A novel next generation sequencing approach to improve sarcoma diagnosis

Sarcoma is a rare disease affecting both bone and connective tissue and with over 100 pathologic entities, differential diagnosis can be difficult. Complementing immune-histological diagnosis with current ancillary diagnostic techniques, including FISH and RT-PCR, can lead to inconclusive results in a significant number of cases. We describe here the design and validation of a novel sequencing tool to improve sarcoma diagnosis. A NGS DNA capture panel containing probes for 87 fusion genes and 7 genes with frequent copy number changes was designed and optimized. A cohort of 113 DNA samples extracted from soft-tissue and bone sarcoma FFPE material with clinical FISH and/or RT-PCR results positive for either a translocation or gene amplification was used for validation of the NGS method. Sarcoma-specific translocations or gene amplifications were confirmed in 110 out of 113 cases using FISH and/or RT-PCR as gold-standard. MDM2/CDK4 amplification and a total of 25 distinct fusion genes were identified in this cohort of patients using the NGS approach. Overall, the sensitivity of the NGS panel is 97% with a specificity of 100 and 0% failure rate. Targeted NGS appears to be a feasible and cost-effective approach to improve sarcoma subtype diagnosis with the ability to screen for a wide range of genetic aberrations in one test.

THU0008 DEVELOPMENT OF A NOVEL TRANSLATIONAL IN SILICO INDICATION DISCOVERY FRAMEWORK: EXEMPLIFIED BY THE CLINICAL COMPOUND CENERIMOD

Background:

To explore the full therapeutic spectrum of a drug it is crucial to consider its potential effectiveness in all diseases. Serendipitous clinical observations have often shown that approved drugs and those in development to be efficacious in indications different to those originally tested for. Traditional approaches to match a drug candidate with possible indications are mostly based on matching drug mechanistic knowledge with disease pathophysiology. Proof-of-concept trials or elaborate pre-clinical studies in animal models do not allow for a broad assessment due to high costs and slow progress. Gene expression changes in patients or animal models represent a good proxy to comprehensively assess both disease and drug effects. Furthermore, this data type can be integrated with a plethora of publicly available data.

Objectives:

Generation of a novel in silico framework to support the selection and expansion of potential indications which associate with a compound or approved drug. The framework was exemplified by the clinical compound cenerimod, a potent, selective, and orally active sphingosine-1-phosphate receptor 1 modulator (Piali et al., 2017).

Methods:

A total of ~13’000 public patient gene expression datasets from ~140 diseases were evaluated against cenerimod gene expression data generated in mouse disease models. To improve comparability of studies across platforms and species, computer algorithms (neural networks) were trained and employed to reduce noise within the data sets and improve signal. The predicted response to cenerimod for individual patients was contrasted against clinical patient characteristics.

Results:

The neural network algorithm efficiently reduced experimental noise and improved sensitivity in the gene expression data. The results predicted cenerimod to be efficacious in several auto-immune diseases foremost SLE. Additionally, focused analysis on individual patients rather than disease cohorts revealed potential determinants predictive of maximal clinical response, with the highest predicted clinical response for cenerimod in patients with severe inflammatory endotype and/or high SLE Disease Activity Index (SLEDAI).

Conclusion:

Combining preclinical compound data with the wealth of public disease gene expression data, provides great potential to support indication selection. The novel in silico framework identified SLE as a prime potential indication for cenerimod and supported the cenerimod phase 2b clinical trial in patients with SLE (CARE study,NCT03742037).

References:

[1]Piali, L., Birker-Robaczewska, M., Lescop, C., Froidevaux, S., Schmitz, N., Morrison, K., … Nayler, O. (2017). Cenerimod, a novel selective S1P1 receptor modulator with unique signaling properties. Pharmacology Research & Perspectives, 5(6), 1–12.https://doi.org/10.1002/prp2.370

Disclosure of Interests:

Dominik Hartl Shareholder of: Idorsia shares, Employee of: Idorsia employee, Marcel Keller Shareholder of: Idorsia options/shares, Employee of: Idorsia employee, Axel Klenk Shareholder of: Idorsia option/shares, Employee of: Idorsia employee, Mark Murphy Shareholder of: Idorsia shares and stock options, Employee of: Idorsia employee, Marianne Martinic Shareholder of: Idorsia options/shares, Employee of: Idorsia employee, Gabin Pierlot Shareholder of: Idorsia options/shares, Employee of: Idorsia employee, Peter Groenen Shareholder of: Idorsia options/shares, Employee of: Idorsia employee, Daniel Strasser Shareholder of: Idorsia options/shares, Employee of: Idorsia employee

Disease-biased and shared characteristics of the immunoglobulin gene repertoires in marginal zone B cell lymphoproliferations

The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Clinical impact of recurrently mutated genes on lymphoma diagnostics: state-of-the-art and beyond

Similar to the inherent clinical heterogeneity of most, if not all, lymphoma entities, the genetic landscape of these tumors is markedly complex in the majority of cases, with a rapidly growing list of recurrently mutated genes discovered in recent years by next-generation sequencing technology. Whilst a few genes have been implied to have diagnostic, prognostic and even predictive impact, most gene mutations still require rigorous validation in larger, preferably prospective patient series, to scrutinize their potential role in lymphoma diagnostics and patient management. In selected entities, a predominantly mutated gene is identified in almost all cases (e.g. Waldenström's macroglobulinemia/lymphoplasmacytic lymphoma and hairy-cell leukemia), while for the vast majority of lymphomas a quite diverse mutation pattern is observed, with a limited number of frequently mutated genes followed by a seemingly endless tail of genes with mutations at a low frequency. Herein, the European Expert Group on NGS-based Diagnostics in Lymphomas (EGNL) summarizes the current status of this ever-evolving field, and, based on the present evidence level, segregates mutations into the following categories: i) immediate impact on treatment decisions, ii) diagnostic impact, iii) prognostic impact, iv) potential clinical impact in the near future, or v) should only be considered for research purposes. In the coming years, coordinated efforts aiming to apply targeted next-generation sequencing in large patient series will be needed in order to elucidate if a particular gene mutation will have an immediate impact on the lymphoma classification, and ultimately aid clinical decision making.

Molecular evidence for antigen drive in the natural history of mantle cell lymphoma

To further our understanding about antigen involvement in mantle cell lymphoma (MCL), we analyzed the expression levels of activation-induced cytidine deaminase (AID), a key player in B-cell responses to antigen triggering, in 133 MCL cases; assessed the functionality of AID by evaluating in vivo class switch recombination in 52 MCL cases; and sought for indications of ongoing antigen interactions by exploring intraclonal diversification within 14 MCL cases. The AID full-length transcript and the most frequent splice variants (AID-ΔE4a, AID-ΔE) were detected in 128 (96.2%), 96 (72.2%), and 130 cases (97.7%), respectively. Higher AID full-length transcript levels were significantly associated (P < 0.001) with lack of somatic hypermutation within the clonotypic immunoglobulin heavy variable (IGHV) genes. Median AID transcript levels were higher in lymph node material compared to cases in which peripheral blood was analyzed, implying that clonal behavior is influenced by the microenvironment. Switched tumor-derived IGHV-IGHD-IGHJ transcripts were identified in 5 of 52 cases (9.6%), all of which displayed somatic hypermutation and AID-mRNA expression. Finally, although most cases exhibited low levels of intraclonal diversification, analysis of the mutational activity revealed a precise targeting of somatic hypermutation indicative of an active, ongoing interaction with antigen(s). Collectively, these findings strongly allude to antigen involvement in the natural history of MCL, further challenging the notion of antigen naivety.

Guidance for laboratories performing molecular pathology for cancer patients

Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.

Bigenic heterozygosity and the development of steroid-resistant focal segmental glomerulosclerosis

BACKGROUND

Focal segmental glomerulosclerosis (FSGS) is a major cause of steroid-resistant nephrotic syndrome in childhood with a central role for the podocytes in the pathogenesis. Mutated proteins expressed in podocytes cause proteinuria. The role of combined gene defects in the development of FSGS is less clear.

METHODS

We analysed seven podocyte genes known to cause proteinuria and FSGS in a group of 19 non-familial childhood-onset steroid-resistant FSGS patients. These genes include NPHS1, NPHS2, ACTN4, CD2AP, WT-1, TRPC6 and PLCE1. We also screened for the mitochondrial A3243G DNA transition associated with the MELAS syndrome (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes), and occasionally FSGS.

RESULTS

No mutations were found in the ACTN4 and TRPC6 genes, and no mitochondrial A3243G DNA transition was found in our group of patients. Two patients showed mutations in the CD2AP gene, one combined with an NPHS2 mutation. A tri-allelic hit was found in a patient carrying compound heterozygous NPHS2 mutations and a heterozygous NPHS1 mutation. In another patient a de novo WT-1 mutation was found combined with a heterozygous NPHS1 mutation, and finally two patients showed three heterozygous PLCE1 mutations.

CONCLUSIONS

In our rather small group of 19 steroid-resistant FSGS patients, we found 11 mutations in podocyte genes in 6 patients. In four of them the found mutations could explain the pathology. Our data suggest that combined gene defects in podocyte genes may play a role in the development of FSGS.

Promoter methylation of PARG1, a novel candidate tumor suppressor gene in mantle-cell lymphomas

BACKGROUND AND OBJECTIVES

Mantle cell lymphoma (MCL), a mature B-cell neoplasm, is genetically characterized by the translocation t(11;14)(q13;q32). However, secondary alterations are required for malignant transformation. The identification of inactivated tumor suppressor genes contributing to the development of MCL may lead to further elucidation of the biology of this disease and help to identify novel targets for therapy.

DESIGN AND METHODS

Whole genome microarray-based gene expression profiling on treated versus untreated MCL cell lines was used to identify genes induced by 5-aza-2'-deoxycytidine. The degree of promoter methylation and transcriptional silencing of selected genes was then proven in MCL cell lines and primary cases by methylation-specific polymerase chain reaction (PCR) techniques, real-time PCR and gene expression profiling.

RESULTS

After 5-aza-2'-deoxycytidine treatment, we identified more than 1000 upregulated genes, 16 of which were upregulated > or =3-fold. Most of them were not known to be silenced by methylation in MCL. A low expression of ING1, RUNX3 and BNIP3L was observed in three of the five the MCL cell lines. In addition, the expression of PARG1, which is located in the frequently deleted region 1p22.1, was substantially reduced and displayed at least partial promoter methylation in all investigated MCL cell lines as well as in 31 primary MCL cases.

INTERPRETATION AND CONCLUSIONS

In summary, we identified interesting novel candidate genes that probably contribute to the progression of MCL and suggest that PARG1 is a strong candidate tumor suppressor gene in MCL.

Steroid and G protein binding characteristics of the seatrout and human progestin membrane receptor alpha subtypes and their evolutionary origins

A novel progestin receptor (mPR) with seven-transmembrane domains was recently discovered in spotted seatrout and homologous genes were identified in other vertebrates. We show that cDNAs for the mPR alpha subtypes from spotted seatrout (st-mPRalpha) and humans (hu-mPRalpha) encode progestin receptors that display many functional characteristics of G protein-coupled receptors. Flow cytometry and immunocytochemical staining of whole MDA-MB-231 cells stably transfected with the mPRalphas using antibodies directed against their N-terminal regions show the receptors are localized on the plasma membrane and suggest the N-terminal domain is extracellular. Both recombinant st-mPRalpha and hu-mPRalpha display high affinity (Kd 4.2-7.8 nm), limited capacity (Bmax 0.03-0.32 nm), and displaceable membrane binding specific for progestins. Progestins activate a pertussis toxin-sensitive inhibitory G protein (G(i)) to down-regulate membrane-bound adenylyl cyclase activity in both st-mPRalpha- and hu-mPRalpha-transfected cells. Coimmunoprecipitation experiments demonstrate the receptors are directly coupled to the G(i) protein. Similar to G protein-coupled receptors, dissociation of the receptor/G protein complex results in a decrease in ligand binding to the mPRalphas and mutation of the C-terminal, and third intracellular loop of st-mPRalpha causes loss of ligand-dependent G protein activation. Phylogenetic analysis indicates the mPRs are members of a progesterone and adipoQ receptor (PAQR) subfamily that is only present in chordates, whereas other PAQRs also occur in invertebrates and plants. Progesterone and adipoQ receptors are related to the hemolysin3 family and have origins in the Eubacteria. Thus, mPRs arose from Eubacteria independently from members of the GPCR superfamily, which arose from Archeabacteria, suggesting convergent evolution of seven-transmembrane hormone receptors coupled to G proteins.

Quantitative microsatellite analysis to delineate the commonly deleted region 1p22.3 in mantle cell lymphomas

The molecular pathogenesis of mantle cell lymphomas (MCL), a subset of B-cell non-Hodgkin's lymphomas with a poor prognosis, is still poorly understood. In addition to the characteristic primary genetic alteration t(11;14)(q13;q32), several further genetic changes are present in most cases. One of the most frequent genomic imbalances is the deletion of 1p22.1-p31.1 observed in nearly one-third of MCL cases. This might indicate the presence of tumor suppressor gene(s) in this critical region of deletion. Quantitative microsatellite analysis (QuMA) is a real-time PCR-based method to detect DNA copy number changes. Since QuMA has the resolving power to detect subtle genomic alterations, including homozygous deletions, this may help to identify candidate tumor suppressor genes from deleted regions. To gain more insight into the molecular pathogenesis of MCL, QuMA was performed on genomic DNA from 57 MCL cases. Eight microsatellite loci mapping to the chromosomal region 1p22.3 were analyzed. Losses were observed in 51 of the 57 ( approximately 89.5%) samples. Two cases showed a homozygous deletion at the locus containing the gene SH3GLB1, which plays a key role in Bax-mediated apoptosis. Two hotspots with copy number losses were detected at chromosomal localizations 85.4 and 86.6 Mb encompassing BCL10 and CLCA2. Both the genes seem to be attractive candidates to study tumor suppressor function in MCL.

Lack of Bcl-2 expression in follicular lymphoma may be caused by mutations in the BCL2 gene or by absence of the t(14;18) translocation

Follicular lymphoma (FL), except grade 3B, is characterized by the chromosomal translocation t(14;18)(q32;q21), which results in over-expression of the Bcl-2 protein. Ten per-cent of all FLs, however, do not show Bcl-2 protein expression with standard immunohistochemistry using a monoclonal Bcl-2 antibody against residues 41-54 of the Bcl-2 protein. In this study, the biological background of 18 Bcl-2-negative FL cases grade I, II, or IIIa was investigated by immunohistochemical staining and western blot analysis with alternative antibodies. Bcl-2 protein was demonstrated in five of the 18 cases and all of these carried the t(14;18) translocation. Of the 13 cases that were Bcl-2 negative with alternative antibodies, 12 lacked the t(14;18) translocation. PCR and subsequent sequence analysis of cDNA demonstrated that three cases with a t(14;18) contained somatic mutations in the translocated BCL2 gene, resulting in amino acid replacements in the region of the epitope recognized by the antibody. In conclusion, the majority of Bcl-2-negative FL lack a t(14;18) but a significant subset of these tumours are false negative due to mutations in the BCL2 gene. These findings may have consequences for the use of Bcl-2 immunohistochemistry for diagnostic purposes.

Recurrent involvement of chromosomal region 6q21 in heterotaxy

We present a patient with heterotaxy and a de novo, apparently balanced reciprocal translocation with breakpoints at 6q21 and 20p13. Another patient with heterotaxy was previously reported with a de novo balanced translocation involving chromosome band 6q21. The breakpoints in both patients on 6q21 were found to be located in the same chromosomal region spanning maximally 2 Mb. We speculate that the two breakpoints lead to the disruption of the function of a single gene, either directly or through long distance effects. Alternatively, the present observation suggests additional heterogeneity in heterotaxy in humans.

Comparative study of ASCA (Anti-Saccharomyces cerevisiae antibody) assays in inflammatory bowel disease

BACKGROUND & AIMS

Anti-Saccharomyces cerevisiae antibody (ASCA) is a serologic marker associated with Crohn's disease (CD). Although there is still discussion on its clinical value, several companies each promote their own ASCA assay to be used in the gastroenterologist's practice at considerable expense. The aim of this study was to determine whether different ASCA assays agree sufficiently well for the results to be used interchangeably.

METHODS

Blood obtained from a large cohort of IBD patients with inflammatory bowel disease (IBD; 100 with CD, 100 with ulcerative colitis [UC]) and 178 controls (100 healthy blood donors and 78 patients with non-IBD diarrheal illnesses) was studied with 4 different ASCA assays. Sensitivity, specificity, and positive predictive value were compared. Agreement between assays was evaluated.

RESULTS

Sensitivity of ASCA for CD ranged between 41% and 76%. Sensitivity was inversely related to specificity and positive predictive value. Results correlated well overall (range = 0.54-0.90) and the different ROC curves showed good agreement. When recalculated cutoff points were used, interchangeability increased. However, large differences were seen when absolute values were compared.

CONCLUSIONS

A large range in sensitivities and specificities of ASCA for CD is seen with different ASCA assays, mainly as a consequence of the cutoff value chosen for each individual assay. Although agreement between and within assays is good, caution is important when absolute values are used. Standardization of ASCA measurements is greatly needed.

NIPP1-mediated interaction of protein phosphatase-1 with CDC5L, a regulator of pre-mRNA splicing and mitotic entry

NIPP1 is a regulatory subunit of a species of protein phosphatase-1 (PP1) that co-localizes with splicing factors in nuclear speckles. We report that the N-terminal third of NIPP1 largely consists of a Forkhead-associated (FHA) protein interaction domain, a known phosphopeptide interaction module. A yeast two-hybrid screening revealed an interaction between this domain and a human homolog (CDC5L) of the fission yeast protein cdc5, which is required for G(2)/M progression and pre-mRNA splicing. CDC5L and NIPP1 co-localized in nuclear speckles in COS-1 cells. Furthermore, an interaction between CDC5L, NIPP1, and PP1 in rat liver nuclear extracts could be demonstrated by co-immunoprecipitation and/or co-purification experiments. The binding of the FHA domain of NIPP1 to CDC5L was dependent on the phosphorylation of CDC5L, e.g. by cyclin E-Cdk2. When expressed in COS-1 or HeLa cells, the FHA domain of NIPP1 did not affect the number of cells in the G(2)/M transition. However, the FHA domain blocked beta-globin pre-mRNA splicing in nuclear extracts. A mutation in the FHA domain that abolished its interaction with CDC5L also canceled its anti-splicing effects. We suggest that NIPP1 either targets CDC5L or an associated protein for dephosphorylation by PP1 or serves as an anchor for both PP1 and CDC5L.

GATA3 haplo-insufficiency causes human HDR syndrome

Terminal deletions of chromosome 10p result in a DiGeorge-like phenotype that includes hypoparathyroidism, heart defects, immune deficiency, deafness and renal malformations. Studies in patients with 10p deletions have defined two non-overlapping regions that contribute to this complex phenotype. These are the DiGeorge critical region II (refs 1, 2), which is located on 10p13-14, and the region for the hypoparathyroidism, sensorineural deafness, renal anomaly (HDR) syndrome (Mendelian Inheritance in Man number 146255), which is located more telomeric (10p14-10pter). We have performed deletion-mapping studies in two HDR patients, and here we define a critical 200-kilobase region which contains the GATA3 gene. This gene belongs to a family of zinc-finger transcription factors that are involved in vertebrate embryonic development. Investigation for GATA3 mutations in three other HDR probands identified one nonsense mutation and two intragenic deletions that predicted a loss of function, as confirmed by absence of DNA binding by the mutant GATA3 protein. These results show that GATA3 is essential in the embryonic development of the parathyroids, auditory system and kidneys, and indicate that other GATA family members may be involved in the aetiology of human malformations.

The phenotypic spectrum of the 10p deletion syndrome versus the classical DiGeorge syndrome

We reviewed 36 patients with a deletion of the short arm of chromosome 10 and a partial DiGeorge syndrome. We compared the phenotypes observed in these del(10p) patients with the classical DiGeorge phenotype associated with del(22q11), pointing out both similarities and differences. Some features, such as sensorineural hearing loss, seem to be highly associated with a deletion of 10p but are absent in the classical DiGeorge spectrum caused by del(22q11).

Partial DiGeorge syndrome in two patients with a 10p rearrangement

We describe 2 patients with a partial DiGeorge syndrome (facial dysmorphism, hypoparathyroidism, renal agenesis, mental retardation) and a rearrangement of chromosome 10p. The first patient carries a complex chromosomal rearrangement, with a reciprocal insertional translocation between the short arm of chromosome 10 and the long arm of chromosome 8, with karyotype 46, XY ins(8;10) (8pter 8q13::10p15-->10p14::8q24.1-->8qter) ins(10:8) (10pter--> 10p15::8q24.1-->8q13::10p14-->10qter). The karyotype of the second patient shows a terminal deletion of the short arm of chromosome 10. In both patients, the breakpoints on chromosome 10p reside outside the previously determined DiGeorge critical region II (DGCRII). This is in agreement with previous reports of patients with a terminal deletion of 10p with breakpoints distal to the DGCRII and renal malformations/hypoparathyroidism, and thus adds to evidence that these features may be caused by haploinsufficiency of one or more genes distal to the DGCRII.

Expanding complexity in myotonic dystrophy

Myotonic dystrophy (DM) is a highly variable multisystemic disease belonging to the rather special class of trinucleotide expansion disorders. DM results from dynamic expansion of a perfect (CTG)n repeat situated in a gene-dense region on chromosome 19q. Based on findings in patient materials or cellular and animal models, many mechanisms for the causes and consequences of repeat expansion have been proposed; however, none of them has enjoyed prolonged support. There is now circumstantial evidence that long (CTG)n repeats may affect the expression of any of at least three genes, myotonic dystrophy protein kinase (DMPK), DMR-N9 (gene 59), and a DM-associated homeodomain protein (DMAHP). Furthermore, the new findings suggest that DM is not a simple gene-dosage or gain-or-loss-of-function disorder but that entirely new pathological pathways at the DNA, RNA, or protein level may play a role in its manifestation.

Can event-related potentials be evoked by extra-cochlear stimulation and used for selection purposes in cochlear implantation?

To investigate whether electrically evoked event-related responses (P300) could be elicited by extra-cochlear stimulation, measurements were performed on a group of adults fitted with the single-channel extra-cochlear implant. To optimize measurement conditions, and because of the low number of subjects still using an extra-cochlear device in our cochlear implant programme, measurements were also performed on a group of experienced users fitted with the intra-cochlear Nucleus multichannel device. For reference purposes, subjects with normal hearing (control group) were also included in the study. Reproducible late latency responses (N1 and P2 peaks) were found in the five extra-cochlear implant users, while P300s were present in four out of these five subjects. The latencies were longer than those of the control group, but were similar to those obtained in the intra-cochlear implant group. Significant correlations were found for most N1, P2 and P300 measurements evoked by the tonal stimuli and by speech stimuli. The P300 amplitudes, evoked by either tonal or speech stimuli, appeared to be related to speech perception ability. This led to the conclusion that N1, P2 and P300 measurements may have potential as a clinical tool for preoperative prediction and postoperative evaluation of sound processing on a cortical level.

Vesico-ureteral reflux: a genetic condition?

Vesico-ureteral reflux (VUR) is a frequent condition, but in most instances, the precise cause is unknown. We here review the evidence of a genetic aetiology of VUR, inherited as an autosomal dominant trait, with variable expression. We discuss the possible pathogenetic relationship between VUR and other types of uropathies and possible strategies towards the identification of genes underlying VUR are presented. The isolation of the gene(s) responsible for uropathies will not only lead to a better insight into the embryology of the urological system, the pathogenesis of uropathies, but also to a renewed interest from clinicians in congenital uropathies.

Formant transition duration and place perception in misarticulating children and adolescents

The explanation of articulatory problems as an output speech disorder does not preclude the possibility that auditory processing problems are associated. Identification of brief auditory spectral cues in a place-of-articulation continuum was studied in children with articulation problems. First, it was shown that formant transition durations smaller than 20·0 ms dramatically decreased phonemic identification rates for alveolar stop consonants in control subjects. Identification tasks based on two place-of-articulation continua /pαk/-/tαk/ with F2/F3 transition durations of 52 and 20 ms were administered to groups of misarticulating children and adolescents and two control groups (children and adults). For all subject groups there was poorer phonetic processing with shorter transition durations of F2 and F3. The misarticulating subjects demonstrated poorer phonetic processing of formant transitions than did the control subjects. Shortening F2/F3 transition duration did not differentially influence perceptual behaviour between the experimental and the control groups. In determining the causal link between perception and production, an explanation of perception preceding production was favoured. It was argued that, in addition to assessing the specificity between perception and production mechanisms, assessment of perception of formant transitions may have potential as a clinical tool for evaluating phonetic processing.

Electrically evoked auditory middle latency responses versus perception abilities in cochlear implant users

Electrical auditory middle latency responses (EAMLRs) were recorded in a group of 12 postlingually and 4 congenitally deaf cochlear implant users. The EAMLRs of the postlingually deaf cochlear implant users were compared to behavioral measures of speech perception. All the cochlear implant users showed pronounced EAMLR morphology and amplitude. EAMLRs of congenitally deaf cochlear implant users were remarkably similar to those of postlingually deaf cochlear implant users. The difference in speech perception ability between congenitally deaf and postlingually deaf cochlear implant users did not seem to be caused by integrity differences of the neural generators of the auditory middle latency response. For the postlingually deaf subjects, EAMLR amplitude variation and interlatency variation seemed to be related to specific aspects of speech perception. The poorer performers demonstrated more diversity in the amplitude of the EAMLR component peaks and a more diffuse EAMLR peak latency organization across the electrodes than the better performers.

The specific relation between perception and production errors for place of articulation in developmental apraxia of speech

Developmental apraxia of speech is a disorder of phonological and articulatory output processes. However, it has been suggested that perceptual deficits may contribute to the disorder. Identification and discrimination tasks offer a fine-grained assessment of central auditory and phonetic functions. Seventeen children with developmental apraxia (mean age 8:9, years:months) and 16 control children (mean age 8:0) were administered tests of identification and discrimination of resynthesized and synthesized monosyllabic words differing in place-of-articulation of the initial voiced stop consonants. The resynthetic and synthetic words differed in the intensity of the third formant, a variable potentially enlarging their clinical value. The results of the identification task showed equal slopes for both subject groups, which indicates no phonetic processing deficit in developmental apraxia of speech. The hypothesized effect of the manipulation of the intensity of the third formant of the stimuli was not substantiated. However, the children with apraxia demonstrated poorer discrimination than the control children, which suggests affected auditory processing. Furthermore, analyses of discrimination performance and articulation data per apraxic subject demonstrated a specific relation between the degree to which auditory processing is affected and the frequency of place-of-articulation substitutions in production. This indicates the interdependence of perception and production. The results also suggest that the use of perceptual tasks has significant clinical value.

On the clinical relevance of mismatch negativity: results from subjects with normal hearing and cochlear implant users

Mismatch negativity (MMN) provides an objective measure for evaluating subjects with problems related to speech processing. For a valid neurophysiological profile of speech-processing mechanisms, an efficient procedure to elicit MMNs is needed. In Experiment 1 of this study, MMN recordings were conducted in adults with normal hearing on the effects of decreasing the duration of the interstimulus interval (ISI). Shortening ISI duration does not seem to have a high impact on the individual MMN quality, whereas it does influence group MMN quality. In Experiment 2, MMNs were elicited in a group of cochlear implant users by using a speech sound contrast/ba/-/da/. A group of good performers produced a significant MMN, whereas a group of moderate performers did not. There seems to be a relation between speech perception ability and MMN quality. To fundamentally understand the effects of electrical stimulation of the inner ear and to clinically adjust rehabilitation, diverse data are needed on different aspects of auditory processing. Optimizing the procedure to elicit and MMN is therefore of great clinical value.

Perception of voicing cues by children with early otitis media with and without language impairment

Research on the relationship between early otitis media with effusion (OME), language impairment, and central auditory processing has been equivocal. Identification and discrimination tasks provide us with a sensitive method of assessing speech perception on both an auditory and a phonetic level. The present study examined identification and discrimination of initial bilabial stop consonants differing in voicing by 9-year-old children with a history of severe OME. The groups studied were controlled for language impairment. The ability of these children to perceive major and minor voicing cues was examined using multiple voicing cues. Long-term effects of OME were found for both identification and discrimination performance. Children with OME produced an overall inconsistency in categorization, which suggests poorer phonetic processing. Discrimination was measured by means of "just noticeable differences" (JND). Children with early OME experience demonstrated a greater mean JND than children without early OME experience. Finally, in cases of language impairment with early OME, there was no additional deterioration of auditory or phonetic processing. It appears that either early OME or language impairment can lead to poorer perception.