Abstract 3401: Whole genome cell-free tumor DNA mutational signatures for noninvasive monitoring of pediatric brain cancers

Introduction: Liquid biopsy offers a noninvasive approach to monitor cancer burden during therapy and surveillance period. However, in pediatric brain cancers, liquid biopsy methods from the blood have been unsuccessful due to a low tumor burden and low number of mutations in coding regions. We hypothesized that a whole genome sequencing (WGS)-derived patient specific mutational signature from a matched tumor-normal WGS can provide a sensitive and specific approach to detect mutations in circulating cell free tumor DNA (ctDNA) and provide blood-based monitoring in pediatric patients with brain tumor.

Methods: All tumors were analyzed and molecularly subclassified using whole genome DNA methylation profiling and machine learning classifier. Tumor DNA was extracted from pathology tissue and normal germline DNA from the white blood cells, while ctDNA was extracted from 1-2 mL of post-surgery or follow-up plasma samples, WGS was applied to sequence DNA from matched tumor-normal and plasma samples. WGS coverage was 40x for matched tumor-normal DNA and 20x for ctDNA. Using the C2i assay, we derived a personalized mutational pattern for each tumor and used an AI-based error suppression model for quantification and ultra-sensitive detection of ctDNA in plasma samples. A patient-specific personalized genome-wide compendium of somatic mutations was established and ctDNA tested at 1 to 3 available time points during the therapy or surveillance period. An AI-based error suppression model was implemented to filter out the noise in the cell free DNA (cfDNA) while the personalized mutational signature was used to detect the ctDNA in the cfDNA and to amplify the somatic signal contained in it. The ctDNA Tumor Fraction (TF) was compared to the clinical status and MR-based imaging.

Results: We profiled 7 pediatric brain tumors, including 2 medulloblastomas (one Group 3, one Group 4), 3 pediatric glioblastomas IDH wild-type, 1 ependymoma PFA subtype and one low grade ganglioglioma. Tumor specific signatures were identified and detected in the plasma of 5 patients with clinical disease with a TF range 0.02-0.0005 but not in 2 patients with no tumor at the time of blood collection. In two children with a medulloblastoma and glioblastoma, the decrease of tumor fraction in ctDNA over 2 (TF: 0.002 to 0.0009) and 3 time points (TF: 0.0005 to undetectable), respectively, correlated with response to therapy based on imaging.

Conclusions: Patient-specific WGS tumor signature in ctDNA from blood can be used for sensitive monitoring of children with brain tumors.

Citation Format: Ivy Tran, Kristyn Galbraith, Guisheng Zhao, Robyn Borsuk, Joyce Varkey, Sharon Gardner, Jeffrey Allen, David Harter, Jeffrey Wisoff, Eveline T. Hidalgo, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, G. Praveen Raju, Theodore Nicolaides, Asaf Zviran, Matija Snuderl. Whole genome cell-free tumor DNA mutational signatures for noninvasive monitoring of pediatric brain cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3401.

Abstract 1959: Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients

Background: While detection of circulating tumor DNA (ctDNA) is associated with poor cancer prognosis, the clinical utility for guiding treatment decisions is unresolved. Patients with minimal residual disease (MRD) often have less than one genome equivalent of ctDNA per 10 mL blood. Consequently, it is stochastic whether a 10 mL sample contains ctDNA from a particular genomic locus. Consequently, the sensitivity of ctDNA detection methods targeting a limited number of tumor loci is heavily affected by sampling bias. To overcome this challenge, we developed MRDetect; a whole genome sequencing (WGS) approach, which detects ctDNA using the patient-specific cumulative signal from tens of thousands of mutations throughout the genome. Recently, we showed how MRDetect found ctDNA fractions down to 10-4. Here, we performed a validation study to confirm the prognostic impact of MRDetect.

Aim: Validation of MRDetect for sensitive ctDNA detection to monitor residual disease in stage III colorectal cancer (CRC) patients treated with curative intent.

Methods: From a large, uniform cohort of stage III CRC patients n = 146), we had plasma samples collected every third month (n = 938, median = 9 per patient) and a median follow-up of 34 months. For each patient, a genome-wide mutational signature was established by WGS of tumor and matched normal DNA. Enhanced by an AI-based error suppression model, this signature was used to detect ctDNA in 1-2 mL plasma samples using WGS (20x coverage). We used de-novo point mutation and copy number variation analysis to investigate cancer evolution after treatment. To evaluate the reproducibility of MRDetect, aliquot samples (n = 2x190 samples) from 5 recurrence and 10 non-recurrence patients were processed and sequenced at two independent laboratories. Outcome measures: ctDNA status, tumor fraction, false positive rate, Time To ctDNA Recurrence (TTcR), and Time To radiological Recurrence (TTrR).

Results: Analysis of paired samples showed great reproducibility with high agreement between both ctDNA status calls (Cohens Kappa = 0.81) and the estimated tumor fractions (r2 = 0.99). MRDetect revealed post-operative ctDNA in all recurrence patients (5/5) with detected tumor fractions down to 2 x 10-4. Median TTcR was 0.9 month (range 0.5 - 7.3 months) while median TTrR was 12.8 months (range 11.3 - 31.1 months). The false positive rate was 1% (1/100), assessed in longitudinal samples from the 10 non-relapsing patients. Tumor evolution dynamics in plasma samples revealed novel amplification and deletions, which were absent in the primary tissue but confirmed in metachronous metastases. We will present results from the full cohort at AACR 2022.

Conclusion: MRDetect detects ctDNA with high sensitivity and specificity and enables effective postoperative assessment of MRD, cancer evolution dynamics and early relapse detection.

Citation Format: Amanda Frydendahl, Thomas Reinert, Jesper Nors, Sunil Deochand, Dillon Maloney, Noah Friedman, Tomer Lauterman, Danielle Afterman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Ravi Kandasamy, Iman Tavassoly, Jonathan Rosenfeld, Anders Husted Andersen, Uffe S. Løve, Per V. Andersen, Ole Thorlacius-Ussing, Lene Hjerrild Iversen, Kåre Andersson Gotschalck, Boris Oklander, Asaf Zviran, Claus Lindbjerg Andersen. Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1959.

Abstract 540: Genome-wide circulating tumor DNA for monitoring treatment response and metastatic relapse in bladder cancer

Background: Neoadjuvant chemotherapy (NAC) followed by radical cystectomy (CX), is gold standard treatment in localized muscle-invasive bladder cancer (MIBC). About 45% of patients with MIBC develop metastatic relapse within 2 years after CX. The response rate to chemotherapy and immune checkpoint inhibitors (ICI) is relatively low, and biomarker tests for monitoring response are needed. Furthermore, biomarkers for early detection of minimal residual disease (MRD) after CX is needed to enable earlier treatment initiation. Tumor-informed detection of mutations in cell-free DNA (cfDNA) from peripheral blood has shown promising results in its ability to monitor MRD. However, the low tumor fraction after surgery and limited input material obtained from a typical plasma sample limits the probability of detecting low metastatic burden scenarios. Here we implemented and applied locally a whole-genome sequencing (WGS) approach to circulating tumor DNA (ctDNA) monitoring for improving ctDNA detection.

Methods: A total of 140 MIBC patients undergoing NAC and CX were enrolled, including a test cohort (n=19) and a validation cohort (n=120). cfDNA was extracted from ~1mL plasma (n=1100) and procured from longitudinal plasma sampling during NAC (response measure), pre-cystectomy (response measure), post-surgery (relapse monitoring) and during immunotherapy (ICI treatment). WGS was applied to tumor/germline pairs (coverage >30x/20x) and plasma cfDNA (>20x) facilitating detection of genome wide genomic alterations and quantification of ctDNA using the MRDetect method.

Results: We developed a personalized tumor-informed WGS model by integrating genome-wide mutation and copy number variation data coupled with advanced signal processing and AI-based error suppression. Patient-specific somatic variant patterns were then used for detecting and measuring the ctDNA levels in low-input blood samples by WGS. The assay sensitivity allowed for detection of tumor fractions down to 8*10-5. Furthermore, in our test cohort of 19 patients, we detected ctDNA after CX in 7 of 8 patients with clinical relapse (88% sensitivity) and detected no ctDNA in 11 of 11 patients with no clinical relapse (100% specificity). We observed a positive lead-time for MRD-based recurrence detection compared to CT-based reccurence detection (9 months on average). The full dataset is currently being processed and will be presented at the AACR 2022 meeting.

Conclusions: For precision oncology, we need to develop quantitative and non-invasive methodologies to help tailor the treatments to individual patients and monitor them for further clinical decision-making. The results indicate the clinical potential of personalized genome-wide mutation integration as an ultra-sensitive, non-invasive method for MRD detection and treatment response monitoring which could aid in clinical management of patients with bladder cancer.

Citation Format: Iver Nordentoft, Karin Birkenkamp-Demtröder, Emil Christensen, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Sia Viborg, Mads Agerbæk, Jørgen Bjerggaard Jensen, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, Asaf Zviran, Lars Dyrskjøt. Genome-wide circulating tumor DNA for monitoring treatment response and metastatic relapse in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 540.

Abstract 5114: Ultra-sensitive detection of minimal residual disease (MRD) through whole genome sequencing (WGS) using an AI-based error suppression model in resected early-stage non-small cell lung cancer (NSCLC)

Background: Early detection of recurrence and monitoring of MRD post-surgery is critical for clinical decision-making to tailor adjuvant therapy. In early-stage NSCLC, circulating tumor DNA (ctDNA) detection is especially challenging, requiring highly sensitive and specific assays. Therefore, we used a WGS approach (MRDetect) for ultra-sensitive ctDNA detection in NSCLC patients (pts) undergoing curative surgery.

Methods: We conducted a pilot study to evaluate the MRDetect approach in serial plasma samples (including pre-surgery, post-surgery and follow-up [f/u] timepoints) from resected stage IB-IIIA NSCLC pts. Pts underwent routine surveillance by computed tomography scans. ctDNA was extracted from ~1mL plasma. MRDetect uses WGS by a tumor-informed approach (sequencing coverage 40x for tumor, 20x for plasma DNA) combined with AI-based error suppression models (trained and calibrated with a non-cancer cohort, n=17) to increase the signal to noise ratio for precise ctDNA detection, and improve the accuracy of readouts especially for low tumor burden scenarios. The assay reports the detection and quantification of ctDNA burden in blood with a prognostic value for risk of recurrence. The ability of the assay to predict recurrence from a single sample, taken at the clinical landmark point (median 1.6 mths post-surgery, range 0.1-6.5) was evaluated.

Results: Overall, 52 NSCLC pts were enrolled (n=88 plasma samples) with median clinical f/u of 32.6 mths (range 3.1-98.6). There were 43 pts with post-surgery landmark samples, with median age 62 years, 70% were male, 79% were adenocarcinoma and 49% were EGFR mutated. 26% were stage IB and 37% each were stage II and III. There were 15/18 (sensitivity 83%) pts with confirmed radiological recurrence in which MRDetect was positive, including 6/7 (86%) EGFR mutated pts. The median RFS in MRDetect positive pts was 15.2 mths (range 3.7-33.4). Among 25 pts with no recurrence (median f/u 25.6 mths), MRDetect reported 4 pts to be MRD positive (specificity 84%). These results were consistent between EGFR mutated (sensitivity 86%, specificity 86%) and wildtype pts (sensitivity 82%, specificity 82%). For longitudinal samples (n=17 pts), negative ctDNA was associated with absence of recurrence in 14/15 pts (specificity 93%). At the AACR meeting, results from a planned larger validation study will be presented.

Conclusion: Using a robust WGS implemented AI-based computational platform (MRDetect), we demonstrate high sensitivity and specificity detection of MRD in both EGFR mutated and wildtype NSCLC. With an increasing number of therapeutic options in the adjuvant setting for NSCLC, an ultra-sensitive MRD assay has the potential to facilitate personalized clinical decision-making for tailoring both the need and choice of adjuvant therapies.

Citation Format: Aaron C. Tan, Stephanie P. Saw, Gillianne G. Lai, Kevin L. Chua, Angela Takano, Boon-Hean Ong, Tina P. Koh, Amit Jain, Wan Ling Tan, Quan Sing Ng, Ravindran Kanesvaran, Tanujaa Rajasekaran, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, Asaf Zviran, Wan-Teck Lim, Eng-Huat Tan, Anders J. Skanderup, Mei-Kim Ang, Daniel S. Tan. Ultra-sensitive detection of minimal residual disease (MRD) through whole genome sequencing (WGS) using an AI-based error suppression model in resected early-stage non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5114.

Accuracy of point-of-care ultrasound by pediatric emergency physicians for testicular torsion

INTRODUCTION

Acute scrotum is a common presentation to the pediatric emergency department, and ultrasound is frequently used to narrow the differential diagnosis. Point-of-care ultrasound (POCUS) is increasingly used by urologists and emergency physicians and could potentially be used to detect pediatric testicular torsion.

OBJECTIVES

This study aimed to determine the accuracy of POCUS by pediatric emergency physicians in diagnosing testicular torsion and the agreement between point-of-care ultrasound and final diagnosis for other causes of acute scrotum.

STUDY DESIGN

A chart review of patients presenting to the study emergency department who received POCUS by a pediatric emergency physician, as well as radiology department ultrasound and/or surgery, was performed. Charts were reviewed for POCUS diagnoses, final diagnoses, and imaging time metrics.

RESULTS

A total of 120 patients met study criteria, with 12 cases of testicular torsion. The diagnostic accuracy of POCUS for testicular torsion is described in the summary table. For all causes of acute scrotum, point-of-care ultrasound agreed with final diagnosis in 70% (95% confidence interval [CI] 62-78%) of cases, and more experienced point-of-care ultrasound users displayed higher agreement with final diagnosis. Point-of-care ultrasound results were generated a median of 73 min (Q1 = 51, Q3 = 112) before radiology department ultrasound results.

DISCUSSION

Scrotal POCUS performed by pediatric emergency physicians appears to be an accurate tool to detect testicular torsion in children with acute scrotum and saves time compared with radiology ultrasound. The study results may not be generalizable to hospitals without a multidisciplinary POCUS system for quality assurance and image sharing. Future work on POCUS for acute scrotum should investigate its impact on patient outcomes, cost-effectiveness, and family satisfaction.

CONCLUSION

Point-of-care ultrasound by pediatric emergency physicians is accurate for detecting testicular torsion in children with acute scrotum and could expedite diagnosis of this time-sensitive condition.

Effect of patient and nurse ethnicity on emergency department analgesia for children with appendicitis in israeli government hospitals

BACKGROUND

Ethnicity is a risk factor for disparate Emergency Department (ED) analgesia. We aimed to explore ethnic variations in the administration of ED analgesia to children with acute appendicitis in Israeli government hospitals.

METHODS

Children discharged with an International Classification of Disease-Ninth Revision diagnosis of acute appendicitis between 2010 and 2015 were included. The association between patient ethnicity (Jewish, Arab) and analgesia administration (any, opioid) was assessed. Age, gender, triage category, pain score and time of arrival were tested as possible confounders. The effect of patient-nurse ethnic discordance (PNED) was examined.

RESULTS

Overall, 4714 children with acute appendicitis, 3520 Jewish and 1194 Arab, were cared for in the EDs; 1516 (32.2%) received any analgesia and 368 (7.8%) opioid analgesia. Stratified by pain score, no statistical differences were found in the administration of any or opioid analgesia between Jewish and Arab patients with either severe pain or moderate pain. In multivariate modelling adjusted for pain score and triage category, the rates of any analgesia for Arab and Jewish patients were 31.8% (95% CI, 30.9-32.6) and 36.5% (95% CI, 36.0-36.9), adjusted OR (aOR) = 1.16 (95% CI, 0.98-1.38), respectively. The rates of opioid analgesia for Arab and Jewish patients were 8.5% (95% CI, 8.2-8.9) and 7.9% (95% CI, 7.3-8.7), aOR = 0.77; (95% CI, 0.59-1.22), respectively. Jewish and Arab nurses treated proportionally fewer patients from the opposite ethnicity with any analgesia (p < 0.01).

CONCLUSION

Emergency Department analgesia was markedly low, and not associated with patient ethnicity. PNED was associated with decreased rates of analgesia.

SIGNIFICANCE

Emergency Department analgesia for children with acute appendicitis in Israeli government hospitals is markedly low. Patient-provider ethnic discordance may negatively influence the provision of analgesia. Significant efforts should be undertaken in order to increase analgesia provision rates and reduce social inequality.

Measurements of the stabilities of isolated retinal chromophores

The barrier energies for isomerization and fragmentation were measured for a series of retinal chromophore derivatives using a tandem ion mobility spectrometry approach. These measurements allow us to quantify the effect of charge delocalization on the rigidity of chromophores. We find that the role of the methyl group on the C13 position is pivotal regarding the ground state dynamics of the chromophore. Additionally, a correlation between quasi-equilibrium isomer distribution and fragmentation pathways is observed.

Linear Dichroism Spectroscopy of Retinal with Picosecond Time Resolution

For the first time linear dichroism spectroscopy has been extended to the picosecond time regime. 11-cis retinal, all-trans retinal and 1,8-diphenyl-1,3,5,7-octatetraene (DPOT) are incorporated into polyethylene films and oriented by stretching the films. By measuring picosecond transient absorption spectra polarized parallel and perpendicular to the stretching direction and calculating the dichroic ratio we get informations about the molecular geometry in excited singlet and triplet states. The results may have relevance to vision.

Refinement of the Region for Split Hand/Foot Malformation 5 on 2q31.1

Background: Deletions that encompass 2q31.1 have been proposed as a microdeletion syndrome with common clinical features, including intellectual disability/developmental delay, microcephaly, cleft palate, growth delay, and hand/foot anomalies. In addition, several genes within this region have been proposed as candidates for split hand-foot malformation 5 (SHFM5). Methods: To delineate the genotype-phenotype correlation between deletions of this region, we identified 14 individuals with deletions at 2q31.1 detected by microarray analysis for physical and developmental disabilities. Results: All subjects for whom detailed clinical records were available had neurological deficits of varying degree. Seven subjects with deletions encompassing the HOXD cluster had hand/foot anomalies of varying severity, including syndactyly, brachydactyly, and ectrodactyly. Of 7 subjects with deletions proximal to the HOXD cluster, 5 of which encompassed DLX1/DLX2, none had clinically significant hand/foot anomalies. In contrast to previous reports, the individuals in our study did not display a characteristic gestalt of dysmorphic facial features. Conclusion: The absence of hand/foot anomalies in any of the individuals with deletions of DLX1/DLX2 but not the HOXD cluster supports the hypothesis that haploinsufficiency of the HOXD cluster, rather than DLX1/DLX2, accounts for the skeletal abnormalities in subjects with 2q31.1 microdeletions.

Case series: 2q33.1 microdeletion syndrome--further delineation of the phenotype

Recurrent deletions of 2q32q33 have recently been reported as a new microdeletion syndrome, clinical features of which include significant learning difficulties, growth retardation, dysmorphic features, thin and sparse hair, feeding difficulties, and cleft or high palate. Haploinsufficiency of one gene within the deleted region, SATB2, has been suggested to be responsible for most of the features of the syndrome. This article describes seven previously unreported patients with deletions at 2q33.1, all partially overlapping the previously described critical region for the 2q33.1 microdeletion syndrome. The deletions ranged in size from 35 kb to 10.4 Mb, with the smallest deletion entirely within the SATB2 gene. Patients demonstrated significant developmental delay and challenging behaviour, a particular behavioural phenotype that seems to be emerging with more reported patients with this condition. One patient in this cohort has a deletion entirely within SATB2 and has a cleft palate, whereas several patients with larger deletions have a high arched palate. In addition, one other patient has significant orthopaedic problems with ligamentous laxity. Interestingly, this patient has a deletion that lies just distal to SATB2. The orthopaedic problems have not been reported previously and are possibly an additional feature of this syndrome. Overall, this report provides further evidence that the SATB2 gene is the critical gene in this microdeletion syndrome. In addition, because the individuals in this study range in age from 3-19 years, these patients will help define the natural progression of the phenotype in patients with this microdeletion.

Blood mononuclear cell gene expression signature of postpartum depression

In sorrow thou shalt bring forth children (Genesis 3:16) seems as relevant today, with one of seven mothers afflicted by a depressive episode, constituting the most common medical complication after delivery. Why mothers are variably affected by mood symptoms postpartum remains unclear, and the pathogenesis and early molecular indicators of this divergent outcome have not been described. We applied a case-control design comparing differential global gene expression profiles in blood mononuclear cells sampled shortly after delivery at the time of inception of postpartum depression (PD). Nine antidepressant naive mothers showing high depressive scores and developing a persisting major depressive episode with postpartum onset were compared with 10 mothers showing low depressive scores and no depressive symptoms on prospective follow-up. A distinctive gene expression signature was observed after delivery among mothers with an emergent PD, with a significant overabundance of transcripts showing a high-fold differential expression between groups, and correlating with depressive symptom severity among all mothers. Early expression signatures correctly classified the majority of PD patients and controls. Those developing persisting PD exhibit a relative downregulation of transcription after delivery, with differential immune activation, and decreased transcriptional engagement in cell proliferation, and DNA replication and repair processes. Our data provide initial evidence indicating that blood cells sampled shortly after delivery may harbor valuable prognostic information for identifying the onset of persisting PD. Some of the informative transcripts and pathways may be implicated in the differential vulnerability that underlies depression pathogenesis.

Circadian characteristics of serum calcium, magnesium and eight trace elements and of their metallo-moieties in urine of healthy middle-aged men

OBJECTIVE

To monitor the around-the-clock distribution of serum and urine concentrations of calcium, magnesium and eight trace elements and of those same elements in urine after their dialysis, and to statistically describe their circadian characteristics by chronobiological procedures.

MATERIALS AND METHODS

Serum and urine samples were collected every 3h over a single 24h period from eleven clinically-healthy male subjects, 41-60 years of age, and were analyzed for calcium (Ca), magnesium (Mg), iron (Fe), copper (Cu), zinc (Zn), lead (Pb), cadmium (Cd), cobalt (Co), chromium (Cr), and nickel (Ni). Urines were also sequentially dialyzed against ammonium-barbituric acid buffer at pH 7.35+/-0.02 using a 12.000-14.000 molecular weight exclusion sieve and then reanalyzed for the same elements. Urine concentrations were adjusted by urine volume to reflect a 3h excretion rate. Time-series were analyzed for circadian time-effect by ANOVA and for rhythm characteristics by the single cosinor fitting procedure.

RESULTS

The dialysis effectively removed 90% of total solids, 97% of urea, 92% creatinine, 72% uric acid, and essentially all of glucose. It also removed 99% of potassium (K), 96% of sodium (Na), 65% of Ca and P, 55% of Mg, 41% of Zn and 88% of Ni. A significant or borderline-significant 24h rhythm in serum was detected for Ca, Mg, Fe, Cu, Zn, Cd and Cr; in untreated urine for Ca, Fe, Cu, Zn, Ni, creatinine and volume; and in dialyzed urine for Ca, Fe, Cu, Zn, Pb, Cr, Cd and Ni. A 12h component was significant or borderline-significant in serum for Mg, Fe, Zn, and Cd; in untreated urine for volume, creatinine, Ca, Mg, Cu, and Ni; and in dialyzed urine for Ca, Mg, Fe, Cu, Zn, and Cr. In general, values in serum were lowest near the onset of sleep and highest in the first half of the day (between 02:28 and 13:56 h), while highest values in untreated or dialyzed urine were found several hours later in the day and at night.

CONCLUSIONS

Significant circadian variations were found in levels of nearly every element that was measured in blood and urine of 11 healthy men, but with highest and lowest levels occurring at different times. This suggests not only that urine concentrations need to be adjusted for collection time interval and urine volume, but that different biological limits at different times of the 24h day should be applied for serum and urinary monitoring of trace elements. We also found that the non-dialyzable segments of these elements in urine represent metallo-moieties composed of proteinacious matter greater than 12,000-14,000 Daltons. Further studies would be of interest to reveal time specificity for metabolic functions associated with any of these trace elements.

Uric acid and renal function in multiple sclerosis

OBJECTIVE

The purpose of this study was to examine the circadian distribution of creatinine and uric acid clearances in subjects with Multiple Sclerosis.

MATERIALS AND METHODS

Eleven subjects with MS, 6 women (48+/-7y) and 5 men (58+/-5y) volunteered for this circadian study. Thirteen healthy females (39+/-11y) served as controls. Data of seven healthy male controls (64+/-8 y) were extracted from a similar circadian study conducted previously. Each MS patient, and each male control had blood samples drawn around the clock, at 3h intervals (8/24h), and each collected urines over 3h periods (8/24h). Each female control contributed only one blood sample and one complete 24h urine collection. Blood and urine samples were analyzed for a number of relevant analytes: ELAM, IL-6, NO, insulin, ACTH, aldosterone, cortisol, electrolytes, lymphocytes, monocytes including creatinine and uric acid clearances. Those were standardized to an average body surface area of 1.73 m2.

RESULTS

The relevant analytes demonstrated increased synthesis of insulin, IL-6, ELAM, monocytes, and reduced concentrations of serum NO. The creatinine clearances were significantly lower in MS females than in female controls, 63+/-22 vs.108+/-18 ml/min. They were also lower than those of MS males and male controls, 107.8+/-17, 97.5+/-8.2 ml/min. Uric acid clearances in MS females were also lower 6.9+/-2.4 vs. 10.5+/-4.4 ml/min. The uric acid clearance in MS males was higher than in male controls, 7.0+/-4.5 vs. 4.0+/-1.0 ml/min.

CONCLUSIONS

The alterations in selected relevant analytes and the reduced creatinine and uric acid clearances in females but not in males, suggest a renal dysfunction in MS females. These observations may contribute to understanding better the mechanism of renal dysfunction in female patients and perhaps this may be an additional factor contributing to greater frequency of MS in females than in male subjects.

Horizontal gaze palsy with progressive scoliosis can result from compound heterozygous mutations in ROBO3

BACKGROUND

Horizontal gaze palsy with progressive scoliosis (HGPPS) is an autosomal recessive disorder characterised by congenital absence of horizontal gaze, progressive scoliosis, and failure of the corticospinal and somatosensory axon tracts to decussate in the medulla. We previously reported that HGPPS patients from consanguineous pedigrees harbour homozygous mutations in the axon guidance molecule ROBO3.

METHODS

We now report two sporadic HGPPS children of non-consanguineous parents who harbour compound heterozygous mutations in ROBO3. The mother of one of the children also had scoliosis DNA was extracted from a blood sample from each participant using a standard protocol, and the coding exons of ROBO3 were amplified and sequenced as previously described.

RESULTS

Each patient harboured two unique heterozygous mutations in ROBO3, having inherited one mutation from each parent.

CONCLUSIONS

HGPPS can result from compound heterozygous mutations. More comprehensive examinations of parents and siblings of HGPPS patients are required to determine if the incidence of scoliosis in individuals harbouring heterozygous ROBO3 mutations is greater than in the general population.

Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption

A visible-pump/UV-probe transient absorption is used to characterize the ultrafast dynamics of bacteriorhodopsin with 80-fs time resolution. We identify three spectral components in the 265- to 310-nm region, related to the all-trans retinal, tryptophan (Trp)-86 and the isomerized photoproduct, allowing us to map the dynamics from reactants to products, along with the response of Trp amino acids. The signal of the photoproduct appears with a time delay of approximately 250 fs and is characterized by a steep rise ( approximately 150 fs), followed by additional rise and decay components, with time scales characteristic of the J intermediate. The delayed onset and the steep rise point to an impulsive formation of a transition state on the way to isomerization. We argue that this impulsive formation results from a splitting of a wave packet of torsional modes on the potential surface at the branching between the all-trans and the cis forms. Parallel to these dynamics, the signal caused by Trp response rises in approximately 200 fs, because of the translocation of charge along the conjugate chain, and possible mechanisms are presented, which trigger isomerization.

Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors

Trauma survivors show marked differences in the severity and persistence of post-traumatic stress disorder (PTSD) symptoms. Early symptoms subside in most, but persist as acute and chronic PTSD in a significant minority. The underlying molecular mechanisms or outcome predictors determining these differences are not known. Molecular markers for identifying any mental disorder are currently lacking. Gene expression profiling during the triggering and development of PTSD may be informative of its onset and course. We used oligonucleotide microarrays to measure peripheral blood mononuclear cell (PBMC) gene expression of trauma survivors at the emergency room and 4 months later. Gene expression signatures at both time points distinguished survivors who met DSM-IV diagnostic criteria for PTSD at 1 and 4 months, from those who met no PTSD criterion. Expression signatures at both time points correlated with the severity of each of the three PTSD symptom clusters assessed 4 months following exposure among all survivors. Results demonstrate a general reduction in PBMCs' expression of transcription activators among psychologically affected trauma survivors. Several differentiating genes were previously described as having a role in stress response. These findings provide initial evidence that peripheral gene expression signatures following trauma identify an evolving neuropsychiatric disorder and are informative of its key clinical features and outcome. Replications in larger samples, as well as studies focusing on specific markers within the signatures discovered, are warranted to confirm and extend the diagnostic utility and pathogenetic implications of our results.

CIS: compound importance sampling method for protein-DNA binding site p-value estimation

MOTIVATION

A key aspect of transcriptional regulation is the binding of transcription factors to sequence-specific binding sites that allow them to modulate the expression of nearby genes. Given models of such binding sites, one can scan regulatory regions for putative binding sites and construct a genome-wide regulatory network. In such genome-wide scans, it is crucial to control the amount of false positive predictions. Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge.

RESULTS

We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data.

AVAILABILITY

The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http://compbio.cs.huji.ac.il/CIS/ CONTACT: nir@cs.huji.ac.il.

Inferring quantitative models of regulatory networks from expression data

MOTIVATION

Genetic networks regulate key processes in living cells. Various methods have been suggested to reconstruct network architecture from gene expression data. However, most approaches are based on qualitative models that provide only rough approximations of the underlying events, and lack the quantitative aspects that are critical for understanding the proper function of biomolecular systems.

RESULTS

We present fine-grained dynamical models of gene transcription and develop methods for reconstructing them from gene expression data within the framework of a generative probabilistic model. Unlike previous works, we employ quantitative transcription rates, and simultaneously estimate both the kinetic parameters that govern these rates, and the activity levels of unobserved regulators that control them. We apply our approach to expression datasets from yeast and show that we can learn the unknown regulator activity profiles, as well as the binding affinity parameters. We also introduce a novel structure learning algorithm, and demonstrate its power to accurately reconstruct the regulatory network from those datasets.

Increasing asthma awareness among physicians: impact on patient management and satisfaction

Our objective was to investigate the impact of increased asthma awareness among primary care physicians on the asthma control and satisfaction of their patients. Physicians attended an asthma education session with emphasis on patient-physician partnership followed by 4 month monitored follow-up of patients aged 5-44 years with mild to moderate asthma. Findings were compared with a group of patients whose physician attended the session but did not participate in the follow-up and two other control groups. The study included pediatricians and general practitioners of Maccabi Healthcare Services and their patients. Asthma symptoms were rated by patients and physicians. Data on drug prescription and use were derived from the Maccabi central database. Patient response and satisfaction and physician satisfaction were evaluated by telephone interviews. Mean asthma symptom score improved from 2.0 to 1.1 in the study group of patients (p < 0.001). The use of reliever drugs decreased concomitantly with a rise in controller drugs in all patients. An improvement in asthma status was reported by 64% of the study patients and 39% of non-participating patients (p = 0.007). Fifty-eight percent of the patients rated their competence to deal with asthma as high before the intervention compared to 62% of the participating and 55% of the non-participating patients after the intervention (p = 0.002). Most physicians claimed that simply increasing their awareness on asthma led to beneficial results in their patients. Physician education followed by monitored follow-up enhanced asthma control and patient satisfaction. Nevertheless, physician education alone appears to have a significant isolated impact on asthma control.

Evidence-based medicine: the key to guidelines, disease and care management programmes

INTRODUCTION

Evidence-based medicine (EBM) is based on the concept of applying best practice to the diagnosis or treatment of a single patient or clinical question, one patient at one time. Although this is useful as a practitioner seeing patients one at a time, it is limited in its application to populations or to single patients with multiple diseases. I will review how to apply EBM to the structure and implementation of population-based care management programmes.

METHODS

A review of the existing literature on the topic was undertaken in preparation for the First National Disease Management Conference-"Achieving seamless quality care across the continuum"-held between May 25 and 26, 2001. This material has been combined with experience and evidence of the author.

RESULTS

EBM and practice form the basis of the development of evidence-based guidelines that help lay the path for populations of patients with specific conditions. Care and disease management are the programmes that have been developed to implement evidence-based guidelines and best practice and to produce optimal outcomes in populations with chronic conditions, either single or multiple. Examples are presented to further the understanding of the reader.

CONCLUSIONS

To optimally improve the health of a population, chronic collaborative care programmes must be built and implemented that utilise best practice as defined by evidence in the literature.

Clinical, genetic and histopathologic findings in two siblings with muscle-eye-brain disease

PURPOSE

We present the clinical, genetic and histopathologic findings in two siblings with Muscle-Eye-Brain Disease (MEB-D), an autosomal recessive disease characterized by mental retardation, muscular dystrophy, retinal hypoplasia and brain abnormalities.

METHODS

Clinical, histopathologic and gene mapping studies of a family with two normal and two children with MEB-D.

RESULTS

Two siblings presented in the first few months of life with developmental delay, hypotonia, and strabismus. MRI of the brain showed colpocephaly, pontine and cerebellar atrophy, and diffuse white matter disease. Both patients were blind and had high myopia, strabismus, and retinal and optic nerve abnormalities. The older boy had glaucoma. Both children died from uncontrolled seizures. There was retinal, choroidal and RPE atrophy and optic nerve hypoplasia on ocular histopathology. Both patients shared the same parental haplotypes at the MEB locus on chromosome 1p, while an unaffected sibling did not, indicating possible linkage to the MEB locus.

CONCLUSIONS

Patients with MEB-D have severe visual impairment from retinal and optic nerve hypoplasia. High myopia appears to be a consistent finding. The ocular manifestations of MEB-D appear to be distinct from those of patients with Walker-Warburg syndrome.

Rich probabilistic models for gene expression

Clustering is commonly used for analyzing gene expression data. Despite their successes, clustering methods suffer from a number of limitations. First, these methods reveal similarities that exist over all of the measurements, while obscuring relationships that exist over only a subset of the data. Second, clustering methods cannot readily incorporate additional types of information, such as clinical data or known attributes of genes. To circumvent these shortcomings, we propose the use of a single coherent probabilistic model, that encompasses much of the rich structure in the genomic expression data, while incorporating additional information such as experiment type, putative binding sites, or functional information. We show how this model can be learned from the data, allowing us to discover patterns in the data and dependencies between the gene expression patterns and additional attributes. The learned model reveals context-specific relationships, that exist only over a subset of the experiments in the dataset. We demonstrate the power of our approach on synthetic data and on two real-world gene expression data sets for yeast. For example, we demonstrate a novel functionality that falls naturally out of our framework: predicting the "cluster" of the array resulting from a gene mutation based only on the gene's expression pattern in the context of other mutations.

Inferring subnetworks from perturbed expression profiles

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways.

Observation of islands of stability in soft wall atom-optics billiards

We report on numerical and experimental observations of islands of stability induced in a Bunimovich stadium atom-optics billiard by a soft wall repulsive potential. A deviation from exponential decay of the survival probability of atoms in an open billiard is observed, and explained by the presence of these stable islands and a sticky region surrounding them. We also investigate islands in dispersing billiards with soft walls, and predict a new mechanism for their formation.

Non-isomerizable artificial pigments: implications for the primary light-induced events in bacteriorhodopsin

The primary events in the photosynthetic retinal protein bacteriorhodopsin (bR) are reviewed in light of photophysical and photochemical experiments with artificial bR in which the native retinal polyene is replaced by a variety of chromophores. Focus is on retinals in which the "critical" C13=C14 bond is locked with respect to isomerization by a rigid ring structure. Other systems include retinal oxime and non-isomerizable dyes noncovalently residing in the binding site. The early photophysical events are analyzed in view of recent pump-probe experiments with sub-picosecond time resolution comparing the behavior of bR pigments with those of model protonated Schiff bases in solution. An additional approach is based on the light-induced cleavage of the protonated Schiff base bond that links retinal to the protein by reacting with hydroxylamine. Also described are EPR experiments monitoring reduction and oxidation reactions of a spin label covalently attached to various protein sites. It is concluded that in bR the initial relaxation out of the Franck-Condon (FC) state does not involve substantial C13=C14 torsional motion and is considerably catalyzed by the protein matrix. Prior to the decay of the relaxed fluorescent state (FS or I state), the protein is activated via a mechanism that does not require double bond isomerization. Most plausibly, it is a result of charge delocalization in the excited state of the polyene (or other) chromophores. More generally, it is concluded that proteins and other macromolecules may undergo structural changes (that may affect their chemical reactivity) following optical excitation of an appropriately (covalently or non-covalently) bound chromophore. Possible relations between the light-induced changes due to charge delocalization, and those associated with C13=C14 isomerization (that are at the basis of the bR photocycle), are discussed. It is suggested that the two effects may couple at a certain stage of the photocycle, and it is the combination of the two that drives the cross-membrane proton pump mechanism.

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin: mechanism and evidence for two M species

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin is investigated both for the native pigment and its D96N mutant. The experimental setup is based on creating the M intermediate by a first pulse, followed by a (blue) laser pulse which drives the back photoreaction of M. Experiments are carried out varying the delay between the two pulses, as well as the temperature over the -25 degrees C-20 degrees C range. It is found that the kinetic patterns of the M back photoreaction change with time after the generation of this intermediate. The data provide independent evidence for the suggestion of a photocycle mechanism based on two distinct M intermediates. They are thus in keeping with the consecutive model of Varo and Lanyi (Biochemistry 30, 5016-5022; 1991), although they cannot exclude other models such as those based on branched or parallel cycles. More generally, we offer a "photochemical" approach to discriminating between intermediate stages in the photocycle which does not depend on spectroscopic and/or kinetic data. While markedly affecting the rate of the M --> N transition in the photocycle, the rate of the thermal step in back photoreaction of M, at both room and low temperatures, is not significantly affected by the D96N mutation. It is proposed that while Asp 96 is the Schiff-base protonating moiety in the M --> N transition, another residue (most probably Asp 85) reprotonates the Schiff base following light absorption by M.

Evaluation of the consumer model: relationship between patients' expectations, perceptions and satisfaction with care

OBJECTIVE

To evaluate the consumer model in a health care system, by studying the relationship between four variables: expectations, perceived degree of fulfillment, satisfaction and changing of physicians.

DESIGN

Cross-sectional study; telephone interview of patients who had visited a primary care physician 1-2 months previously.

SETTING

The Maccabi health plan, Israel.

STUDY PARTICIPANTS

A random sample of 759 patients, aged 18 and over residing in two towns in Israel. Response rate to telephone interview was 50.7% (n=385).

MAIN OUTCOME MEASURES

Expectation, perceived expectations fulfilled by the physician, satisfaction with the visit to the primary care physician and intention to change physician.

RESULTS

The gap between the expectations and their fulfillment showed a low correlation with satisfaction. For attributes where a large difference was found, no correlation was found with patient satisfaction. Attributes such as 'diagnosis', 'preventive health care' and 'answering questions' presented correlation coefficients of 0.3. The correlation between the perceived fulfillment of these attributes and satisfaction presented higher correlation coefficients (between 0.4-0.5). This limits the consumer model as a way to predict satisfaction. Satisfaction correlated highly with intention to change physician. The mean score for the satisfaction of those intending to change doctors was 3.8 compared to 5.5 in the group of consumers not intending to change doctors.

CONCLUSION

The consumer model is able to explain only to a modest extent the variation in satisfaction, but dissatisfaction is a good predictor of the intention to change doctors.

Acousto-optic lens with very fast focus scanning

We propose and experimentally demonstrate an acousto-optic cylindrical lens with a very fast (400-kHz) focal scanning. The lens is realized by use of two adjacent acousto-optic scanners with counterpropagating acoustic waves that have the same frequency modulation but a pi phase difference. This scheme completely suppresses the lateral scan but adds the linear chirp of the two waves and thus functions as a fast focal-scan lens. We also demonstrate the use of this scanning lens in a very fast confocal profilometer.

Caustic soda ingestion -- a case presentation and review of the literature

We present a case report of a 2-year-old child with a hypopharyngeal stricture secondary to caustic soda ingestion. We discuss the initial and long-term management of caustic soda ingestion. In this case the hypopharynx was successfully reconstructed using a pedicled pectoralis major flap. We demonstrate the versatility of this flap, which is traditionally known for its use in adult head and neck surgery.

Using Bayesian networks to analyze expression data

DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a "snapshot" of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998).

Tissue classification with gene expression profiles

Constantly improving gene expression profiling technologies are expected to provide understanding and insight into cancer-related cellular processes. Gene expression data is also expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. In this work we examine three sets of gene expression data measured across sets of tumor(s) and normal clinical samples: The first set consists of 2,000 genes, measured in 62 epithelial colon samples (Alon et al., 1999). The second consists of approximately equal to 100,000 clones, measured in 32 ovarian samples (unpublished extension of data set described in Schummer et al. (1999)). The third set consists of approximately equal to 7,100 genes, measured in 72 bone marrow and peripheral blood samples (Golub et al, 1999). We examine the use of scoring methods, measuring separation of tissue type (e.g., tumors from normals) using individual gene expression levels. These are then coupled with high-dimensional classification methods to assess the classification power of complete expression profiles. We present results of performing leave-one-out cross validation (LOOCV) experiments on the three data sets, employing nearest neighbor classifier, SVM (Cortes and Vapnik, 1995), AdaBoost (Freund and Schapire, 1997) and a novel clustering-based classification technique. As tumor samples can differ from normal samples in their cell-type composition, we also perform LOOCV experiments using appropriately modified sets of genes, attempting to eliminate the resulting bias. We demonstrate success rate of at least 90% in tumor versus normal classification, using sets of selected genes, with, as well as without, cellular-contamination-related members. These results are insensitive to the exact selection mechanism, over a certain range.

Observation of chaotic and regular dynamics in atom-optics billiards

We report on experimental observations of chaotic and regular motion of ultracold atoms confined by a billiard-shaped optical dipole potential induced by a rapidly scanning laser beam. To investigate the dynamics of the atoms confined by such an "atom-optics" billiard we measure the decay of the number of trapped atoms through a hole on the boundary. A fast and purely exponential decay, the clear signature of chaotic motion, is found for a stadium billiard, but not for a circular or an elliptical billiard, in agreement with theory. We also investigated the effects of decoherence, velocity spread, and gravity on regular and chaotic motion.