Looking beyond year 1 in the molecular era of pediatric brain tumor diagnosis: confirmatory testing of germline variants found on tumor sequencing

Purpose

Somatic molecular profiling of pediatric brain tumors aids with the diagnosis and treatment of patients with a variety of high- and low-grade central nervous system neoplasms. Here, we report follow-up targeted germline evaluation for patients with possible germline variants following tumor only testing in the initial year in which somatic molecular testing was implemented at a single institution.

Patients and Methods

Somatic testing was completed for all tumors of the central nervous system (CNS) undergoing diagnostic workup at Seattle Children's Hospital during the study period of November 2015 to November 2016. Sequencing was performed in a College of American Pathologists-accredited, Clinical Laboratory Improvements Amendments-certified laboratory using UW-OncoPlex™ assay (version 5), a DNA-based targeted next generation sequencing panel validated to detect genetic alterations in 262 cancer-related genes. We tracked subsequent clinical evaluation and testing on a subgroup of this cohort found to have potential germline variants of interest.

Results

Molecular sequencing of 88 patients' tumors identified 31 patients with variants that warranted consideration of germline testing. To date, 19 (61%) patients have been tested. Testing confirmed germline variants for ten patients (31% of those identified for testing), one with two germline variants (NF1 and mosaic TP53). Eight (26%) patients died before germline testing was sent. One patient (13%) has not yet had testing.

Conclusion

Clinically validated molecular profiling of pediatric brain tumors identifies patients who warrant further germline evaluation. Despite this, only a subset of these patients underwent the indicated confirmatory sequencing. Further work is needed to identify barriers and facilitators to this testing, including the role of genetic counseling and consideration of upfront paired somatic-germline testing.

Therapeutic HDAC inhibition in hypermutant diffuse intrinsic pontine glioma

Constitutional mismatch repair deficiency (CMMRD) is a cancer predisposition syndrome associated with the development of hypermutant pediatric high-grade glioma, and confers a poor prognosis. While therapeutic histone deacetylase (HDAC) inhibition of diffuse intrinsic pontine glioma (DIPG) has been reported; here, we use a clinically relevant biopsy-derived hypermutant DIPG model (PBT-24FH) and a CRISPR-Cas9 induced genetic model to evaluate the efficacy of HDAC inhibition against hypermutant DIPG. We screened PBT-24FH cells for sensitivity to a panel of HDAC inhibitors (HDACis) in vitro, identifying two HDACis associated with low nanomolar IC50s, quisinostat (27 nM) and romidepsin (2 nM). In vivo, quisinostat proved more efficacious, inducing near-complete tumor regression in a PBT-24FH flank model. RNA sequencing revealed significant quisinostat-driven changes in gene expression, including upregulation of neural and pro-inflammatory genes. To validate the observed potency of quisinostat in vivo against additional hypermutant DIPG models, we tested quisinostat in genetically-induced mismatch repair (MMR)-deficient DIPG flank tumors, demonstrating that loss of MMR function increases sensitivity to quisinostat in vivo. Here, we establish the preclinical efficacy of quisinostat against hypermutant DIPG, supporting further investigation of epigenetic targeting of hypermutant pediatric cancers with the potential for clinical translation. These findings support further investigation of HDAC inhibitors against pontine high-grade gliomas, beyond only those with histone mutations, as well as against other hypermutant central nervous system tumors.

Current Utilization of Electron Microscopy in the Pediatric Pathology Setting: A Survey by the SPP Practice Committee

BACKGROUND

Electron microscopy (EM), once an important component in diagnosing pediatric diseases, has experienced a decline in its use. To assess the impact of this, pediatric pathology practices were surveyed regarding EM services.

METHODS

The Society of Pediatric Pathology Practice Committee surveyed 113 society members from 74 hospitals. Settings included 36 academic tertiary, 32 free-standing children's, and 6 community hospitals.

RESULTS

Over 60% maintained in-house EM services and had more than 2 pathologists interpreting EM while reporting a shortage of EM technologists. Freestanding children's hospitals had the most specimens (100-200 per year) and more diverse specimen types. Hospitals with fewer than 50 yearly specimens often used reference laboratories. Seventeen had terminated all in-house EM services. Challenges included decreasing caseloads due to alternative diagnostic methods, high operating costs, and shortages of EM technologists and EM-proficient pathologists. Kidney, liver, cilia, heart, and muscle biopsies most often required EM. Lung/bronchoalveolar lavage, tumor, skin, gastrointestinal, nerve, platelet, and autopsy samples less commonly needed EM.

CONCLUSIONS

The survey revealed challenges in maintaining EM services but demonstrated its sustained value in pediatric pathology. Pediatric pathologists may need to address the centralization of services and training to preserve EM diagnostic proficiency among pathologists who perform ultrastructural interpretations.

Intraventricular B7-H3 CAR T Cells for Diffuse Intrinsic Pontine Glioma: Preliminary First-in-Human Bioactivity and Safety

Diffuse intrinsic pontine glioma (DIPG) remains a fatal brainstem tumor demanding innovative therapies. As B7-H3 (CD276) is expressed on central nervous system (CNS) tumors, we designed B7-H3-specific chimeric antigen receptor (CAR) T cells, confirmed their preclinical efficacy, and opened BrainChild-03 (NCT04185038), a first-in-human phase I trial administering repeated locoregional B7-H3 CAR T cells to children with recurrent/refractory CNS tumors and DIPG. Here, we report the results of the first three evaluable patients with DIPG (including two who enrolled after progression), who received 40 infusions with no dose-limiting toxicities. One patient had sustained clinical and radiographic improvement through 12 months on study. Patients exhibited correlative evidence of local immune activation and persistent cerebrospinal fluid (CSF) B7-H3 CAR T cells. Targeted mass spectrometry of CSF biospecimens revealed modulation of B7-H3 and critical immune analytes (CD14, CD163, CSF-1, CXCL13, and VCAM-1). Our data suggest the feasibility of repeated intracranial B7-H3 CAR T-cell dosing and that intracranial delivery may induce local immune activation.

SIGNIFICANCE

This is the first report of repeatedly dosed intracranial B7-H3 CAR T cells for patients with DIPG and includes preliminary tolerability, the detection of CAR T cells in the CSF, CSF cytokine elevations supporting locoregional immune activation, and the feasibility of serial mass spectrometry from both serum and CSF. This article is highlighted in the In This Issue feature, p. 1.

Two cases of pineal anlage tumor with molecular analysis

Pineal anlage tumor is a rare pediatric tumor with clinical and histological features overlapping with pineoblastoma. Two patients with pineal anlage tumor, a 13-month-old female and an 11-month-old male, underwent subtotal resection, high-dose chemotherapy with autologous stem cell rescue, and radiation. Neither had tumor progression 50 months after diagnosis. The tumors underwent next-generation sequencing on a panel of 340 genes. Chromosomal copy gains and losses were present and differed between the tumors. No mutations or amplifications, including none specific to pineoblastoma, were identified.

Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor

Polynucleotide Kinase-Phosphatase (PNKP) is a bifunctional enzyme that possesses both DNA 3'-phosphatase and DNA 5'-kinase activities, which are required for processing termini of single- and double-strand breaks generated by reactive oxygen species (ROS), ionizing radiation and topoisomerase I poisons. Even though PNKP is central to DNA repair, there have been no reports linking PNKP mutations in a Microcephaly, Seizures, and Developmental Delay (MSCZ) patient to cancer. Here, we characterized the biochemical significance of 2 germ-line point mutations in the PNKP gene of a 3-year old male with MSCZ who presented with a high-grade brain tumor (glioblastoma multiforme) within the cerebellum. Functional and biochemical studies demonstrated these PNKP mutations significantly diminished DNA kinase/phosphatase activities, altered its cellular distribution, caused defective repair of DNA single/double stranded breaks, and were associated with a higher propensity for oncogenic transformation. Our findings indicate that specific PNKP mutations may contribute to tumor initiation within susceptible cells in the CNS by limiting DNA damage repair and increasing rates of spontaneous mutations resulting in pediatric glioma associated driver mutations such as ATRX and TP53.

Neuropathology of Pediatric Brain Tumors: A Concise Review

Pediatric brain tumors are an incredibly diverse group of neoplasms and neuropathological tumor classification is an essential part of patient care. Classification of pediatric brain tumors has changed considerably in recent years as molecular diagnostics have become incorporated with routine histopathology in the diagnostic process. This article will focus on the fundamental major histologic, immunohistochemical, and molecular features that neuropathologists use to make an integrated diagnosis of pediatric brain tumors. This concise review will focus on tumors that are integral to the central nervous system in pediatric patients including: embryonal tumors, low and high grade gliomas, glioneuronal tumors, ependymomas, and choroid plexus tumors.

Predictors of mortality and tumor recurrence in desmoplastic infantile ganglioglioma and astrocytoma-and individual participant data meta-analysis (IPDMA)

PURPOSE

Desmoplastic infantile astrocytoma (DIA) and desmoplastic infantile ganglioglioma (DIG) are classified together as grade I neuronal and mixed neuronal-glial tumor of the central nervous system by the World Health Organization (WHO). These tumors are rare and have not been well characterized in terms of clinical outcomes. We aimed to identify clinical predictors of mortality and tumor recurrence/progression by performing an individual patient data meta-analysis (IPDMA) of the literature.

METHODS

A systematic literature review from 1970 to 2020 was performed, and individualized clinical data for patients diagnosed with DIA/DIG were extracted. Aggregated data were excluded from collection. Outcome measures of interest were mortality and tumor recurrence/progression, as well as time-to-event (TTE) for each of these. Participants without information on these outcome measures were excluded. Cox regression survival analyses were performed to determine predictors of mortality and tumor recurrence / progression.

RESULTS

We identified 98 articles and extracted individual patient data from 188 patients. The cohort consisted of 58.9% males with a median age of 7 months. The majority (68.1%) were DIGs, while 24.5% were DIAs and 7.5% were non-specific desmoplastic infantile tumors; DIAs presented more commonly in deep locations (p = 0.001), with leptomeningeal metastasis (p = 0.001), and was associated with decreased probability of gross total resection (GTR; p = 0.001). Gender, age, and tumor pathology were not statistically significant predictors of either mortality or tumor recurrence/progression. On multivariate survival analysis, GTR was a predictor of survival (HR = 0.058; p = 0.007) while leptomeningeal metastasis at presentation was a predictor of mortality (HR = 3.27; p = 0.025). Deep tumor location (HR = 2.93; p = 0.001) and chemotherapy administration (HR = 2.02; p = 0.017) were associated with tumor recurrence/progression.

CONCLUSION

Our IPDMA of DIA/DIG cases reported in the literature revealed that GTR was a predictor of survival while leptomeningeal metastasis at presentation was associated with mortality. Deep tumor location and chemotherapy were associated with tumor recurrence / progression.

Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models

BACKGROUND

Diffuse midline gliomas (DMGs), including diffuse intrinsic pontine gliomas (DIPGs), have a dismal prognosis, with less than 2% surviving 5 years postdiagnosis. The majority of DIPGs and all DMGs harbor mutations altering the epigenetic regulatory histone tail (H3 K27M). Investigations addressing DMG epigenetics have identified a few promising drugs, including the HDAC inhibitor (HDACi) panobinostat. Here, we use clinically relevant DMG models to identify and validate other effective HDACi and their biomarkers of response.

METHODS

HDAC inhibitors were tested across biopsy-derived treatment-naïve in vitro and in vivo DMG models with biologically relevant radiation resistance. RNA sequencing was performed to define and compare drug efficacy and to map predictive biomarkers of response.

RESULTS

Quisinostat and romidepsin showed efficacy with low nanomolar half-maximal inhibitory concentration (IC50) values (~50 and ~5 nM, respectively). Comparative transcriptome analyses across quisinostat, romidepsin, and panobinostat showed a greater degree of shared biological effects between quisinostat and panobinostat, and less overlap with romidepsin. However, some transcriptional changes were consistent across all 3 drugs at similar biologically effective doses, such as overexpression of troponin T1 slow skeletal type (TNNT1) and downregulation of collagen type 20 alpha 1 chain (COL20A1), identifying these as potential vulnerabilities or on-target biomarkers in DMG. Quisinostat and romidepsin significantly (P < 0.0001) inhibited in vivo tumor growth.

CONCLUSIONS

Our data highlight the utility of treatment-naïve biopsy-derived models; establishes quisinostat and romidepsin as effective in vivo; illuminates potential mechanisms and/or biomarkers of DMG cell lethality due to HDAC inhibition; and emphasizes the need for brain tumor-penetrant versions of potentially efficacious agents.

Laser interstitial thermal therapy for pediatric atypical teratoid/rhabdoid tumor: case report

Herein, the authors describe the successful use of laser interstitial thermal therapy (LITT) for management of metastatic craniospinal disease for biopsy-proven atypical teratoid/rhabdoid tumor in a 16-month-old boy presenting to their care. Specifically, LITT was administered to lesions of the right insula and left caudate. The patient tolerated 2 stages of LITT to the aforementioned lesions without complication and with evidence of radiographic improvement of lesions at the 2- and 6-month follow-up appointments. To the authors' knowledge, this represents the first such published report of LITT for management of atypical teratoid/rhabdoid tumor.

A Protocol for the Generation of Treatment-naïve Biopsy-derived Diffuse Intrinsic Pontine Glioma and Diffuse Midline Glioma Models

Diffuse intrinsic pontine glioma (DIPG) is a universally fatal tumor of the brainstem, most commonly affecting young children. Due to its location, surgical resection is not achievable, but consideration of a biopsy has become standard practice at children’s hospitals with the appropriate neurosurgical expertise. While the decision to obtain a biopsy should be directed by the presence of atypical radiographic features that call the diagnosis of DIPG into question or the requirement of biopsy tissue for clinical trial enrollment, once this precious tissue is available its use for research should be considered. The majority of DIPG and diffuse midline glioma, H3 K27M-mutant (DMG) models are autopsy-derived or genetically-engineered, each of which has limitations for translational studies, so the use of biopsy tissue for laboratory model development provides an opportunity to create unique model systems. Here, we present a detailed laboratory protocol for the generation of treatment-naïve biopsy-derived DIPG/DMG models.

A Protocol for the Generation of Treatment-naïve Biopsy-derived Diffuse Intrinsic Pontine Glioma and Diffuse Midline Glioma Models

Diffuse intrinsic pontine glioma (DIPG) is a universally fatal tumor of the brainstem, most commonly affecting young children. Due to its location, surgical resection is not achievable, but consideration of a biopsy has become standard practice at children's hospitals with the appropriate neurosurgical expertise. While the decision to obtain a biopsy should be directed by the presence of atypical radiographic features that call the diagnosis of DIPG into question or the requirement of biopsy tissue for clinical trial enrollment, once this precious tissue is available its use for research should be considered. The majority of DIPG and diffuse midline glioma, H3 K27M-mutant (DMG) models are autopsy-derived or genetically-engineered, each of which has limitations for translational studies, so the use of biopsy tissue for laboratory model development provides an opportunity to create unique model systems. Here, we present a detailed laboratory protocol for the generation of treatment-naïve biopsy-derived DIPG/DMG models.

Heme oxygenase-1 deficiency presenting with interstitial lung disease and hemophagocytic flares

BACKGROUND

Heme oxygenase-1 (HMOX1) catalyzes the metabolism of heme into carbon monoxide, ferrous iron, and biliverdin. Through biliverdin reductase, biliverdin becomes bilirubin. HMOX1-deficiency is a rare autosomal recessive disorder with hallmark features of direct antibody negative hemolytic anemia with normal bilirubin, hyperinflammation and features similar to macrophage activation syndrome. Clinical findings have included asplenia, nephritis, hepatitis, and vasculitis. Pulmonary features and evaluation of the immune response have been limited.

CASE PRESENTATION

We present a young boy who presented with chronic respiratory failure due to nonspecific interstitial pneumonia following a chronic history of infection-triggered recurrent hyperinflammatory flares. Episodes included hemolysis without hyperbilirubinemia, immunodeficiency, hepatomegaly with mild transaminitis, asplenia, leukocytosis, thrombocytosis, joint pain and features of macrophage activation with negative autoimmune serologies. Lung biopsy revealed cholesterol granulomas. He was found post-mortem by whole exome sequencing to have a compound heterozygous paternal frame shift a paternal frame shift HMOX1 c.264_269delCTGG (p.L89Sfs*24) and maternal splice donor HMOX1 (c.636 + 2 T > A) consistent with HMOX1 deficiency. Western blot analysis confirmed lack of HMOX1 protein upon oxidant stimulation of the patient cells.

CONCLUSIONS

Here, we describe a phenotype expansion for HMOX1-deficiency to include not only asplenia and hepatomegaly, but also interstitial lung disease with cholesterol granulomas and inflammatory flares with hemophagocytosis present in the bone marrow.

Histopathologic and Molecular Features of Central Nervous System Embryonal Tumors for Integrated Diagnosis Reporting

Embryonal tumors of the pediatric central nervous system are challenging clinically and diagnostically. These tumors are aggressive, and patients often have poor outcomes even with intense therapy. Proper tumor classification is essential to patient care, and this process has undergone significant changes with the World Health Organization recommending histopathologic and molecular features be integrated in diagnostic reporting. This has especially impacted the workup of embryonal tumors because molecular testing has resulted in the identification of clinically relevant tumor subgroups and new entities. This review summarizes recent developments and provides a framework to workup embryonal tumors in diagnostic practice.

Year 1 in the Molecular Era of Pediatric Brain Tumor Diagnosis: Application of Universal Clinical Targeted Sequencing in an Unselected Cohort of Children

Purpose

Next-generation sequencing is gaining acceptance as a clinical tool to aid diagnosis and guide treatment of pediatric cancer. Prior pilot studies have evaluated the feasibility and utility of clinical genomic profiling in a subset of selected patients with brain tumors. Here, we report an unselected prospective cohort study to evaluate the clinical use of universal targeted sequencing in pediatric patients with brain tumors.

Methods

We applied a universal sequencing protocol for all tumors of the CNS undergoing diagnostic workup at Seattle Children’s Hospital during the study period of November 2015 to November 2016. All tumors were sequenced using the UW-OncoPlex platform, which is a multiplexed targeted deep gene sequencing panel that detects genetic alterations in 262 cancer-related genes performed in a College of American Pathologists–accredited Clinical Laboratory Improvements Amendments–certified laboratory.

Results

Eighty-eight patients underwent diagnostic evaluation during the study period, of which 85 tumors (95%) yielded sufficient DNA for sequencing, including 59 newly diagnosed and 26 relapsed. Clinically relevant genetic alterations were identified in 68 of 85 patients (80%). Of these, 57 (67%) had disease-defining or disease-modifying mutations, 44 (52%) had potentially targetable mutations, and 31 (36%) had mutations requiring germline follow-up. As of the last follow-up, seven patients had been prescribed targeted agents on the basis of sequencing results, and nine had confirmed deleterious germline mutations.

Conclusion

Clinically validated molecular profiling of pediatric brain tumors aids diagnosis and treatment of patients with a variety of high- and low-grade primary and relapsed pediatric brain tumors.

Desmoplastic Infantile Ganglioglioma/Astrocytoma (DIG/DIA) Are Distinct Entities with Frequent BRAFV600 Mutations

Desmoplastic infantile ganglioglioma (DIG) and desmoplastic infantile astrocytoma (DIA) are extremely rare tumors that typically arise in infancy; however, these entities have not been well characterized in terms of genetic alterations or clinical outcomes. Here, through a multi-institutional collaboration, the largest cohort of DIG/DIA to date is examined using advanced laboratory and data processing techniques. Targeted DNA exome sequencing and DNA methylation profiling were performed on tumor specimens obtained from different patients (n = 8) diagnosed histologically as DIG/DIGA. Two of these cases clustered with other tumor entities, and were excluded from analysis. The remaining 16 cases were confirmed to be DIG/DIA by histology and by DNA methylation profiling. Somatic BRAF gene mutations were discovered in 7 instances (43.8%); 4 were BRAFV600E mutations, and 3 were BRAFV600D mutations. Three instances of malignant transformation were found, and sequencing of the recurrence demonstrated a new TP53 mutation in one case, new ATRX deletion in one case, and in the third case, the original tumor harbored an EML4-ALK fusion, also present at recurrence. DIG/DIA are distinct pathologic entities that frequently harbor BRAFV600 mutations. Complete surgical resection is the ideal treatment, and overall prognosis is excellent. While, the small sample size and incomplete surgical records limit a definitive conclusion about the risk of tumor recurrence, the risk appears quite low. In rare cases with wild-type BRAF, malignant progression can be observed, frequently with the acquisition of other genetic alterations.Implications: DIG/DIA are a distinct molecular entity, with a subset frequently harboring either BRAF V600E or BRAF V600D mutations. Mol Cancer Res; 16(10); 1491-8. ©2018 AACR.

Targeted Sequencing of Malignant Supratentorial Pediatric Brain Tumors Demonstrates a High Frequency of Clinically Relevant Mutations

Pediatric brain tumors cause more deaths than any other childhood malignancy, and the identification of potentially actionable genomic alterations in this rare heterogeneous group of tumors may improve treatment and outcome. The genetic landscape of common posterior fossa tumors has been described in the past several years, yet the classification of malignant pediatric supratentorial tumors remains controversial. Next-generation sequencing (NGS) is a promising tool to evaluate multiple genes concurrently. The clinical utility of NGS has not been proven in pediatric brain tumors. We identified patients diagnosed with high-grade supratentorial pediatric brain tumors resected between 2008 and 2012 at our institution. DNA from 12 formalin-fixed paraffin-embedded tumor samples from 9 patients was analyzed, including 3 paired samples from diagnosis and relapse. A panel of 194 cancer-related genes was sequenced using targeted next-generation deep sequencing. Genetic findings were correlated with histology, immunohistochemistry, treatment, and survival. We found one or more pathologic genetic change (mutation, amplification, or deletion) in 8 of 9 (89%) of patients studied. Epidermal Growth Factor Receptor ( EGFR) mutations were found in 3 patients, 2 of which had an exon 20 insertion not previously described in pediatric malignancy. Additional genetic changes were found in EGFR and Platelet-Derived Growth Factor Receptor Alpha ( PDGFRA) at relapse not present in the initial samples. Familial cancer predisposition syndromes were suggested by mutations found in 3 genes in 4 patients, including TP53, MSH2, and CHEK2. Seven of 9 patients in this study died of their disease. In summary, targeted deep sequencing may be used in rare pediatric brain tumors to identify driver mutations for targeted therapy, suggest constitutional and familial testing for cancer predisposition syndromes, and select molecular targets worthy of further study.

Preventing Genetic Testing Order Errors With a Laboratory Utilization Management Program

OBJECTIVES

To characterize error rates for genetic test orders between medical specialties and in different settings by examining detailed order information.

METHODS

We performed a retrospective analysis of a detailed utilization management case database, comprising 2.5 years of data and almost 1,400 genetic test orders. After review by multiple reviewers, we categorized order modifications and cancellations, quantified rates of positive results and order errors, and compared genetics with nongenetics providers and inpatient with outpatient orders.

RESULTS

High cost or problems with preauthorization were the most common reasons for modification and cancellation, respectively. The cancellation rate for nongenetics providers was three times the rate for geneticists, but abnormal result rates were similar between the two groups. The approval rate for inpatient orders was not significantly lower than outpatient orders, and abnormal result rates were similar for these two groups as well. Order error rates were approximately 8% among tests recommended by genetics providers in the inpatient setting, and tests ordered or recommended by nongeneticists had error rates near 5% in both inpatient and outpatient settings.

CONCLUSIONS

Clinicians without specialty training in genetics make genetic test order errors at a significantly higher rate than geneticists. A laboratory utilization management program prevents these order errors from becoming diagnostic errors and reaching the patient.

Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait Loci

Understanding the genetic architecture of evolutionary change remains a long-standing goal in biology. In vertebrates, skeletal evolution has contributed greatly to adaptation in body form and function in response to changing ecological variables like diet and predation. Here we use genome-wide linkage mapping in threespine stickleback fish to investigate the genetic architecture of evolved changes in many armor and trophic traits. We identify >100 quantitative trait loci (QTL) controlling the pattern of serially repeating skeletal elements, including gill rakers, teeth, branchial bones, jaws, median fin spines, and vertebrae. We use this large collection of QTL to address long-standing questions about the anatomical specificity, genetic dominance, and genomic clustering of loci controlling skeletal differences in evolving populations. We find that most QTL (76%) that influence serially repeating skeletal elements have anatomically regional effects. In addition, most QTL (71%) have at least partially additive effects, regardless of whether the QTL controls evolved loss or gain of skeletal elements. Finally, many QTL with high LOD scores cluster on chromosomes 4, 20, and 21. These results identify a modular system that can control highly specific aspects of skeletal form. Because of the general additivity and genomic clustering of major QTL, concerted changes in both protective armor and trophic traits may occur when sticklebacks inherit either marine or freshwater alleles at linked or possible "supergene" regions of the stickleback genome. Further study of these regions will help identify the molecular basis of both modular and coordinated changes in the vertebrate skeleton.

A critique of the usefulness of inferential statistics in applied behavior analysis

Researchers continue to recommend that applied behavior analysts use inferential statistics in making decisions about effects of independent variables on dependent variables. In many other approaches to behavioral science, inferential statistics are the primary means for deciding the importance of effects. Several possible uses of inferential statistics are considered. Rather than being an objective means for making decisions about effects, as is often claimed, inferential statistics are shown to be subjective. It is argued that the use of inferential statistics adds nothing to the complex and admittedly subjective nonstatistical methods that are often employed in applied behavior analysis. Attacks on inferential statistics that are being made, perhaps with increasing frequency, by those who are not behavior analysts, are discussed. These attackers are calling for banning the use of inferential statistics in research publications and commonly recommend that behavioral scientists should switch to using statistics aimed at interval estimation or the method of confidence intervals. Interval estimation is shown to be contrary to the fundamental assumption of behavior analysis that only individuals behave. It is recommended that authors who wish to publish the results of inferential statistics be asked to justify them as a means for helping us to identify any ways in which they may be useful.

Occult androgenetic-biparental mosaicism and sporadic hepatic mesenchymal hamartoma

The incidence of hepatic mesenchymal hamartoma (HMH) is increased in patients with placental mesenchymal dysplasia (PMD), which appears to be caused by androgenetic-biparental mosaicism (ABM). We hypothesized that occult ABM might underlie cases of HMH with no known history of PMD. Formalin-fixed, paraffin-embedded HMH specimens from 10 such patients and liver specimens from 6 non-HMH controls were identified retrospectively from the surgical pathology records of a pediatric hospital. The relative abundance of maternal and paternal alleles was assessed by quantitative polymerase chain reaction amplification of polymorphic short tandem repeats and single nucleotide polymorphisms located on 15 different chromosomes. Androgenetic-biparental mosaicism was diagnosed in one patient based on global allelic imbalances at all informative loci. In that patient, the greatest imbalances were observed in stroma-rich portions of the hamartoma, with no significant imbalance in histologically normal liver or epithelium-rich portions of the hamartoma. A retrospective, unbiased review of the histology and clinical records from all 10 patients revealed no morphologic or clinical correlates to distinguish the affected patient, except that she had multiple cutaneous hemangiomas, which like HMH, appear to be more common in patients with PMD. Our findings suggest that other patients with apparently sporadic HMH, hemangioma, or other lesions seen more frequently with PMD may harbor occult ABM. Recognition of ABM may be important because its long-term consequences are unknown but may be significant.

The genetic architecture of divergence between threespine stickleback species

The genetic and molecular basis of morphological evolution is poorly understood, particularly in vertebrates. Genetic studies of the differences between naturally occurring vertebrate species have been limited by the expense and difficulty of raising large numbers of animals and the absence of molecular linkage maps for all but a handful of laboratory and domesticated animals. We have developed a genome-wide linkage map for the three-spined stickleback (Gasterosteus aculeatus), an extensively studied teleost fish that has undergone rapid divergence and speciation since the melting of glaciers 15,000 years ago. Here we use this map to analyse the genetic basis of recently evolved changes in skeletal armour and feeding morphologies seen in the benthic and limnetic stickleback species from Priest Lake, British Columbia. Substantial alterations in spine length, armour plate number, and gill raker number are controlled by genetic factors that map to independent chromosome regions. Further study of these regions will help to define the number and type of genetic changes that underlie morphological diversification during vertebrate evolution.

A survey of student assessment in U.S. medical schools: the balance of breadth versus fidelity

BACKGROUND

Faced with the challenge to develop models of assessment relevant to work of physicians, medical schools have broadened their assessment of medical student competency.

PURPOSE

U.S. medical schools were surveyed to determine the extent to which student assessments have broadened beyond multiple-choice question (MCQ) examinations and preceptor ratings.

METHODS

A survey mailed to 126 accredited U.S. medical schools asked respondents to indicate the frequency with which a variety of assessment methods were used in each year of the curriculum.

RESULTS

Examinations dominated preclinical assessments. Year 3 relied heavily on faculty ratings, live observations, and MCQs. Preceptor ratings were used most in year 4.

CONCLUSIONS

A variety of competency assessments currently are used; MCQs remain a core assessment method. Year 3 had the greatest breadth of assessment strategies. The findings suggest that educators continue to be challenged to balance the breadth of competencies sampled with the fidelity of the assessment experience.

The prevalence and symptoms of migraine in a consecutive series of patients attending an optometric practice

The purpose of the investigation was to determine the prevalence of migraine in optometric practice and to document the variety of presentation. One thousand consecutively presenting patients of a suburban optometric practice were asked questions to establish whether they experience migraine or have experienced it in the past. Those with a history of migraine were asked further questions to establish the type of migraine and to document the variety of the symptoms they experienced. Eleven percent of male and 23% of female patients currently had migraine or had experienced it in the past. When corrected for the age distribution of the population of the state from which the sample was drawn, it is estimated that the general population prevalence of migraine is 9.5% for men and 19.7% for women. Half of the sample of migraineurs had not experienced a migraine within the last 12 months. A third had a known family history of migraine. Nearly half had not had a formal medical diagnosis of their migraine but only 7 had attended for optometric examination because of their migraine symptoms. Four of these patients had single migraine-like episodes and three had migraine equivalents (acephalic migraine, experiencing the visual aura without headache). Optometrists must be thoroughly familiar with migraine and its varied presentation because of its high prevalence, the explanatory value in offering a formal diagnosis of migraine, and the risk that headache or visual aura may be wrongly ascribed to migraine when there is some more sinister cause of the symptoms.

Can clinical colour vision tests be used to predict the results of the Farnsworth lantern test?

Clinicians usually do not have access to a lantern test when making an occupational assessment of the ability of a person with defective colour vision to recognise signal light colours: they must rely on the results of ordinary clinical tests. While all colour vision defectives fail the Holmes Wright Type B lantern test and most fail the Holmes Wright Type A lantern, 35% of colour vision defectives pass the Farnsworth lantern. Can clinical tests predict who will pass and fail the Farnsworth lantern? We find that a pass (less than two or more diametrical crossings) at the Farnsworth Panel D 15 Dichotomous test has a sensitivity of 0.67 and specificity of 0.94 in predicting a pass or fail at the Farnsworth lantern test: a Nagel range of > 10 has a sensitivity of 0.87 and a specificity of 0.57. We conclude that neither the D 15 nor the Nagel Anomaloscope matching range are satisfactory predictors of performance on the Farnsworth Lantern.

Action on worksite health and safety problems: a follow-up survey of workers participating in a hazardous waste worker training program

In it's worker health and safety training program, the California-Arizona Consortium aims to promote worker action to improve health and safety conditions. To assess action on worker-identified health and safety problems, 278 trainees were interviewed 3-8 months after training. Associations with three outcomes were analyzed: (1) attempted action, (2) problem correction, and (3) trainee participation. Perceived management support was associated with all three outcomes, pointing to its key role in maximizing the impact of training. Odds of attempted action were 2-5 times greater with support than without. Trainees for whom English was not the primary language (mostly Spanish speakers) attempted action as often as English speakers. However, the odds of their correcting problems were half that of the English-speaking workers. It is suggested this was due to a perceived lack of control over organizational resources for change, not simply due to communication barriers.

Effect of VDUs on the eyes: report of a 6-year epidemiological study

One thousand, three hundred and sixteen office workers [692 visual display unit (VDU) users, 624 controls in the first year] were examined once each year over a 6-year period to establish whether or not VDU work was a factor in the occurrence of visual symptoms, ocular abnormalities, or ocular disease. Statistical analysis showed that although there were differences between VDU users and nonusers in the amount of myopia, the prevalence of some symptoms, and the prevalence of signs of fundal or vitreal disease, the differences were small and there were no clear trends or patterns to lend convincing support to the hypothesis that VDU work may be a risk factor. There were no significant differences in the prevalence and incidence of cataract.

HIV-related knowledge and attitudes among medical students in China

A modified version of the 'WHO/KABP Questionnaire for Students' was administered to 302 students at a medical university in China. The instrument included items to assess the students' demographic background, knowledge of AIDS/HIV, attitudes about AIDS, as well as towards people infected with HIV, those groups commonly labelled as 'high risk' and toward sources of information. The average score on the knowledge scale was 80% correct. There was a substantial disparity in knowledge between how HIV is transmitted and how HIV is not transmitted--90% of the former items were answered correctly, while only 72% of the latter were answered correctly. Over 40% of the sample blamed prostitutes for AIDS in China, whereas 22% blamed drug addicts and 6% blamed homosexuals. Two-thirds of the sample indicated that they thought people with AIDS got what they deserve. About one-third of the sample supported quarantine measures as well as keeping infected students out of classrooms. Nearly half of the sample indicated that they did not trust any of the official sources of health information we asked about and 27% said that they thought the government was concealing information about AIDS.

What do color vision defectives say about everyday tasks?

A lengthy questionnaire was administered to 102 people with defective color vision and to an equal number of people with normal color vision. The questionnaire asked about the subjects' awareness of their defect and their knowledge of defective color vision as well as exploring the difficulties they experience with color at work and in pursuing leisure activities. The questionnaire was administered in the consulting room under conditions that might be expected to elicit frank replies. Nearly 90% of dichromats and up to two-thirds of anomalous trichomats reported difficulties with everyday tasks that involve color, nearly one-half of the dichromats and one in five anomalous trichromats reported difficulty with traffic lights, and similar proportions reported color difficulties in their present jobs. Substantial numbers reported that their color vision defect had affected their choice of career and many had been excluded from a chosen occupation. The screening of color vision in schools and provision of appropriate career counselling is urged.

Assessment of contrast sensitivity of patients with macular disease using reduced contrast near visual acuity charts

A set of near Bailey-Lovie logMAR letter charts that varied in contrast from 0.40 dB (C = 0.95) to 58.0 dB (C = 0.001) were used to measure the middle and high spatial frequency range of the contrast sensitivity function (CSF) of 15 subjects with age-related maculopathy (ARM) and 15 age-matched normal subjects. The letter charts were shown to have good test-retest reliability. Compared with measures made using CRT generated square wave gratings of variable contrast and spatial frequency they were also shown to provide a valid measure of CSF in the mid to high spatial frequency range. The 20.0 dB letter chart alone was shown to be a good screening device for macular disease. The letter charts do not provide a measure of the peak of the CSF and a supplementary test of contrast sensitivity is needed to quantify contrast sensitivity at a low spatial frequency. Three measures are proposed as necessary to document foveal visual capability of patients with macular disease: distance logMAR visual acuity to measure high spatial frequency resolution, visual acuity with letter charts of 20 dB contrast to assess mid spatial frequency resolution; and contrast sensitivity for the detection of an edge to estimate contrast sensitivity for larger objects.

Defective colour vision can impede information acquisition from redundantly colour-coded video displays

Earlier findings showed that redundant colour coding decreased response times and reduced errors in carrying out various tasks that required information acquisition from the video display of an electronic flight instrument system. The results of this experiment showed that observers with defective colour vision have slower response times and higher error rates than normal observers for some of the tasks and that their performance is similar to that of colour-normal observers for a monochrome display. However, they were not disadvantaged when blue was used to colour code the target feature. Protanopes were shown to be especially disadvantaged in responding to a red 'fail' message.

Reliability and validity of simple photographic plate tests of contrast sensitivity

Sets of edge and square wave grating photographic plates of varying contrasts were used to measure the mid to low spatial frequency range of the contrast sensitivity function (CSF) of 20 subjects with evident ocular disease and 20 age-matched normal subjects. Both plate tests were shown to have good test-retest reliability and to correlate well with electronic cathode ray tube (CRT) measures of CSF. The edge test, when administered in 2-dB steps of ascending contrast, has optimum sensitivity of 0.70 and specificity of 0.84 for detecting the patient with ocular disease with a fail criterion of less than 38 dB. A measure of edge contrast sensitivity was also shown to be a good predictor of the peak of the CSF, which is shown to be largely independent of the visual acuity of the subject. The 2 c/deg and 4 c/deg plates did not provide more information about the visual difficulties of subjects than the edge test. We advocate the use of an edge test as a simple clinical measure of low spatial frequency contrast sensitivity that provides information about visual dysfunction not provided by a measure of visual acuity.

Origins of colour vision standards within the transport industry

Colour vision standards should reflect changes in our understanding of the nature of these defects as well as technological advances that place less importance upon the visual senses of the human operator. Therefore it is suggested that visual standards be subject to routine reviews in order to assess their suitability for modern work environments. This paper gives a chronological account of the introduction of colour vision standards by several national transport authorities and identifies historical reasons that led to their implementation. It is concluded that the same factors that gave rise to the adoption of early colour vision standards are still relevant for modern transport systems. However the recent deployment of automatic or semi-automatic control or navigational systems has substantially altered man's role from being the primary source of information input to one of a monitoring process. This has generated a good deal of debate and uncertainty regarding the level of responsibility that a human operator has for the control of modern transport vehicles. Nevertheless, it is argued that in the absence of complete automation some type of visual standard is needed whenever visual judgements must be made by human observers.

The effect of variability of background elements on the conspicuity of objects

The effect of complex backgrounds on target visibility was studied by asking observers to locate a disc target presented on a background of randomly arranged discs. A previous paper (Vision Res. 22, 1241-1252, 1982) explored the effect of increasing the density (numerosity) of the background elements when the elements were all the same size and luminance. In this investigation the size or the luminance of the background elements varied although mean size and mean luminance was held constant. Variability of the size of the background elements had a substantial effect on the size contrast necessary to detect the target. The data are well described by a contrast metric CT which assumes that observers detect the target by comparing it to a weighted average of the larger elements. The larger elements that determine the weighted average are those that all appear the same size because, at the eccentricity of target, the observers are unable to distinguish their differences in size. The threshold values of CT for detection of the target at a given level of probability were dependent on eccentricity but independent of the degree of variability of the background elements. The threshold contrast was also the same as the necessary for the more elementary task of discriminating size differences of two discs. In a second experiment it is shown that variability in the luminance of the background elements did not affect target visibility. This result is explained by reference to the data in our earlier paper from which it can be shown that the observers were unable to perceive the differences in luminance in their peripheral visual field so that, within limits, backgrounds that vary in luminance can be validly characterised by mean luminance.

Who fails lantern tests?

A battery of clinical colour vision tests was given to a group of 100 observers with abnormal colour vision who were also tested on the Farnsworth lantern and the Holmes-Wright lanterns types A and B. It was found that clinical colour vision tests are imperfect predictors of lantern test performance. However, observers classified as having a 'severe' colour vision defect were found to fail the lantern tests but only one half to two-thirds of those who fail the lantern tests can be identified in this way. It is not possible to identify with certainty any of the people likely to pass the lantern tests: about one-third to two-thirds of observers classified as being mildly affected fail the lantern tests. The Farnsworth D-15 and City University tests were found to be the best predictors of lantern test performance but other tests such as the Nagel anomaloscope, the H-16, L'Anthony's desaturated test can also be used. The lack of a strong correlation between clinical tests and the recognition of the small coloured stimuli presented by the lantern tests suggests that clinical tests do not test the same aspect of colour vision that is important to the recognition of signal lights. For this reason lantern tests should be retained for occupational testing of colour vision.

A survey and evaluation of lantern tests of color vision

This paper reports a survey of the lantern tests that have been or are used to evaluate the color vision of people who wish to enter occupations that require the ability to recognize colored signal lights reliably. The origin of each lantern is traced and the principal features of each are described. The available data concerning failure rate of normals, the failure rate of people with defective color vision, and the extent to which scores on lantern tests correlate with field trials are summarized. Despite the fact that lantern tests have been used since the turn of the century and that some lanterns have been in use for more than 30 years and some for much longer periods, the available validation data are incomplete and sometimes conflicting. However, the data do indicate that some lanterns may fail a significant proportion of normals and that there is considerable variation between lanterns in the proportion of color vision defectives that will fail. It is noted that most lanterns will pass some protanomals despite their reduced sensitivity to red light and correspondingly short visual range for red signals. The view of Cameron is supported that a more rational approach would be to made a clinical diagnosis of the type of color vision defect, to reject protanopes, deuteranopes, and protanomals and to use a lantern test only to determine which deuteranomals should be accepted.

The effect of the density of background elements on the conspicuity of objects

Engel's concept of conspicuity is formalised to define a conspicuous object as one that will, for a given background, be seen with certainty within a short observation time regardless of the location of the object in relation to the line of sight. Thus for a defined level of probability of seeing and given observation time, the angle of eccentricity at which the defined level of probability of seeing occurs becomes the measure of the conspicuity of the target. Using this measure the conspicuity of disc targets has been determined when the targets are presented in complex backgrounds made up of random arrays of discs. A first experiment determined thresholds for discrimination of size differences and luminance differences for two discs since this was regarded as the elementary task in the detection of the target within a complex background made up of elements of the same shape. In the main experiment the task was the detection of a target disc located in a background consisting of randomly arranged discs. The target disc differed from the background discs in either size or luminance or both. The background array had three densities of background element. When the target discs differed in luminance from the background discs an increase in background density made the target disc less conspicuous but changing background density had no effect on the conspicuity of target discs that differed in size from the background discs. It was found that the task of detecting a luminance difference when there were only two discs (first experiment) was easier than detecting a target disc in the random arrays. However, the detection of a disc of different size in the random arrays appears to be no more difficult than the elementary task of comparing size differences between two discs. This suggests that the visual processes for detecting a target in a complex background by size difference are different from those for detecting the target by luminance difference.

Recognition of the aircraft navigation light color code

Navigation lights are a set of color-coded signals intended to indicate the presence, orientation, and relative direction of aircraft at night, and thereby reduce the possibility of midair collisions. It is known that some people with defective color vision have difficulty with quite simple codes. Accordingly, the International Civil Aviation Organization (ICAO) has recommended -- and most countries apply -- that applicants for pilot's licences demonstrate the ability to recognise colored light signals. Pilots who fail to meet this requirement are restricted from flying at night. But is the navigation light signal system effective? This paper concludes that the navigation light system at night can serve as a crude screening method to categorize intruder aircraft into "potential threat" and "no threat" categories. An experiment is described which shows that observers with normal color vision can determine intruder aircraft orientation and relative direction from the navigation light code with a moderately high degree of reliability. The reliability of judgement is, however, decreased by the higher-intensity presence lights also displayed by aircraft.

A recommendation for illumination of the Farnsworth-Munsell 100-hue test

The effect of illuminance on the performance of the Farnsworth-Munsell 100-hue (FM 100) test has previously been reported for young observers with normal color vision. However, information regarding these effects for older persons is lacking. This study reports the effect of illuminance level, over a wide range, on the FM100 performance of 10 elderly subjects with normal color vision compared to a control group of five young adult normal subjects. A recommendation is made for a standard level of illuminance for administration of the FM100-hue test.

Visual detection of commencement of aircraft takeoff runs

Among other things, airport control towers should be sited so that controllers can readily detect whether an aircraft cleared for takeoff has commenced its takeoff run. The detection of movement is not well enough understood to enable confident prediction that a particular site for a tower will enable commencement of takeoff run to be easily observed. A field study was undertaken to establish detection times for commencement of takeoff run by groups of trained and trainee air traffic controllers and untrained observers. It was found that the mean response of observers occurs when the aircraft is displaced about 5' of arc, a value essentially independent of observer experience, observation distance, aircraft velocity, and the clarity with which the aircraft can be seen. Binoculars reduce the mean response time and response variability, although not as much as might be expected. Domains within which control towers can be located to enable detection of takeoff runs within 2 s and 4 s are defined.

Specification fo road traffic signal light intensity

In a previous communication we reported data supporting the recommendation that a red road traffic signal should have an intensity of 200 cd for optimum recognition from 100 m when the signal is seen against a very bright sky (104cd/m2). This confirmed the earlier result of Boisson and Pagès. The present paper extends the data to include (a) the effect of signal size on optimum signal intensity for a practical range of angular diameters (4.1 to 16.5 min of arc), and (b) the effect of background luminance for a range of luminances of 1.5 ft-L to 2250 ft-L. The results show that optimum signal intensity is independent of signal size and that spatial summation by the visual system is complete. However the same data demonstrate a failure of spatial summation when a conventional threshold criterion (probability of seeing the signal 0.5) is used. It is shown that smaller signals will be more effective than larger ones of the same intensity if their intensity is less than optimum. Optimum signal intensity is shown to be a linear function of background luminances greater than 10 ft-L. A graph relating optimum signal intensity to signalling range for various background luminances summarises the experimental data.