Constitutional Microsatellite Instability, Genotype, and Phenotype Correlations in Constitutional Mismatch Repair Deficiency

Background & aims: Constitutional mismatch repair deficiency (CMMRD) is a rare recessive childhood cancer predisposition syndrome caused by germline mismatch repair variants. Constitutional microsatellite instability (cMSI) is a CMMRD diagnostic hallmark and may associate with cancer risk. We quantified cMSI in a large CMMRD patient cohort to explore genotype-phenotype correlations using novel MSI markers selected for instability in blood.Methods: Three CMMRD, 1 Lynch syndrome, and 2 control blood samples were genome sequenced to >120 7 depth. A pilot cohort of 8 CMMRD and 38 control blood samples and a blinded cohort of 56 CMMRD, 8 suspected CMMRD, 40 Lynch syndrome, and 43 control blood samples were amplicon sequenced to 5000 7 depth. Sample cMSI score was calculated using a published method comparing microsatellite reference allele frequencies with 80 controls.Results: Thirty-two mononucleotide repeats were selected from blood genome and pilot amplicon sequencing data. cMSI scoring using these MSI markers achieved 100% sensitivity (95% CI, 93.6%-100.0%) and specificity (95% CI 97.9%-100.0%), was reproducible, and was superior to an established tumor MSI marker panel. Lower cMSI scores were found in patients with CMMRD with MSH6 deficiency and patients with at least 1 mismatch repair missense variant, and patients with biallelic truncating/copy number variants had higher scores. cMSI score did not correlate with age at first tumor.Conclusions: We present an inexpensive and scalable cMSI assay that enhances CMMRD detection relative to existing methods. cMSI score is associated with mismatch repair genotype but not phenotype, suggesting it is not a useful predictor of cancer risk

Constitutional microsatellite instability, genotype, and phenotype correlations in constitutional mismatch repair deficiency

Background & AimsConstitutional mismatch repair deficiency (CMMRD) is a rare recessive childhood cancer predisposition syndrome caused by germline mismatch repair variants. Constitutional microsatellite instability (cMSI) is a CMMRD diagnostic hallmark and may associate with cancer risk. We quantified cMSI in a large CMMRD patient cohort to explore genotype–phenotype correlations using novel MSI markers selected for instability in blood.MethodsThree CMMRD, 1 Lynch syndrome, and 2 control blood samples were genome sequenced to >120× depth. A pilot cohort of 8 CMMRD and 38 control blood samples and a blinded cohort of 56 CMMRD, 8 suspected CMMRD, 40 Lynch syndrome, and 43 control blood samples were amplicon sequenced to 5000× depth. Sample cMSI score was calculated using a published method comparing microsatellite reference allele frequencies with 80 controls.ResultsThirty-two mononucleotide repeats were selected from blood genome and pilot amplicon sequencing data. cMSI scoring using these MSI markers achieved 100% sensitivity (95% CI, 93.6%–100.0%) and specificity (95% CI 97.9%–100.0%), was reproducible, and was superior to an established tumor MSI marker panel. Lower cMSI scores were found in patients with CMMRD with MSH6 deficiency and patients with at least 1 mismatch repair missense variant, and patients with biallelic truncating/copy number variants had higher scores. cMSI score did not correlate with age at first tumor.ConclusionsWe present an inexpensive and scalable cMSI assay that enhances CMMRD detection relative to existing methods. cMSI score is associated with mismatch repair genotype but not phenotype, suggesting it is not a useful predictor of cancer risk.Perioperative Medicine: Efficacy, Safety and Outcome (Anesthesiology/Intensive Care

The Nachtlichter app: a citizen science tool for documenting outdoor light sources in public space

The relationship between satellite based measurements of city radiance at night and the numbers and types of physical lights installed on the ground is not well understood. Here we present the "Nachtlichter app", which was developed to enable citizen scientists to classify and count light sources along street segments over large spatial scales. The project and app were co-designed: citizen scientists played key roles in the app development, testing, and recruitment, as well as in analysis of the data. In addition to describing the app itself and the data format, we provide a general overview of the project, including training materials, data cleaning, and the result of some basic data consistency checks

Nutraceutical Potential of Apiaceae

Apiaceae family is large, with over 3.000 species worldwide cultivated for many purposes. Some plants in this family such as carrots, parsley, parsnip and celery are common vegetable crops, while other members like anise, caraway, coriander, cumin, fennel, lovage, angelica and dill are famous for their medicinal and aromatic properties. Usage of these plants is very popular in everyday diet because of their documented health benefits. Apiaceae are a very important source of phytochemicals – chemicals with biological activity. However, phytochemicals are non-nutritive plant chemicals, also called nutraceuticals. They are widely used for prevention, treatment or cure of conditions or diseases. Bioactive compounds with nutraceutical potential are polyphenolic compounds, polyacetylenes and terpenoids. The aim of this review is to represent selected plants of Apiaceae family currently used as nutraceuticals and describe their nutritional benefits