Rare variants detected by Next Generation Sequencing in two siblings affected by late onset Parkinson's disease

Background: With the use of Next-Generation Sequencing (NGS) an increasing number of PD related genes have been discovered and this new approach can be used to genetically define unresolved PD clinical cases. Objectives: The objective of the present study was to analyze the DNA of two brothers affected by late onset PD. The first patient suffered from mood depression and panic attacks since he was young. He presented progressive slowness of movements, oro-mandibular and right upper limb tremor from the age of 68 years. The response to L-dopa treatment was good. After six years, he showed rapid deterioration of the motor condition, progressive dementia, fluctuating cognition and recurrent visual hallucinations. His brother presented resting tremor at the right upper limb at the age of 59 years. Methods: After DNA extraction, high coverage targeted NGS data were generated at the NGS-Core of IRIB, CNR, Mangone (CS) by an amplicon-based approach. We used a custom-made panel containing 42 genes PD-related. The enriched libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM) system from ThermoFisher Scientific. The primary bioinformatics analysis was carried out using Ion Torrent Suite vers.5.10. Annotation and filtering/priorization of single-nucleotide variations (SNVs) and copy number variations (CNVs) discovered was made by annovar. Results: Sequencing generated a median of 5.85 *106 reads per run, with a mean depth close to 500 reads, a mean read length of 375 called bases and a chip loading of 71%. After bioinformatics analysis and considering only the common variants identified in the two siblings, we highlighted a heterozygous variation c.2710A>G (p.Lys904Glu) in the alphasynuclein binding domain of SNCAIP gene with MAF<0.01, reported as damaging. In addition, we identified 4 common high confidence and precision CNVs: a deletion in the ATP13A2 gene (chr1p36.13), a deletion in DNAJC6 gene (chr1p31.3), a deletion in ADHC1 gene (chr4q23), and a 12Mb deleted region in 22q11.21-21q12.3. Conclusions: We presented two PD clinical cases in wich NGS analysis allowed us to detect new variants that could be directly involved in the worsening of the complex clinical history of ou two patients.