstrated by the year-round correlations of 0.94 and low RMSE between PA (woodsmoke and ALT-34 conversions) and reference PM2.5 at the NSW Government monitoring sites in Orange and Gunnedah. To ensure the reliability of the PA data, basic quality checks are recommended, including the agreement of the two laser sensors in each PA unit and removing any transient spikes affecting only one sensor. In Armidale, from 2019 to 2022, the continuing high spatial variation in the PM2.5 levels observed during the colder months was many times higher than any discrepancies between the PA and reference measurements. Particularly unhealthy PM2.5 levels were noted in southern and eastern central Armidale. The measurements inside two older weatherboard houses in Armidale showed that high outdoor pollution resulted in high pollution inside the houses within 1-2 h. Daily average PM2.5 concentrations available on the PA website allow air pollution at different sites across regions (and countries) to be compared. Such comparisons revealed major elevations in PA PM2.5 at Gunnedah, Orange, Monash (Australian Capital Territory), and Christchurch (New Zealand) during the wood heating season. The data for Gunnedah and Muswellbrook suggest a slight underestimation of PM2.5 at other times of the year when there are proportionately more dust and other larger particles. A network of appropriately calibrated PA sensors can provide valuable information on the spatial and temporal variation in the air pollution that can be used to identify pollution hotspots, improve estimates of population exposure and health costs, and inform public policy.

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

INTRODUCTION

The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures.

METHODS

In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025.

FINDINGS

Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation.

INTERPRETATION

After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification.

FUNDING

UK Research and Innovation and National Institute for Health Research.

A Review of Artificial Neural Network Models Applied to Predict Indoor Air Quality in Schools

BACKGROUND

Indoor air quality (IAQ) in schools can affect the performance and health of occupants, especially young children. Increased public attention on IAQ during the COVID-19 pandemic and bushfires have boosted the development and application of data-driven models, such as artificial neural networks (ANNs) that can be used to predict levels of pollutants and indoor exposures.

METHODS

This review summarises the types and sources of indoor air pollutants (IAP) and the indicators of IAQ. This is followed by a systematic evaluation of ANNs as predictive models of IAQ in schools, including predictive neural network algorithms and modelling processes. The methods for article selection and inclusion followed a systematic, four-step process: identification, screening, eligibility, and inclusion.

RESULTS

After screening and selection, nine predictive papers were included in this review. Traditional ANNs were used most frequently, while recurrent neural networks (RNNs) models analysed time-series issues such as IAQ better. Meanwhile, current prediction research mainly focused on using indoor PM2.5 and CO2 concentrations as output variables in schools and did not cover common air pollutants. Although studies have highlighted the impact of school building parameters and occupancy parameters on IAQ, it is difficult to incorporate them in predictive models.

CONCLUSIONS

This review presents the current state of IAQ predictive models and identifies the limitations and future research directions for schools.

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

BACKGROUND

No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge.

METHODS

The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing.

FINDINGS

2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters.

INTERPRETATION

The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials.

FUNDING

UK Research and Innovation and National Institute for Health Research.

Analytical evaluation and critical appraisal of early commercial SARS-CoV-2 immunoassays for routine use in a diagnostic laboratory

Background: The objective of this study was to evaluate the performance characteristics of early commercial SARS-CoV-2 antibody assays in mild and asymptomatic subjects to enable the selection of suitable immunoassays for routine diagnostic use.

Methods: We used serum samples from a pre-COVID era patient cohort (n = 50, pre-December 2019), designated SARS-CoV-2 negative, and serum samples from a SARS-CoV-2 RT-PCR-positive cohort (n = 90) taken > 14 days post-symptom onset (April–May 2020). Six ELISA assays were evaluated, including one confirmation assay to investigate antibody specificity. We also evaluated one point-of-care lateral flow device (LFIA) and one high throughput electrochemiluminescence immunoassay (CLIA).

Results: The ELISA specificities ranged from 84% to 100%, with sensitivities ranging from 75.3% to 90.0%. The LFIA showed 100% specificity and 80% sensitivity using smaller sample numbers. The Roche CLIA immunoassay showed 100% specificity and 90.7% sensitivity. When used in conjunction, the Euroimmun nucleocapsid (NC) and spike-1 (S1) IgG ELISA assays had a sensitivity of 95.6%. The confirmation Dia.Pro IgG assay showed 92.6% of samples tested contained both NC and S1 antibodies, 32.7% had NC, S1 and S2 and 0% had either S1 or S2 only.

Conclusions: The Roche assay and the Euroimmun NC and S1 assays had the best sensitivity overall. Combining the assays detecting NC and S1/S2 antibody increased diagnostic yield. These first-generation assays were not calibrated against reference material and the results were reported qualitatively. A portfolio of next-generation SARS-CoV-2 immunoassays will be necessary to investigate herd and vaccine-induced immunity.

Studying bone mineral density in young people: The complexity of choosing a pQCT reference database

BACKGROUND

Many chronic illnesses affect bone health, and commonly lead to mineralization abnormalities in young people. As cortical and trabecular bone may be differentially affected in certain diseases, an imaging technique that allows for detailed study of the bone structure is required. Peripheral quantitative computed tomography (pQCT) overcomes the limitations of dual energy X-ray absorptiometry (DXA) and is perhaps more widely available for use in research than bone biopsy. However, in contrast to DXA, where there are large reference datasets, this is not the case for pQCT.

METHODS

Fifty-five children and young adults aged 7 to 30 years had the non-dominant tibia scanned at the 3% & 4% sites for trabecular bone mineral density and the 38% site for cortical bone mineral density and bone mineral content. Image acquisition and analysis was undertaken according to the protocols of two of the largest reference datasets for tibial pQCT. The Z-scores generated were compared to examine the differences between protocols and the differences from the expected median of zero in a healthy population.

RESULTS

The trabecular bone mineral density Z-scores generated by the two protocols were similar. The same was true for cortical mineral content Z-scores at the 38% site. Cortical bone mineral density was significantly different between protocols and likely affected by differences in the ethnicity of our cohort compared to the reference datasets. Only one reference dataset extended from childhood to young adulthood. Only trabecular bone mineral density, periosteal and endosteal circumference Z-scores from one methodology were not significantly biased when tested for deviation of the median from zero.

CONCLUSIONS

pQCT is a useful tool for studying trabecular and cortical compartments separately but, there are variations in pQCT scanning protocols, analysis methodology, and a paucity of reference data. Reference datasets may not be generalizable to local study populations, even when analysed using identical analysis protocols.

Pandemic products and volatile chemical emissions

The recent pandemic (COVID-19) has seen a sweeping and surging use of products intended to clean and disinfect, such as air sprays, hand sanitizers, and surface cleaners, many of which contain fragrance. However, exposure to fragranced cleaning products has been associated with adverse effects on human health. Products can emit a range of volatile chemicals, including some classified as hazardous, but relatively few ingredients are disclosed to the public. Thus, relatively little is known about the specific emissions from these products. This study investigates the volatile organic compounds (VOCs) emitted from "pandemic products" that are being used frequently and extensively in society. In addition, among these emissions, this study identifies potentially hazardous compounds, compares so-called green and regular versions of products, and examines whether ingredients are disclosed to the public. Using gas chromatography/mass spectrometry, 26 commonly used pandemic products, including 13 regular and 13 so-called green versions, were analyzed for their volatile emissions. Product types included hand sanitizers, air disinfectants, multipurpose cleaners, and handwashing soap. All products were fragranced. The analyses found the products collectively emitted 399 VOCs with 127 VOCs classified as potentially hazardous. All products emitted potentially hazardous compounds. Comparing regular products and green products, no significant difference was found in the emissions of the most prevalent compounds. Further, among the 399 compounds emitted, only 4% of all VOCs and 11% of potentially hazardous VOCs were disclosed on any product label or safety data sheet. This study reveals that pandemic products can generate volatile emissions that could pose risks to health, that could be unrecognized, and that could be reduced, such as by using fragrance-free versions of products.

Biofouling potential and material reactivity in a simulated water distribution network supplied with stormwater recycled via managed aquifer recharge

The injection of stormwater into aquifers for storage and recovery during high water demand periods is a promising technology for augmenting conventional water reserves. Limited information exists regarding the potential impact of aquifer treated stormwater in distribution system infrastructure. This study describes a one year pilot distribution pipe network trial to determine the biofouling potential for cement, copper and polyvinyl chloride pipe materials exposed to stormwater stored in a limestone aquifer compared to an identical drinking water rig. Median alkalinity (123 mg/L) and colour (12 HU) in stormwater was significantly higher than in drinking water (82 mg/L and 1 HU) and pipe discolouration was more evident for stormwater samples. X-ray Diffraction and Fluorescence analyses confirmed this was driven by the presence of iron rich amorphous compounds in more thickly deposited sediments also consistent with significantly higher median levels of iron (∼0.56 mg/L) in stormwater compared to drinking water (∼0.17 mg/L). Water type did not influence biofilm development as determined by microbial density but faecal indicators were significantly higher for polyvinyl chloride and cement exposed to stormwater. Treatment to remove iron through aeration and filtration would reduce the potential for sediment accumulation. Operational and verification monitoring parameters to manage scaling, corrosion, colour, turbidity and microbial growth in recycled stormwater distribution networks are discussed.

Abstract P4-13-04: Upregulation of cell cycle pathway genes without loss of RB1 contributes to acquired resistance to single-agent treatment with palbociclib in breast cancer

Background: The oral cdk4/6 inhibitor, Palbociclib (Palbo), has been shown to prolong progression-free survival when combined with anti-estrogen therapy and have single-agent activity in metastatic breast cancer (MBC). Progressive disease (PD) on therapy does occur, however, and little is known about resistance mechanisms. Preclinical data have suggested that cell cycle gene expression changes are a potential mechanism of resistance. We performed comprehensive genomic analyses on serial tumor samples from an exceptional responder to single-agent Palbo to determine whether such changes occur in vivo.

Methods: Serial biopsies were obtained from a 67 year old patient with MBC treated on a phase II trial of single-agent Palbo at the University of Pennsylvania. Tissue was obtained from the primary lesion (1999, Stage 3, ER-/PR+/Her2+) and first recurrence (2005, contralateral breast, bone, lung; ER+/PR-/Her2+, treated with Herceptin/letrozole). At PD (2010), pt received single-agent P, 50 mg daily for 21 days each 28-day cycle, with PR for 33 months. A sample from metastatic skin lesion at PD on P (2013) was obtained. Next generation targeted sequencing was performed at Foundation Medicine using the Heme Panel. RNA was profiled using a 784-gene custom Nanostring array including cell cycle genes and ER pathway genes. Determination of pathway enrichment was performed using GSEA and the statistical significance of network neighborhood over-representation was calculated using cumulative hypergeometric distribution.

Results: There was no genetic evidence suggesting loss of RB1, or alterations in p16, cyclin D1, cdk4, PIK3CA or ESR1, and the genomic profile did not change between the primary and recurrent tissue samples. As expected, amplification of ERRB2 was present in all samples. In contrast, expression of cell cycle-regulated genes (PLK1, TOP2A, CDK1, BUB1, CDC20, CCNA2, CCNE2, CCNB1 BIRC5) increased more than two-fold at PD on Palbo compared to pre-Palbo, along with evidence of activation of the FOXM1 network.

Conclusion: Gene expression changes associated with cell cycle activation and FOXM1 activation may lead to acquired resistance to Palbociclib, despite wild-type RB1. These data demonstrate the importance of pre-/post-treatment biopsies and the feasibility of high-level genomic assessment in archival tissues to elucidate resistance mechanisms of novel therapies.

Citation Format: DeMichele A, Shih NNC, Koehler M, Huang Bartlett C, Jiang Y, Harwick J, Huang D, Zheng X, Clark AS, Colameco C, Feldman MD, Gallagher M, Goodman N, O'Dwyer P, Rejto P. Upregulation of cell cycle pathway genes without loss of RB1 contributes to acquired resistance to single-agent treatment with palbociclib in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-13-04.

Abstract P6-07-05: Mutational spectrum and tumor response in metastatic breast cancer

Background: While several comprehensive genomic sequencing tests are clinically available for breast cancer(BC), little is known about the spectrum of findings reported in the general population and clinical utility of findings for patients(pts). Here we report tumor sequencing from the METAMORPH study, a comprehensive genomic testing approach in pts with metastatic(met) BC.

Methods: Pts with either known or suspected BC mets consented to and clinically underwent concurrent diagnostic and research tumor biopsies(bx). FFPE specimens were profiled via Illumina TruSeq Cancer Panel next generation sequencing platform covering 212 amplicons in 47 cancer genes. Pathology, treatment and outcome data were prospectively collected and tracked. Aside from Her2-directed treatment, therapy was not mutation (mut)-matched.

Results: 64 pts enrolled between 11/2013 – 05/2015. Of these, 48 had bx successfully sequenced (75%). Of those without sequencing, 5 had negative/insufficient tissue, 2 had insufficient DNA, remainder no bx/pending. Median age of those sequenced was 56 (range 31-78); 81% Caucasian, 17% African American. 25% (12 pts) presented with de novo stage IV disease. Of those with recurrence (n=36), 83% had prior adjuvant chemotherapy; 81% hormone receptor positive(HR+) had prior endocrine therapy. Median # prior lines of therapy for met disease was 2 (IQR 0 – 8). Tumor characteristics, including mut analyses, are shown in Table 1. # muts did not differ significantly by subtype(p=0.22). Frequency of TP53 and PIK3CA hotspot muts was nearly identical to TCGA. Median # muts was 1 for pts with both de novo mets and recurrence(p=0.79). # of muts was not associated with time to recurrence(p=0.80). Excluding pts found to have TP53 mut only or ERBB2 alterations in known Her2+ disease, 42% of pts were identified as having at least one potentially actionable alteration (PIK3CA mut, AKT1 mut or EGFR amplification). Median time to treatment failure(TTF) on subsequent therapy was 4.1 months for overall group, and 4.1, 6.2, and 1.6 months for HR+/Her2-, any Her2+ and TN, respectively, adjusted for line of therapy(p=0.03). After adjustment for # lines of prior met therapy, TTF was 4.7 vs. 4.1 months for pts with any mut vs. none(p=0.89); 5.7 vs 4.1 months for PIK3CA+ vs. not (p=0.94); 3.3 vs. 6.5 months for TP53+ vs. not (p=0.03).

Conclusion: Pts with met BC have frequent and potentially actionable muts.While overall # of muts did not affect response, tumors with TP53 muts had shorter response to subsequent therapy in this cohort. Additional data are needed to determine the clinical utility of mut testing in met BC, for both standard and mut-matched therapy.

 Total (n=48)HR+/Her2- (n=28)Any HER2+ (n=7)TN (n=13)Receptor concordant with primary 100%78%77%# Mutations Median (Range)1 (0-4)1 (0-3)1 (1-2)1 (0-4)014 (29%)10 (36 %)04 (31%)118 (38%)11 (39%)4 (57%)3 (23%)213 (27%)5 (18%)3 (43%)5 (38%)3+3 (6%)2 (7%)01 (8%)Prevalent Mutations (&gt;20%)TP53 (38%), PIK3CA (35%)PIK3CA (50%), TP53 (25%)TP53 (60%), ERBB2amp (86%)TP53 (62%),PIK3CA (23%)Other Alterations (#)ATM (1), KIT (1), PDGFRA (1), PTEN(1), RB1 (1), SMAD4 (1), SMO (1), STK11 (1)AKT1 (1), ATM VUS (1), ERBB2 (1), PTEN (1), SMAD4 VUS (1), SMO VUS (1)ERBB2 (1), STK11(1)EGFR amp (2), KIT amp (1),PDGFRA amp (1), RB1 VUS (1)

Citation Format: Soucier-Ernst D, Colameco C, Troxel AB, Clark C, Shih N, Maxwell KN, Morrissette J, Lieberman D, Feldman M, Goodman N, Bradbury A, Clark A, Domchek S, Fox K, Glick J, Matro J, Nathanson K, Chodosh L, DeMichele A. Mutational spectrum and tumor response in metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-05.

Headspace gas chromatography with flame ionization detection (HS-GC-FID) for the determination of dissolved methane in wastewater

There is currently a need for a simple, accurate and reproducible method that quantifies the amount of dissolved methane in wastewater in order to realize the potential methane that can be recovered and account for any emissions. This paper presents such a method, using gas chromatography with flame ionization detection fitted with a GS-Gas PRO column coupled with a headspace auto sampler. A practical limit of detection for methane of 0.9 mg L(-1), with a retention time of 1.24 min, was obtained. It was found that the reproducibility and accuracy of the method increased significantly when samples were collected using an in-house constructed bailer sampling device and with the addition of 100 μL hydrochloric acid (HCl) and 25% sodium chloride (NaCl) and sonication for 30 min prior to analysis. Analysis of wastewater samples and wastewater sludge collected from a treatment facility were observed to range from 12.51 to 15.79 mg L(-1) (relative standard deviation (RSD) 8.1%) and 17.56 to 18.67 mg L(-1) (RSD 3.4%) respectively. The performance of this method was validated by repeatedly measuring a mid-level standard (n=8; 10 mg L(-1)), with an observed RSD of 4.6%.

A genomic-based approach identifies FXYD domain containing ion transport regulator 2 (FXYD2)gammaa as a pancreatic beta cell-specific biomarker

AIMS/HYPOTHESIS

Non-invasive imaging of the pancreatic beta cell mass (BCM) requires the identification of novel and specific beta cell biomarkers. We have developed a systems biology approach to the identification of promising beta cell markers.

METHODS

We followed a functional genomics strategy based on massive parallel signal sequencing (MPSS) and microarray data obtained in human islets, purified primary rat beta cells, non-beta cells and INS-1E cells to identify promising beta cell markers. Candidate biomarkers were validated and screened using established human and macaque (Macacus cynomolgus) tissue microarrays.

RESULTS

After a series of filtering steps, 12 beta cell-specific membrane proteins were identified. For four of the proteins we selected or produced antibodies targeting specifically the human proteins and their splice variants; all four candidates were confirmed as islet-specific in human pancreas. Two splice variants of FXYD domain containing ion transport regulator 2 (FXYD2), a regulating subunit of the Na(+)-K(+)-ATPase, were identified as preferentially present in human pancreatic islets. The presence of FXYD2gammaa was restricted to pancreatic islets and selectively detected in pancreatic beta cells. Analysis of human fetal pancreas samples showed the presence of FXYD2gammaa at an early stage (15 weeks). Histological examination of pancreatic sections from individuals with type 1 diabetes or sections from pancreases of streptozotocin-treated Macacus cynomolgus monkeys indicated a close correlation between loss of FXYD2gammaa and loss of insulin-positive cells.

CONCLUSIONS/INTERPRETATION

We propose human FXYD2gammaa as a novel beta cell-specific biomarker.

Meta-analysis of gene expression in human pancreatic islets after in vitro expansion

Pancreatic islet transplantation as a potential cure for type 1 diabetes (T1D) cannot be scaled up due to a scarcity of human pancreas donors. In vitro expansion of beta-cells from mature human pancreatic islets provides an alternative source of insulin-producing cells. The exact nature of the expanded cells produced by diverse expansion protocols and their potential for differentiation into functional beta-cells remain elusive. We performed a large-scale meta-analysis of gene expression in human pancreatic islet cells, which were processed using three different previously described protocols for expansion and for which redifferentiation was attempted. All three expansion protocols induced dramatic changes in the expression profiles of pancreatic islets; many of these changes are shared among the three protocols. Attempts at redifferentiation of expanded cells induce a limited number of gene expression changes. Nevertheless, these fail to restore a pancreatic islet-like gene expression pattern. Comparison with a collection of public microarray datasets confirmed that expanded cells are highly comparable to mesenchymal stem cells. Genes induced in expanded cells are also enriched for targets of transcription factors important for pluripotency induction. The present data increase our understanding of the active pathways in expanded and redifferentiated islets. Knowledge of the mesenchymal stem cell potential may help development of drug therapeutics to restore beta-cell mass in T1D patients.

Results of the ALEGRIA study in Luxembourg. An epidemiological, observational study to describe symptom impact and control in patients with GERD and an evaluation of the GERD Impact Scale

BACKGROUND AND STUDY AIMS

The aim of this observational study was to perform the first epidemiology study in a primary care patient population with GERD in the Grand Duchy of Luxembourg and to evaluate the added value of the GERD Impact Scale (GIS) patient questionnaire.

PATIENTS AND METHODS

152 Patients with symptoms of GERD from 20 study centers were included. At visit 1, demographic data including lifestyle factors and the patients' symptoms were recorded. GERD symptoms and their severity, treatment changes and the GIS were all assessed at baseline (visit 1), visit 2 (4-6 weeks) and visit 3 (8-14 weeks). Analyses were performed on an intent-to-treat basis.

RESULTS

142 patients were included in the analysis, which comprised 50% men and 50% women with a mean BMI of 27 kg/m2. Documented lifestyle factors included consumption of caffeine-containing beverages (87% of patients), stress (62%) and alcohol consumption (53%); 44% of patients were smokers or ex-smokers. The median duration of GERD was 2.0 years. Upon inclusion, 46% were receiving, or had received, proton pump inhibitors (PPIs), antacids (44%), H2-receptor antagonists (21%) or no treatment (21%). PPIs were prescribed at the first visit in the majority of cases (94%) with 75% of patients being prescribed esomeprazole with a median daily dose of 40 mg. The GIS score correlated well with the clinician's judgment of symptom severity and was reported to help determine the appropriate treatment and evaluate the patient's response in approximately 80% of patients.

CONCLUSIONS

In this, the first epidemiological study on GERD patients in the Grand Duchy of Luxembourg, data was obtained as planned. The novel patient questionnaire was judged to be helpful by the physician and data shows that the GIS may have an added value over current assessments.

Pre-eclampsia is associated with airway hyperresponsiveness

Several large retrospective cohort studies demonstrate that pre-eclampsia is common in asthmatics. Whether airway hyperresponsiveness (AHR), a hallmark of asthma, is associated with pre-eclampsia is unknown. We measured AHR, using a methacholine challenge, and atopy in 19 women 3-60 months postpartum following pre-eclamptic or normotensive pregnancies. The geometric mean (95% CI) concentration of methacholine required to produce a >20% fall in the forced expiratory volume in 1 second (PC20 FEV1) was 8.9 (2.2-36) mg/ml in pre-eclamptics versus 72 (32-131) mg/ml in controls (P = 0.01) and 9 (1.9-40) mg/ml in atopic pre-eclamptics without asthma versus 54 (17-174) mg/ml (P = 0.038) in matched controls. Therefore, AHR was increased in women who have had pre-eclampsia. This association and its possible mechanisms warrant further investigation.

Assessment of differences in HLA-A, -B, and -DRB1 allele mismatches among African-American and non-African-American recipients of deceased kidney transplants

Among recipients of deceased donor kidney transplants, African-Americans experience a more rapid rate of kidney allograft loss than non-African-Americans. The purpose of this study was to characterize and quantify the HLA-A, -B, and -DRB1 allele mismatches and amino acid substitutions at antigen recognition sites among African-American and non-African-American recipients of deceased donor kidney transplants matched at the antigen level. In recipients with zero HLA antigen mismatches, the degree of one or two HLA allele mismatches for both racial groups combined was 47%, 29%, and 11% at HLA-DRB1, HLA-B, and HLA-A, respectively. There was a greater number of allele mismatches in African-Americans than non-African-Americans at HLA-A (P < .0001), -B (P = .096), and -DRB1 loci (P < .0001). For both racial groups, the HLA allele mismatches were predominantly at A2 for HLA-A; B35 and B44 for HLA-B; but multiple specificities for HLA-DRB1. The observed amino acid mismatches were concentrated at a few functional positions in the antigen binding site of HLA-A and -B and -DRB1 molecules. Future studies are ongoing to assess the impact of these HLA mismatches on kidney allograft loss.

Long-range destruction of Der p 1 using experimental and commercially available ionizers

BACKGROUND

To reduce the risk of sensitization and the elicitation of allergy symptoms, it is important to reduce the level of allergens in the home. It has previously been demonstrated that corona discharge, the process by which ionizers produce ions, can destroy the major house dust mite allergen Der p 1.

OBJECTIVE

In this paper the denaturing efficacy of an experimental ionizer and two commercially available products are evaluated.

METHODS

The first test was conducted in an electrically grounded chamber with samples of Der p 1 placed in various positions for 1, 2 and 3 weeks. The second test was conducted in situ in an unoccupied, furnished office room for 1 week. Der p 1 concentration was quantified by two-site monoclonal antibody enzyme-linked immunosorbent assay (ELISA).

RESULTS

All ionizers in both tests caused significant reductions in allergen concentration (P < 0.05), reaching a maximum of 92% with the experimental ionizer in the chamber after 3 weeks. The percentage reductions observed in situ with the experimental and the larger commercial ionizer were similar, reaching a maximum of 32% at a distance of 4 m away from the experimental ionizer after 1 week of exposure.

CONCLUSION

With a revised protocol for use, air ionizers may offer a simple, efficient and inexpensive way to reduce allergen levels in the domestic environment.

The effect of corona discharge on Der p 1

BACKGROUND

Reduction of house dust mite allergens in the domestic environment can play an important part in reducing sensitization and in the amelioration of symptoms in atopic individuals. Chemical and physical methods have been tried with varied levels of success. The present paper presents a novel electrostatic way of destroying Der p 1, the major mite allergen.

OBJECTIVE

To assess the efficacy of negative Trichel, negative continuous glow, positive pulse and positive continuous glow corona in destroying Der p 1. To determine whether ozone has any effect on the integrity of Der p 1 in the experimental conditions present.

METHODS

A simple point-to-plane apparatus was used to irradiate samples of Der p 1 for periods of 1, 15, 30, 45, 60, 120, 180, 240 and 300 min. Controls were exposed to the atmosphere with no corona products present for the equivalent time. The effect of the corona by-product ozone was investigated alone by exposing samples of Der p 1 to molecular ozone for 60 min. Der p 1 concentration was quantified by two-site monoclonal antibody ELISA.

RESULTS

High current negative glow resulted in a 67.37% reduction in Der p 1 concentration after 300 min compared with a 50.5% reduction from a low current Trichel regime. High current positive glow corona gave a reduction of 25.22% while a low current positive pulse corona caused a 13.72% reduction after 300 min. All these reductions were statistically significant (P < 0.05) compared with unexposed controls. Negative corona always gave greater percentage reductions in Der p 1 concentration for each time exposure investigated. The pattern of percentage reduction follows an exponential rise to maximum relationship in respect to time. Samples of Der p 1 were not affected by exposure to molecular ozone.

CONCLUSION

These data indicate corona products to be a powerful new method of destroying Der p 1 allergen that is not dependent on the presence of the oxidizing corona product ozone.

Biological data becomes computer literate: new advances in bioinformatics

Bioinformatics is an art and science concerned with the use of computing in biological research areas such as genomics, transcriptomics, proteomics, genetics, and evolution. This review paints a broad picture of bioinformatics, drawing examples from genomic sequencing and microarray analysis. I highlight the role of bioinformatics at multiple points along the path from high-tech data generation to biological discovery.

The riddle of femininity: the interplay of primary femininity and the castration complex in analytic listening

This study elucidates the application of an analytic attitude to questions of gender and sexuality. The paper reports on a study group's exploration of the relative heuristic use of two important organising concepts in analytic work with female analysands: primary feminity and the phallic castration complex. A tendency to cling to one position over the other skews analytic listening. Two cases are presented of women struggling to consolidate positive feminine identifications and, to that end, working through conflicting feminine identifications and defences against a resolution of the awareness of gender differences. Analytic listening requires a view of each psychic construction as a layer to be understood in its own right yet as a cloak soon to reveal the next layer--a different construction. The study includes observations on perverse fantasies in women.

Uniform integration of genome mapping data using intersection graphs

MOTIVATION

The methods for analyzing overlap data are distinct from those for analyzing probe data, making integration of the two forms awkward. Conversion of overlap data to probe-like data elements would facilitate comparison and uniform integration of overlap data and probe data using software developed for analysis of STS data.

RESULTS

We show that overlap data can be effectively converted to probe-like data elements by extracting maximal sets of mutually overlapping clones. We call these sets virtual probes, since each set determines a site in the genome corresponding to the region which is common among the clones of the set. Finding the virtual probes is equivalent to finding the maximal cliques of a graph. We modify a known maximal-clique algorithm such that it finds all virtual probes in a large dataset within minutes. We illustrate the algorithm by converting fingerprint and Alu-PCR overlap data to virtual probes. The virtual probes are then analyzed using double-linkage intersection graphs and structure graphs to show that methods designed for STS data are also applicable to overlap data represented as virtual probes. Next we show that virtual probes can produce a uniform integration of different kinds of mapping data, in particular STS probe data and fingerprint and Alu-PCR overlap data. The integrated virtual probes produce longer double-linkage contigs than STS probes alone, and in conjunction with structure graphs they facilitate the identification and elimination of anomalies. Thus, the virtual-probe technique provides: (i) a new way to examine overlap data; (ii) a basis on which to compare overlap data and probe data using the same systems and standards; and (iii) a unique and useful way to uniformly integrate overlap data with probe data.

Treatment of high-grade low-stage prostate cancer by high-dose-rate brachytherapy

BACKGROUND AND PURPOSE

The best management of patients with low-stage, high-grade prostate cancer remains unclear. In an attempt to improve the outcomes of this high-risk group, we have offered those with Gleason > or =7 cancers removable-source high-dose-rate (HDR) brachytherapy in combination with external-beam radiation.

PATIENTS AND METHODS

We reviewed the clinical histories of 61 consecutive patients with high-grade clinical stage T1-T2 lesions who received the combination radiation therapy between March 1997 and November 1998. The average Gleason score was 7.5. The HDR brachytherapy was given in three sessions with removable-source afterloaded (192)Ir to a minimum peripheral dose of 6 Gy. Conformal external-beam radiation in 25 fractions to a dose of 50 Gy was given beginning 1 week later. Patients with prostate volumes >40 cc received a luteinizing hormone-releasing hormone analog before brachytherapy.

RESULTS

Among the 52 patients available for follow-up (average duration 11.8 months), there has been one death from prostate cancer. After treatment, only one patient had an initial rise in serum prostate specific antigen (PSA) concentration. In addition to the patient who died, there have been three confirmed treatment failures. Toxicity was mild, with only two patients having RTOG grade 3 or 4 effects. Neither of them required surgery.

CONCLUSION

Although long-term results are not available, available data suggest that HDR brachytherapy plus external-beam radiation is at least as effective as any single therapy for high-risk, low-stage prostate cancer. The toxicity is acceptable.

Revealing hidden interval graph structure in STS-content data

MOTIVATION

STS-content data for genomic mapping contain numerous errors and anomalies resulting in cross-links among distant regions of the genome. Identification of contigs within the data is an important and difficult problem.

RESULTS

This paper introduces a graph algorithm which creates a simplified view of STS-content data. The shape of the resulting structure graph provides a quality check - coherent data produce a straight line, while anomalous data produce branches and loops. In the latter case, it is sometimes possible to disentangle the various paths into subsets of the data covering contiguous regions of the genome, i.e. contigs. These straight subgraphs can then be analyzed in standard ways to construct a physical map. A theoretical basis for the method is presented along with examples of its application to current STS data from human genome centers.

AVAILABILITY

Freely available on request.

The LabFlow system for workflow management in large scale biology research laboratories

LabFlow is a workflow management system designed for large scale biology research laboratories. It provides a workflow model in which objects flow from task to task under programmatic control. The model supports parallelism, meaning that an object can flow down several paths simultaneously, and sub-workflows which can be invoked subroutine-style from a task. The system allocates tasks to Unix processes to achieve requisite levels of multiprocessing. The system uses the LabBase data management system to store workflow-state and laboratory results. LabFlow provides a Per15 object-oriented framework for defining workflows, and an engine for executing these. The software is freely available.

A model system for studying the integration of molecular biology databases

MOTIVATION

Integration of molecular biology databases remains limited in practice despite its practical importance and considerable research effort. The complexity of the problem is such that an experimental approach is mandatory, yet this very complexity makes it hard to design definitive experiments. This dilemma is common in science, and one tried-and-true strategy is to work with model systems. We propose a model system for this problem, namely a database of genes integrating diverse data across organisms, and describe an experiment using this model.

RESULTS

We attempted to construct a database of human and mouse genes integrating data from GenBank and the human and mouse genome-databases. We discovered numerous errors in these well-respected databases: approximately 15% of genes are apparently missing from the genome-databases; links between the sequence and genome-databases are missing for another 5-10% of the cases; about a third of likely homology links are missing between the genome-databases; 10-20% of entries classified as 'genes' are apparently misclassified. By using a model system, we were able to study the problems caused by anomalous data without having to face all the hard problems of database integration.

CONTACT

nat@jax.org

The LabBase system for data management in large scale biology research laboratories

MOTIVATION

The development of laboratory information management systems (LIMSs) for large scale biology research projects can be a challenging problem. Many such projects generate complex datasets via complex procedures that undergo continuous refinement. A key software challenge is to simplify the database-development task so that databases can be built and modified quickly enough to keep pace with changing project-requirements.

RESULTS

LabBase extends the facilities offered by relational database systems to simplify the task of creating databases for large scale biology research projects. LabBase provides a structural object data model, similar to ACEDB, and adds to this the concepts of Materials, Steps, and States: Materials are objects representing the identifiable things that participate in a laboratory protocol; Steps are objects reporting the results of a laboratory or analytical procedure; and States are objects denoting places in a laboratory protocol. The system provides a data definition language for succinctly defining laboratory databases, and operations for conveniently storing and retrieving data in such databases. The system also provides support for workflow management. LabBase is implemented in Perl5 and provides a natural interface for laboratory application programs written in Perl.

AVAILABILITY

The software is freely available. Contact the authors.

CONTACT

nat@jax.org

A map of 75 human ribosomal protein genes

We mapped 75 genes that collectively encode >90% of the proteins found in human ribosomes. Because localization of ribosomal protein genes (rp genes) is complicated by the existence of processed pseudogenes, multiple strategies were devised to identify PCR-detectable sequence-tagged sites (STSs) at introns. In some cases we exploited specific, pre-existing information about the intron/exon structure of a given human rp gene or its homolog in another vertebrate. When such information was unavailable, selection of PCR primer pairs was guided by general insights gleaned from analysis of all mammalian rp genes whose intron/exon structures have been published. For many genes, PCR amplification of introns was facilitated by use of YAC pool DNAs rather than total human genomic DNA as templates. We then assigned the rp gene STSs to individual human chromosomes by typing human-rodent hybrid cell lines. The genes were placed more precisely on the physical map of the human genome by typing of radiation hybrids or screening YAC libraries. Fifty-one previously unmapped rp genes were localized, and 24 previously reported rp gene localizations were confirmed, refined, or corrected. Though functionally related and coordinately expressed, the 75 mapped genes are widely dispersed: Both sex chromosomes and at least 20 of the 22 autosomes carry one or more rp genes. Chromosome 19, known to have a high gene density, contains an unusually large number of rp genes (12). This map provides a foundation for the study of the possible roles of ribosomal protein deficiencies in chromosomal and Mendelian disorders.

Informatics--genome and genetic databases

Databases for biologists are becoming increasingly important. Some of these can be regarded as 'core' resources, such as the bibliographic databases, whereas others are of greater interest to specialists. As comparative genomics develops, however, even databases limited in their scope (e.g. to a single organism) are of great interest to a wider community.

A tale of two New Jersey cities

Judging from the social and health measures considered in this article, Newark and Jersey City face similar challenges as other large cities. For Newark, the challenges are more extreme. The high rates of poverty and violence, coupled with a low rate of high school graduation and a large number of single parent households bode ill for the city. The hospitals in Newark and Jersey City have undergone major changes in meeting the needs of their communities. They have adjusted their size, shortened their lengths of stay, and provided more intensive care services and outpatient services. Of special concern for New Jersey's hospitals is the reliance on Medicaid financing. If dramatic changes are made to the Medicaid program, Newark hospitals should be on high alert. Legislatures need to tread carefully in designing policies that address the needs of New Jersey's large cities. The state is undergoing major changes in its health care system. The demise of the all-payer rate setting system, the establishment of the Health Care Subsidy Fund to finance uncompensated care and subsidize insurance for low and middle-income families, modifications to the community rating system for private insurance, and changes to the welfare system that affect eligibility for Medicaid all require legislators to consider the context in which these programs operate.

Current status of the Plasmodium falciparum genome project

The Plasmodium falciparum Genome Project is a collaborative effort by many laboratories that will provide detailed molecular information about the parasite, which may be used for developing practical control measures. Initial goals are to prepare an electronically indexed clone bank containing partially sequenced clones representing up to 80% of the parasite's genes and to prepare an ordered set of overlapping clones spanning each of the parasite's 14 chromosomes. Currently, clones of genomic DNA, prepared as yeast artificial chromosomes, are arranged into contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than 20% of the parasite's genes, and approximately 5% of the parasite's genes are tentatively identified from similarity searches of entries in the international sequence databases. A total of > 0.5 Mb of P. falciparum sequence tag data is available. The gene sequence tags are presently being used to complete YAC contig assembly and localize the cloned genes to positions on the physical map in preparation for sequencing the genome. Routes of access to project information and services are described.

Good maps are straight

This paper proposes a simplified approach to the assembly of large physical genome maps. The approach focuses on two key problems: (i) the integration of diverse forms of data from numerous sources, and (ii) the detection and removal of errors and anomalies in the data. The approach simplifies map assembly by dividing it into three phases-overlap, linkage and ordering. In the first phase, all forms of overlap data are integrated into a simple abstract structure, called clusters, where each cluster is a set of mutually-overlapping DNA segments. This phase filters out many questionable overlaps in the mapping data. In the second phase, clusters are linked together into a weighted intersection graph. False links between widely separated regions of the genome show up as crooked, branching structures in the graph. Removing these false links produces graphs that are straight, reflecting the linear structure of chromosomes. From these straight graphs, the third phase constructs a physical map. Graph algorithms and graph visualization play key roles in implementing the approach. At present, the approach is at an early stage of development: it has been tested on real and simulated mapping data, and the results look promising. This paper describes the first two phases of the approach in detail, and reports on our progress to date.

An STS-based map of the human genome

A physical map has been constructed of the human genome containing 15,086 sequence-tagged sites (STSs), with an average spacing of 199 kilobases. The project involved assembly of a radiation hybrid map of the human genome containing 6193 loci and incorporated a genetic linkage map of the human genome containing 5264 loci. This information was combined with the results of STS-content screening of 10,850 loci against a yeast artificial chromosome library to produce an integrated map, anchored by the radiation hybrid and genetic maps. The map provides radiation hybrid coverage of 99 percent and physical coverage of 94 percent of the human genome. The map also represents an early step in an international project to generate a transcript map of the human genome, with more than 3235 expressed sequences localized. The STSs in the map provide a scaffold for initiating large-scale sequencing of the human genome.