A cross-sectional study of patients referred for HNF1B-MODY genetic testing due to cystic kidneys and diabetes.

BACKGROUND/OBJECTIVES: Patients referred for HNF1B testing present very heterogeneous phenotypes. Despite suggestive characteristics, many do not harbor mutations in HNF1B. Our objective was to evaluate the clinical characteristics of probands referred for HNF1B genetic testing through a nationwide monogenic diabetes screening program. METHODS: Probands tested for HNF1B mutations in the 2005-2018 period (N = 50) were identified in the Polish Monogenic Diabetes Registry, which prospectively recruits primarily pediatric patients and their families on a nationwide scale. Variants that had been reported pathogenic were reassessed using criteria of the American College of Medical Genetics and Genomics (ACMG). A structured medical interview was performed with all available individuals, their parents, and/or their physicians. For each patient, HNF1B score was calculated based on available clinical information. RESULTS: The study group numbered 36 unrelated probands (28% lost to follow-up): 14 with pathogenic or likely-pathogenic variants in HNF1B, one with a variant of uncertain significance, and 21 negative for HNF1B mutations. Presence of cystic kidneys (OR = 9.17, 95% CI:1.87-44.92), pancreatic abnormalities (OR = 15, 95% CI:1.55-145.23), elevated liver enzymes (OR = 15, 95% CI:1.55-145.23) best discriminated HNF1B-positive cases from the negative ones. Presence of impaired glucose tolerance coupled with kidney disease in the proband and one parent was also highly predictive for HNF1B mutations (OR = 11.11, 95% CI:1.13-109.36). HNF1B-score with recommended cutoff distinguished patients with and without HNF1B findings with 100% sensitivity and 47.6% specificity. Addition of four clinical variables to select patients based on HNF1B score improved specificity to 71.4% (95% CI:47.8%-88.7%) while retaining 100% sensitivity. CONCLUSIONS: Detailed medical interview may enable more accurate patient selection for targeted genetic testing.

Clinical use of NGS data from the targeted gene panel for mitochondrial diseases screening.

BACKGROUND AND OBJECTIVE: Mitochondrial diseases are a frequent cause of inherited genetic disorders caused by mutations in both the mitochondrial and nuclear human genome. The new technique of high-throughput sequencing, which is used more and more frequently around the world, is most often focused on nuclear DNA. In some cases, such data after proper IT processing could also allow to determine alterations in mtDNA genome. In our work, we want to verify that off-target reads from targeted gene panels are sufficient data to determine pathogenic variants in the mitochondrial genome. METHODS: We analyzed 50 patients who underwent routine diagnostics with the Illumina's TruSight One Sequencing Panel. In the entire bioinformatic analysis process, we have used only free, user-friendly and generally available online tools that do not require specialized IT knowledge. RESULTS: Most of the data obtained were suitable for determining the presence of homoplasmic variants in mtDNA; 84% of the data met the minimum 20-fold coverage requirement as defined in the scientific literature for clinical data. We managed to identify 16 pathogenic variants in the examined genetic material (mtDNA) according to the ClinVar database. CONCLUSIONS: In conclusion, we have outlined that off-target reads from targeted gene panel (TruSight One Sequencing Panel) may also be suitable for determining potentially pathogenic homoplasmic variants in mtDNA. We also described a simple pipeline based only on free tools available online. Introducing such a pipeline into a standard procedure of clinical units which carry out such research undoubtedly can extend the diagnostic potential by information about mtDNA, especially when it is based on purely free tools that do not require specialized bioinformatic knowledge.