A family-centered orthodontic screening approach using a machine learning-based mobile application.

Background/purpose: Skeletal orthodontic deformities can have functional and aesthetic consequences, making early detection critical. This study aimed to address the issue of parents bringing their children for routine orthodontic checkups after the ideal treatment age has passed. To address this, we developed a mobile application that uses machine-learning to make a preliminary diagnosis of skeletal malocclusion using just one photograph. Materials and methods: A retrospective study was conducted on 524 pre-pubertal children, aged between 5 and 12 years, to evaluate the accuracy of the machine learning based mobile application. The application detects multiple points in photographs taken from the mobile camera and generates a signal indicating the diagnosis of skeletal malocclusion. Results: The final accuracy of the Class III vs not Class III model deployed to the mobile application was above 81%, indicating its ability to accurately identify skeletal malocclusion. On a separate validation dataset of 145 patients diagnosed by 5 different clinicians, the accuracy of Class II vs Class I model was 69%; And pg 4, ln 61: as Class II vs Class I with 69% accuracy. Conclusion: The application provides parents with important information about the orthodontic problem, age of treatment, and various treatment options. This enables parents to seek further advice from an orthodontist at an earlier stage and make informed decisions. However, the diagnosis should still be confirmed by an orthodontist. This approach has the potential to improve access to orthodontic care, especially in underserved communities.

BloodSpot 3.0: a database of gene and protein expression data in normal and malignant haematopoiesis.

BloodSpot is a specialised database integrating gene expression data from acute myeloid leukaemia (AML) patients related to blood cell development and maturation. The database and interface has helped numerous researchers and clinicians to quickly get an overview of gene expression patterns in healthy and malignant haematopoiesis. Here, we present an update to our framework that includes protein expression data of sorted single cells. With this update we also introduce datasets broadly spanning age groups, which many users have requested, with particular interest for researchers studying paediatric leukaemias. The backend of the database has been rewritten and migrated to a cloud-based environment to accommodate the growth, and provide a better user-experience for our many international users. Users can now enjoy faster transfer speeds and a more responsive interface. In conclusion, the continuing popularity of the database and emergence of new data modalities has prompted us to rewrite and futureproof the back-end, including paediatric centric views, as well as single cell protein data, allowing us to keep the database updated and relevant for the years to come. The database is freely available at www.bloodspot.eu.

A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data.

Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. Relevant CNVs are hard to detect because common structural variations define large parts of the human genome. CNV calling from short-read sequencing would allow single protocol full genomic profiling. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard-SNP-array based CNV calling. Additionally, for nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Several tools had better performance for NA12878, which could be a result of overfitting. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Reducing the total number of called variants could potentially be assisted by the use of background panels for filtering of frequently called variants.