Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort

PURPOSE

Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively.

METHODS

ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID.

RESULTS

The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis.

CONCLUSION

Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.

The clinical significance of oropharyngeal cultures in young children with cystic fibrosis

In children with cystic fibrosis (CF) the associations between oropharyngeal swabs (OPSs) for detection of Pseudomonas and lung disease have not been evaluated.OPS and bronchoalveolar lavage (BAL) samples were obtained annually in children with CF from 2005 to 2017. OPS test characteristics were calculated using BAL as "gold standard". Results were related to lung inflammation (BAL neutrophil elastase and interleukin-8), structural lung disease (chest computed tomography PRAGMA-CF (Perth-Rotterdam Annotated Grid Morphometric Analysis for CF) scores), respiratory exacerbations and future detection of Pseudomonas on BAL.From 181 patients, 690 paired OPS-BAL cultures were obtained. Prevalence of Pseudomonas in BAL was 7.4%. OPS sensitivity was 23.0% and specificity was 91.4%, reducing the post-test probability for a positive BAL following a negative OPS to 6.3%. Pseudomonas on OPS was not associated with lung inflammation or respiratory exacerbations, but was weakly associated with current PRAGMA-CF %Disease score (p=0.043). Pseudomonas on BAL was associated with positive neutrophil elastase (OR 4.17, 95% CI 2.04-8.53; p<0.001), increased interleukin-8 (p<0.001), increased all baseline PRAGMA computed tomography scores (p<0.001), progression of PRAGMA computed tomography scores (p<0.05) and increased risk of respiratory exacerbations (incidence rate ratio 2.11, 95% CI 1.15-3.87; p=0.017).In children with CF OPSs only marginally change the probability of detecting lower airway Pseudomonas and are not associated with lung disease indices nor exacerbations risk.

Increased lipid oxidation heralds diabetes onset in DR.lyp/lyp rats

AIM

The BB rat model of type 1 diabetes exhibits altered body weight gain and body temperature regulation prior to hyperglycemia onset, implying the existence of as yet unidentified biomarkers of autoimmune processes that destroy pancreatic beta cells. To investigate this hypothesis, we compared the metabolic profile of diabetes-resistant DR.lyp/+ rats and their diabetes-prone, congenic DR.lyp/lyp littermates in the days leading up to diabetes onset.

METHODS

Except for the Gimap5 mutation on chromosome 4, congenic DR.lyp/lyp rats are genetically identical to DR.lyp/+ littermates. They invariably develop hyperglycemia at 46-81 days of age, whereas DR.lyp/+ rats do not develop diabetes. In addition to daily food intake and body weight, indirect calorimetry was performed continuously on male DR.lyp/lyp and DR.lyp/+ rats (n=6/group) for 6-18 days to measure locomotor activity, VO (2), VCO (2) and RQ.

RESULTS

DR.lyp/lyp rats exhibited a progressive decrease of RQ compared to DR.lyp/+ rats 0.005+/-0.001 units/day (p<0.005). Limiting the analysis to the six days prior to diabetes onset revealed a larger decrease of 0.007+/-0.002 units/day (p<0.001) in DR.lyp/lyp animals, whereas RQ of the DR.lyp/+ rats remained unchanged. This metabolic change occurred prior to hyperglycemia onset and was not associated with changes of any other parameter.

CONCLUSIONS

Diabetes onset in DR.lyp/lyp rats is heralded by a progressive shift towards lipid oxidation relative to carbohydrate metabolism.

Operator dependent variability in quantitative analysis of myocardial perfusion images

The purpose of this study was to evaluate variability in the quantification of myocardial perfusion images obtained by a group of experienced operators using two widely used programs. The Cedars Emory quantitative analysis program (CEqual) was used to quantify the size of perfusion defects and the Cedars-Sinai quantitative gated single-photon emission tomography program was used to quantify left ventricular function. Five patients with reversible apical defects, five with fixed apical defects and three patients with normal perfusion were selected. Eight experienced medical laboratory technologists processed the studies from raw projection data. The manual steps consisted of defining two alignment axes parallel to the long axis of the left ventricle, and for the CEqual program selecting apex and base in the short axis slices in the rest and stress studies. Wide variability between the operators in the quantification of reversibility could be seen in all three vascular territories. A range >10% was found in at least one vascular territory for nine of the 13 patients. The differences in left ventricular ejection fraction (LVEF) between operators were <5% for all 13 patients. The large variability in the quantification of reversible apical perfusion defects may influence the clinical interpretation and cause false conclusions. In contrast, inter-operator variability for the quantification of the LVEF was low.

Simple bone cyst: a discrepancy between magnetic resonance imaging and surgical observations

OBJECTIVE

The purpose of this study was to compare magnetic resonance (MR) imaging and surgical observations of fluid in simple bone cysts.

STUDY DESIGN

Findings during MR imaging of 7 simple bone cysts were compared with surgical observations 1 day or 1.8 months (mean) after MR imaging.

RESULTS

All MR images showed cavities filled with fluid. In 2 patients operated on the day after the imaging, surgical observations were in accordance with the MR findings. At surgery 1.8 months after the MR examination, 4 cavities were found to be empty and 1 cavity contained only a minor amount of fluid.

CONCLUSION

A discrepancy between MR imaging and surgical observations of fluid in simple bone cyst cavities was observed that might be dependent on the time between the observations, indicating that a fairly rapid absorption of fluid might occur or that the amount of fluid in a simple bone cyst can vary for unknown reasons.

An evaluation of image quality for the assessment of the marginal bone level in panoramic radiography. A comparison of radiographs from different dental clinics

The diagnostic image quality of panoramic radiographs originating from different clinics was examined. Two samples of 98 and 100 radiographs, respectively, were from a department of oral radiology. The radiographs of one of these samples were checked using immediate subjective analysis of the image quality before inclusion in the study whereas the radiographs of the other sample were randomly selected. A third sample consisted of radiographs from 20 randomly selected dental clinics. The subjective overall image quality of the whole panoramic radiograph was classified as adequate, marginal or inadequate. The three observers also assessed the reason for inferior image quality. The overall image quality of the radiographs was better for the checked sample from the department of oral radiology compared to the sample form the 20 dental clinics. The main reason for unacceptable image quality of the radiographs was too low density and/or contrast irrespective of sample. Other faults were incorrect positioning of the patient but in the sample from the 20 clinics improper film handling was also frequent. We conclude that image quality in panoramic radiography can be improved. Improvement of the image quality is a prerequisite if panoramic radiography in the future is to replace the full-mouth examination.

Comparison of panoramic and intraoral radiography and pocket probing for the measurement of the marginal bone level

Panoramic, bitewing and periapical radiography and probing for measurement of the marginal bone level were compared. Altogether 237 sites of 23 patients were examined. Radiographs were taken with a splint containing steel balls to allow calculation of the enlargement of the radiographs. Probing was done before and during flap surgery using the same splint. The open bone measurement represented the true value. All radiographs were assessed by 5 observers. The mean enlargement of panoramic radiography was 27% in the upper and 26% in the lower arch. For bitewing and periapical radiography, it was 8% in the upper and 4-5% in the lower arch. All methods underestimated the bone loss. Probing bone level before surgery was most accurate, deviating at most 5% from the true value. Periapical radiography was more accurate than panoramic and bitewing radiography (p less than 0.001). Panoramic radiography presented a slightly lower mean accuracy than bitewing radiography (p less than 0.05). The underestimation of the bone loss ranged from 13 to 32% in orthopantomograms, 11-23% in bitewing and 9-20% in periapical radiographs. The interobserver variation of the radiographic methods was substantial.

Measurements of tooth length in panoramic radiographs. 1. The use of indicators

The aim of this study was to investigate both the actual and the radiographic tooth lengths of the maxillary first molar and second premolar and the mandibular premolars in panoramic radiographs. The actual length of 64 extracted teeth was measured. Steel balls were then attached to the cusp and apex and the teeth embedded in plastic moulds. Each pair of plaster casts with their set of teeth was radiographed with an Orthopantomograph twice at an interval of 1 month. The actual and the radiographic tooth length was measured twice by one observer. The mean tooth length of the molar was shorter than that of the premolars. The mean difference between the repeated measurements of the actual tooth length was small and ranged between 0.47 and 1.16% of the tooth length. The mean difference between repeated measurements of the radiographic tooth length was also small, with a method error of 0.13-0.21 mm. The vertical magnification in panoramic radiography was lower for mandibular premolars (13-15%) than for the maxillary second premolar and first molar (17-28%). The palatal root of the maxillary first molar had the highest vertical magnification (28%). Following the second set of radiographs, the mean difference between the measurements was small, except for the palatal root of the maxillary first molar (P < 0.001). Radiographic measurements of this root should therefore be used with caution. The results for the other roots examined indicate that these could be measured with high reproducibility.

Comparison between panoramic and posterior bitewing radiography in the diagnosis of periodontal bone loss

A study is reported comparing the diagnostic yield of panoramic and posterior bitewing radiographs when used to image periodontal bone disease. It is concluded that there is a high concordance between the findings from the two types of radiographs but that the concordance varies with the degree of bone loss and tooth type. Consequently when panoramic radiography is used in clinical practice, the examination should be supplemented by intraoral radiographs in regions when image quality is poor in the panoramic image and where there are structures of special interest.

Marginal bone in periodontal disease: an evaluation of image quality in panoramic and intra-oral radiography

Five observers assessed the panoramic and full-mouth (14 periapical and four posterior bitewing) radiographs of 20 patients each for the ability to interpret and measure the marginal bone level. The image quality of each site was classified as excellent, acceptable or unacceptable. Depiction errors affecting interpretability and measurability were also noted. In the upper arch, the frequency of uninterpretable and non-measurable sites was almost equal for panoramic and periapical radiography. Image quality was better with periapical radiography in the lower arch. In the posterior regions of both arches, more sites could not be measured from panoramic compared with bitewing radiographs. Due to overlapping the distal surface of the maxillary canine and the mesial surface of the first maxillary premolar could often not be interpreted in either panoramic or periapical radiographs, but infrequently in the bitewings. In the lower arch, the most frequent depiction error was inadequate density in the incisor region of panoramic radiographs. On the basis of these results, we proposed that in clinical practice the panoramic radiograph can be supplemented with individually selected periapicals. In epidemiological studies, the panoramic radiograph should be combined with a premolar bitewing radiograph.

Comparison between panoramic and periapical radiography in the diagnosis of periodontal bone loss

Panoramic and periapical radiography was performed on 100 patients. Five observers each registered the scores for marginal bone level, presence of bone defects and furcation involvement in the radiographs of 20 patients and the results were compared. The overall concordance in scoring the marginal bone level was high when panoramic and periapical radiography was compared. In the upper arch, 66% of the sites showed concordant scores, 31% deviated by one and 3% by two score-points. In the lower arch, 74% of sites had concordant scores, 25% deviated by one and 1% by two score-points. The panoramic radiographs more often indicated a more severe bone loss than the periapical radiographs. The concordance was related to the degree of bone loss. In sites with no bone loss the concordance was high whereas it was lower in those with severe bone loss. The concordance of the two radiographic methods for the mandibular canine, premolars and first molar was equally as high as the intra-observer overall agreement, but lowest for the mandibular central incisors and the maxillary molars. Bone defects were more easily identified by periapical radiography.