A clinical molecular genetic service for United Kingdom families with choroideraemia

A diagnosis of choroideraemia (CHM) can be made clinically, based on the fundus examination and a family history consistent with X-linked inheritance. Molecular genetic testing offers a means of confirming the clinical diagnosis, establishing carrier status and allows presymptomatic diagnosis for families who wish to pursue these options. The aim of this study was to examine the uptake and assess the results from a diagnostic molecular genetics service for CHM.We have carried out a comprehensive audit of all molecular genetic results of UK NHS patients and families referred to the North West Regional Molecular Genetics Laboratory in Manchester, UK over a 55 month period.110 people were referred to this service for testing including diagnostic, carrier and predictive requests. Putative pathogenic mutations were identified in 65/83 (78%) of male index cases. The identification of a familial pathogenic change enabled carrier testing in 16 asymptomatic females and predictive testing in 3 males. Case examples illustrate the range of cases referred for testing and also reflect the need for genetic counselling that results from offering a molecular diagnostic service such as this.Clinical molecular testing for CHM is available clinically and can be used to support the clinical diagnosis and management of patients with choroideraemia as well as their families. Case studies demonstrate the need to provide genetic testing to families and the potential clinical utility of testing.     

A sensitive and specific diagnostic test for hearing loss using a microdroplet PCR‐based approach and next generation sequencing

Implementing DNA diagnostics in clinical practice for extremely heterogeneous diseases such as hearing loss is challenging, especially when attempting to reach high sensitivity and specificity in a cost‐effective fashion. Next generation sequencing has enabled the development of such a test, but the most commonly used genomic target enrichment methods such as hybridization‐based capture suffer from restrictions. In this study, we have adopted a new flexible approach using microdroplet PCR‐based technology for target enrichment, in combination with massive parallel sequencing to develop a DNA diagnostic test for autosomal recessive hereditary hearing loss. This approach enabled us to identify the genetic basis of hearing loss in 9 of 24 patients, a success rate of 37.5%. Our method also proved to have high sensitivity and specificity. Currently, routine molecular genetic diagnostic testing for deafness is in most cases only performed for the GJB2 gene and a positive result is typically only obtained in 10–20% of deaf children. Individuals with mutations in GJB2 had already been excluded in our selected set of 24 patients. Therefore, we anticipate that our deafness test may lead to a genetic diagnosis in roughly 50% of unscreened autosomal recessive deafness cases. We propose that this diagnostic testing approach represents a significant improvement in clinical practice as a standard diagnostic tool for children with hearing loss. © 2012 Wiley Periodicals, Inc.     

DIP–STR: Highly Sensitive Markers for the Analysis of Unbalanced Genomic Mixtures

Samples containing highly unbalanced DNA mixtures from two individuals commonly occur both in forensic mixed stains and in peripheral blood DNA microchimerism induced by pregnancy or following organ transplant. Because of PCR amplification bias, the genetic identification of a DNA that contributes trace amounts to a mixed sample represents a tremendous challenge. This means that standard genetic markers, namely microsatellites, also referred as short tandem repeats (STR), and single‐nucleotide polymorphism (SNP) have limited power in addressing common questions of forensic and medical genetics. To address this issue, we developed a molecular marker, named DIP–STR that relies on pairing deletion–insertion polymorphisms (DIP) with STR. This novel analytical approach allows for the unambiguous genotyping of a minor component in the presence of a major component, where DIP–STR genotypes of the minor were successfully procured at ratios up to 1:1,000. The compound nature of this marker generates a high level of polymorphism that is suitable for identity testing. Here, we demonstrate the power of the DIP–STR approach on an initial set of nine markers surveyed in a Swiss population. Finally, we discuss the limitations and potential applications of our new system including preliminary tests on clinical samples and estimates of their performance on simulated DNA mixtures.     

The detection of sensitivity of proprioception by a new clinical test: The dual joint position test

Objectives

To date, very few studies have paid attention to the joint sense (proprioception) of toes other than the big toe. We evaluated the sensitivity of joint position sense at the joint of the great toe in comparison to other digits, and with that determined by the dual digit stimulation test, in a sample of healthy normal controls and patients with clinical diagnosis of the lemniscal system dysfunction.

Material and methods

Seventy-two patients with lemniscal system dysfunction (55 clinically definitive multiple sclerosis, 17 vasculitis) and 110 healthy volunteers participated in the study. All subjects underwent the joint position sense test of all digits of upper and lower extremities. The position sense resulting from the combined operation of the joints of the second and the fourth digits (simultaneous two digits position sense) was also measured and subsequently compared with the results of the great toe position sense.

Results

Upper extremities: no difference was found in recognition of the position sense in the single digits of the upper extremities between patients and healthy volunteers. There was a significant difference in the dual joint position test of the right upper extremity between patients and the case group (p < 0.05) but not in the left upper extremity. Lower extremities: there was no significant difference in proprioception of the great toe neither in the right and nor in the left side between patients and normal subjects. However, the joint position sense of other single digits was deteriorated in the patients, a difference that was significant compared to normal controls (p < 0.05). Additionally, patients and normal controls displayed a difference in dual digit position sense of the right and left lower extremities (p < 0.05).

Conclusions

We show in this paper that the proprioception of simultaneous dual digits is diminished in patients when compared to a single digit position sense. Moreover, the great toe proprioception is less sensitive than other digits. Taken together, these observations lend evidence for a new clinical method which we named as dual joint position test. We suggest this novel method offers clinical utility to demonstrate lemniscal system dysfunction.     

Salivary infectious agents and periodontal disease status

Saygun I, Nizam N, Keskiner I, Bal V, Kubar A, Aç?kel C, Serdar M, Slots J. Salivary infectious agents and periodontal disease status. J Periodont Res 2011; 46: 235–239. © 2011 John Wiley & Sons A/S Background and Objectives: The potential of salivary microorganisms to diagnose periodontal disease and to guide periodontal treatment is a research topic of current interest. This study aimed to determine whether the salivary counts of periodontopathic microbes correlated with the periodontal pocket counts of the same infectious agents, and whether the salivary counts of the test infectious agents could distinguish among individuals with periodontal health and various types of periodontal disease. Material and Methods: The study included 150 systemically healthy adults, of whom 37 were periodontally healthy, 31 had gingivitis, 46 had chronic periodontitis and 36 had aggressive periodontitis. Each study subject contributed microbial samples from the two deepest periodontal pockets of the dentition and from whole saliva. Aggregatibacter actinomycetemcomitans, Campylobacter rectus, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia and Epstein–Barr virus were identified using the TaqMan real‐time PCR methodology. Statistical analysis was performed using the Mann–Whitney U‐test and the receiver operating characteristic statistics. Results: C. rectus, F. nucleatum, P. gingivalis, P. intermedia and T. forsythia occurred with significantly higher copy‐counts in salivary samples from patients with gingivitis, chronic periodontitis and aggressive periodontitis than from periodontally healthy individuals. A. actinomycetemcomitans only showed higher salivary copy‐counts in subjects with aggressive periodontitis compared with subjects with healthy periodontium, and the salivary copy‐counts of Epstein–Barr virus did not reveal any significant difference among the four subject groups studied. The diagnostic sensitivity for periodontitis was 89.19 for P. gingivalis and for T. forsythia and 86.49 for P. intermedia, with specificities ranging from 83.78 to 94.59. The optimal copy‐counts per mL saliva for identifying periodontitis were 40,000 for P. gingivalis, 700,000 for T. forsythia and 910,000 for P. intermedia. Conclusion: Salivary copy‐counts of P. gingivalis, T. forsythia and P. intermedia appear to have the potential to identify the presence of periodontitis, whereas the salivary level of the other test infectious agents may possess little or no diagnostic utility. Longitudinal studies are warranted to determine the ability of salivary copy‐counts of major periodontopathic bacteria to predict future periodontal breakdown.     

Oral rinse MMP‐8 point‐of‐care immuno test identifies patients with strong periodontal inflammatory burden

Oral Diseases (2010) 17 , 115–122 Objective: To determine whether oral rinse matrix metalloproteinase (MMP)‐8 levels, measured by three different methods, tissue inhibitor of matrix metalloprotease‐1 (TIMP‐1) levels and elastase activity differentiate subjects with different periodontal condition; and second, to find out if MMP‐8 levels were comparable among the methods used. Methods: MMP‐8 levels were analysed with an immunofluorometric method (IFMA), dentoELISA and commercial ELISA. Also TIMP‐1 levels and elastase activity were measured. For statistical analysis 214 study subjects were categorized into four groups, specified by the presence and number of moderate (4–5 mm) and deep (≥6 mm) periodontal pockets, and bleeding on probing percentage. Results: MMP‐8 levels especially measured by dentoELISA and adjusted to the number of teeth per subject differentiated the study group with strong periodontal inflammatory burden from groups with lower levels. This was also verified with receiver operating characteristic ( ROC) analysis. Elastase activity associated with higher IFMA and dentoELISA MMP‐8 levels. IFMA MMP‐8/TIMP and dentoELISA MMP‐8/TIMP‐1 tended to be higher with the increasing level of periodontal inflammatory burden. TIMP‐1 levels decreased with increasing age. Conclusions: Oral rinse MMP‐8 together with TIMP‐1 analysis may have potential in complementary periodontal diagnostics. dentoELISA can be applied in quantitative oral rinse chair side biomarker diagnostics.     

Use of high-sensitivity digital ELISA improves the diagnostic performance of circulating brain-specific proteins for detection of traumatic brain injury during triage

ABSTRACT

Background: Historically, limited sensitivity associated with traditional immunoassay methods has prevented the use of brain-specific proteins as blood biomarkers of traumatic brain injury (TBI) during triage, as these proteins exhibit low circulating concentrations. Digital ELISA is a newly-developed technique that is up to 1000 times more sensitive than conventional ELISA methods. The purpose of this study was to determine whether the use of digital ELISA over conventional ELISA improves the performance of brain-specific proteins as blood biomarkers of TBI during triage.

Methods: Blood was sampled from TBI patients (n = 13) at emergency department admission, as well as from neurologically normal controls (n = 72). Serum levels of two brain-specific proteins, neurofilament light chain (NfL) and Tau, were measured via digital ELISA. Estimated conventional ELISA measures were generated by adjusting values according to the lower limits of detection achievable with commercially available conventional ELISA assays, and receiver operating characteristic (ROC) analysis was used to compare the diagnostic performance of digital ELISA measures to estimated conventional ELISA measures in terms of their ability to discriminate between TBI patients and controls.

Results: Used in combination, digital ELISA measures of NfL and Tau could discriminate between groups with 100% sensitivity and 91.7% specificity. Estimated conventional ELISA measures could only discriminate between groups with 7.7% sensitivity and 94.4% specificity. This difference in diagnostic performance was statistically significant when comparing areas under ROC curves.

Conclusions: The use of digital ELISA over conventional ELISA methods improves the diagnostic performance of circulating brain-specific proteins for detection of TBI during triage.     

Application of salivary noncoding microRNAs for the diagnosis of oral cancers

Oral cancer is on the rise globally and survival rates, despite improvements in clinical care, have not significantly improved. Early detection followed by immediate intervention is key to improving patient outcomes. The use of biomarkers has changed the diagnostic landscape for many cancers. For oral cancers, visual inspection followed by a tissue biopsy is standard practice. The discovery of microRNAs as potential biomarkers has attracted clinical interest but several challenges remain. These microRNAs can be found in bodily fluids such as blood and saliva which have been investigated as potential sources of biomarker discovery. As oral cancer is localized within the oral cavity, saliva may contain clinically relevant molecular markers for disease detection. Our review provides an outline of the current advances for the application of salivary microRNAs in oral cancer. We also provide a technical guide for the processing of salivary RNAs to ensure accurate clinical measurement and validation.     

Potential Impact of Microarray Diagnosis of T Cell–Mediated Rejection in Kidney Transplants: The INTERCOM Study

We previously developed a microarray‐based test for T cell‐mediated rejection (TCMR) in a reference set of 403 biopsies. To determine the potential impact of this test in clinical practice, we undertook INTERCOM, a prospective international study of 300 indication biopsies from 264 patients ( ClinicalTrials.gov NCT01299168). Biopsies from six centers—Baltimore, Barcelona, Edmonton, Hannover, Manchester and Minneapolis—were analyzed by microarrays, assigning TCMR scores by an algorithm developed in the reference set and comparing TCMR scores to local histology assessment. The TCMR score correlated with histologic TCMR lesions—tubulitis and interstitial infiltration. The accuracy for primary histologic diagnoses (0.87) was similar to the reference set (0.89). The TCMR scores reclassified 77/300 biopsies (26%): 16 histologic TCMR were molecularly non‐TCMR; 15 histologic non‐TCMR were molecularly TCMR, including 6 with polyoma virus nephropathy; and all 46 “borderline” biopsies were reclassified as TCMR (8) or non‐TCMR (38). Like the reference set, discrepancies were primarily in situations where histology has known limitations, for example, in biopsies with scarring and inflammation/tubulitis potentially from other diseases. Neither the TCMR score nor histologic TCMR was associated with graft loss. Thus the molecular TCMR score has potential to add new insight, particularly in situations where histology is ambiguous or potentially misleading.