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Additional file 2: Fig S1. Identifying regulatory variants in trans with pLoF variants in GEL.

Background Diagnostic use of gene panel next-generation sequencing (NGS) techniques is commonplace for individuals with inherited retinal dystrophies (IRDs), a highly genetically heterogeneous group of disorders. However, these techniques have often failed to capture the complete spectrum of genomic variation causing IRD, including CNVs. This study assessed the applicability of introducing CNV surveillance into first-tier diagnostic gene panel NGS services for IRD. Methods Three read-depth algorithms were applied to gene panel NGS data sets for 550 referred individuals, and informatics strategies used for quality assurance and CNV filtering. CNV events were confirmed and reported to referring clinicians through an accredited diagnostic laboratory. Results We confirmed the presence of 33 deletions and 11 duplications, determining these findings to contribute to the confirmed or provisional molecular diagnosis of IRD for 25 individuals. We show that at least 7% of individuals referred for diagnostic testing for IRD have a CNV within genes relevant to their clinical diagnosis, and determined a positive predictive value of 79% for the employed CNV filtering techniques. Conclusion Incorporation of CNV analysis increases diagnostic yield of gene panel NGS diagnostic tests for IRD, increases clarity in diagnostic reporting and expands the spectrum of known disease-causing mutations.

Background Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide.Methods We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC).Results Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals.Conclusions Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.

Table S1. Genes and transcripts included in multigene panel tests for retinal dystrophy and childhood cataracts. Table S2. Clinical and in silico evaluation of small (⠤21 nucleotides) in-frame insertions/deletions identified by panel-based genetic diagnostic testing in 486 probands with retinal dystrophy and 181 probands with childhood cataract. Table S3. Previously reported disease-associated small in-frame insertions/deletions in genes found to have clinically reported variants in the present study. (PDF 241 kb)

Background and Purpose: Research has shown that the risk of low back dysfunctions in runners is related to the increased mileage of distance running. Repetitive shock loading of the spinal structures during running has been indicated as one of the important biomechanical mechanisms underlying such injury. Acute changes in foot strike pattern, like those seen during minimalist style running, have been shown to lead to modifications in lumbar range of motion. Minimalist style running could lead to changes in lumbar biomechanics and muscle activation, potentially reducing the loading on the musculoskeletal structures of the lower back. However, the long term effects of minimalist style running on lumbar biomechanics have not been evaluated. The purpose of this study was to investigate the effects a 4-week training program aimed at transitioning recreational runners to minimalist style footwear would have on lower back kinematics and lumbar paraspinal muscle activation. Subjects: 17 volunteers between the ages of 18-45 years who were habitually shod runners and averaged running 10-50 km per week participated in the study. Data from 15 volunteers was used in the analysis of the biomechanics. Inclusion and exclusion criteria were used to determine the appropriateness of each volunteer for this study. Methods: Subjects participated in three data collection sessions at the beginning, during (2-week), and at the end of a 4-week training program. The training consists of progressively increasing the distance each runner ran in the minimalist shoes up to 30-50% of their regular running distance while maintaining the overall distance (minimalist + normal shoes) comparable to before training. Running trials were collected with the subject wearing their normal running shoes. Subjects were asked to run at a prescribed speed (11.2 km/h), and a blinded self-selected speed. During running, kinematics of the lower back in the sagittal plane was recorded using an electro-goniometer. Surface EMG was used to monitor the activation of the lower back (L3 level) paraspinal muscles. Data collected during 10 stance phases were averaged and used for analysis. One-way repeated measures ANOVA tests were used to analyze the effect of training on lumbar kinematics and lumbar paraspinal muscle activation. Results: For the 11.2 km/h running speed, statistically significant differences were found in mean lower back posture (PRE = 1.9 ± 15.3 degrees, MID = 0.4 ± 13.0 degrees, POST = -6.0 ± 13.3 degrees, p = 0.001) and contralateral lumbar paraspinal muscle activation (PRE = 47.0 ± 34.0%, MID = 24.9 ± 8.2%, POST = 29.4 ± 11.3%, p = 0.039) after training. For the self-selected running speed, statistically significant differences were found in mean lower back posture (PRE = 2.3 ± 15.5 degrees, MID = 0.9 ± 13.9 degrees, POST = -5.7 ± 14.2 degrees, p = 0.002) and contralateral lumbar paraspinal muscle activation (PRE = 41.6 ± 28.6%, MID = 23.4 ± 6.2%, POST = 30.3 ± 11.6%, p = 0.047) after training. During both speeds, lower back posture became more extended and contralateral lumbar paraspinal muscle activation decreased. No significant differences were noted in overall lower back range of motion or ipsilateral paraspinal muscle activation over the training period at either speed. Conclusions: Including minimalist running shoes and barefoot exercises into a runners' training regime can alter the lumbar spinal kinematics and muscle activation. Specifically the runners adapted a more extended lumbar posture and reduced the lumbar paraspinal muscle activation after training. This effect carried over to shod running.