DNA sequencing involves the extraction of genomic DNA from specimens collected in approved containers and provided the specimen meets required sample minimum quantity (e.g. volume, weight, etc). This is followed by quantification and qualification to ensure the adequacy of amount and purity for sequencing. Subsequently, whole exome sequencing is conducted on an Illumina^TM short read sequencing (SRS) platform (e.g., NovaSeq X Plus^TM) at Psomagen, Inc.’s laboratories (CLIA # 21D2062464, CAP # 8742212).

DNA sequence alignment, variant calling, and variant filtering are performed utilizing the Illumina DRAGEN^TM bioinformatics pipeline (version 4.2.4.) and various tool sets, which align reads to the human reference genome (GRCh38) and identify single nucleotide variants (SNVs) and small insertions/deletions (indels). Variant annotations are performed using a pipeline available in Fabric Enterprise. Variant review and interpretation are conducted according to the standards and guidelines set forth by the American College of Medical Genetics and Genomics (Richards S, et al., Genet Med., 2015) by Fabric Clinical Labs (CLIA #45D2281059, CAP # 9619501). Only variants classified as pathogenic or likely pathogenic are reported. The following quality filters are applied to all variants: coverage <40x, allele balance outside 0.3-0.7. Variants in the following genes are reported: APP, ATP13A2, ATP1A3, C9orf72, CSF1R, DCTN1, DNMT1, EIF4G1, FBXO7, GBA, GCH1, GRN, HTRA2, LRRK2, MAPT, NOTCH3, PARK7, PINK1, PLA2G6, POLG, PRKN, PRKRA, PRNP, PSEN1, PSEN2, SLC6A3, SNCA, SNCB, TAF1, TH, TREM2, TYROBP, UCHL1, VPS35, APOE, CHCHD10, CHMP2B, CTSF, FUS, HNRNPA2B1, OPTN, SQSTM1, TARDBP, TBK1, TIA1, TMEM106B, UBQLN1, UBQLN2, VCP.