Dragen germline pipeline v3

DNA samples from five family members were exome sequenced at Omega Bioservices (Norcross, GA, USA); these samples were obtained from two affected individuals (Figure 1A, II.1, and II.3), their parents (I.1, and I.2), and one unaffected sibling (II.4). Library preparation was performed with an Illumina Nextera Rapid Capture Exome Kit^® (Illumina, San Diego, CA, USA) following the manufacturer’s instructions, and the resulting libraries were hybridized with a 37 Mb probe pool to enrich exome sequences. Sequencing was performed on an Illumina HiSeq 2500 sequencer using the pair-end 150 bp run format. Sequencing data were processed using the Illumina DRAGEN Germline Pipeline v3.2.8. Briefly, high-quality reads were aligned to the human reference genome GRCh37/hg19 using the DRAGEN software version 05.021.408.3.4.12, and, after sorting and duplicate marking, variants were called, and individual genomic variant call format (gvcf) files were generated. Joint single nucleotide variant (SNV) and Insertion/Deletion (Indel) variant calling was performed using the genome analysis toolkit (GATK) software v4.0.6.0 [17 (link)]. The sex of each individual was verified using plinkv1.9 [18 (link)]. Familial relationships for all members were verified via Identity-by-Descent sharing (plinkv1.9) and the Kinship-based INference for Gwas (KING) algorithm [18 (link),19 (link)].

Sequencing data were processed using Omega Bioservices (Norcross, GA, USA) developed pipelines on the Illumina DRAGEN Germline Pipeline v3.2.8. Briefly, high-quality reads were aligned to the human reference genome GRCh37/hg19 using DRAGEN software version 05.021.408.3.4.12. After sorting and duplicate marking, the base quality scores were recalibrated using the genome analysis toolkit (GATK v4.0.6.0) [20 (link)]. Variants were called using GATKHaplotypeCaller, and individual genomic variant call format (gvcf) files were generated. Joint variant calling was then performed using GATK GenotypeGVCF [21 (link)]. The sex of each individual was verified using Plink version 1.9 [21 (link)]. The familial relationships for all members were verified using the Kinship-based INference for Gwas (KING) algorithm [22 (link)].

DNA samples, from the two affected members of Family 1, underwent whole-exome sequencing at OmegaBioservices (Norcross, GA, USA). An Illumina Nextera Rapid Capture Kit^® (37Mb; San Diego, CA, USA) was used for library preparation, according to the manufacturer’s instructions. The library was then sequenced using the Illumina HiSeq 2500 sequencer using the pair-end 150bp run format. The sequencing data were processed using the Illumina DRAGEN Germline Pipeline v3.2.8.