Paired end cluster kit v4

Whole blood was collected for genomic DNA extraction. Genomic DNA was quantified with a Qubit fluorescence assay (Thermo Fisher Scientific) and sheared with an S2 instrument (Covaris). Library preparation was carried out using the TruSeq DNA PCR-Free HT Kit (Illumina). Individual DNA libraries were measured by 2100 Bioanalyzer (Agilent) qPCR and Qubit (Thermo Fisher Scientific). Normalized DNA libraries were combined into five-sample pools per flow cell in all eight lanes and clustered on a cBot instrument (Illumina) with Paired-End Cluster Kit V4 (Illumina). All flow cells were sequenced on the HiSeq2500 sequencer (Illumina) using the SBS Kit V4 chemistry (Illumina). FastQC was used to check read quality, and the resulting reads were aligned to the hg19 reference genome with the BWA-MEM algorithm (10 (link)). Single nucleotide variants (SNVs) and indel identification and genotyping were performed across all samples simultaneously using standard hard filtering parameters or variant quality score recalibration according to GATK Best Practices recommendations. WGS was presented with a minimum, median coverage of 30X.

Whole blood was collected for genomic DNA extraction. Genomic DNA was quantified with a Qubit fluorescence assay (Thermo Fisher Scientific) and sheared with a S2 instrument (Covaris). Library preparation was carried out using the TruSeq DNA PCR-Free HT kit (Illumina). Individual DNA libraries were measured by 2100 Bioanalyzer (Agilent) qPCR and Qubit (Thermo Fisher Scientific). Normalized DNA libraries were combined into five-sample pools per flow cell in all eight lines and clustered on a cBot instrument (Illumina) with Paired-End Cluster Kit V4 (Illumina). All flow cells were sequenced on the HiSeq. 2500 sequencer (Illumina) using SBS kit V4 chemistry (Illumina). FastQC was used to check read quality, and the resulting reads were aligned to the hg19 reference genome with the BWA-MEM algorithm¹⁶ . SNV and indel identification and genotyping were performed across all samples simultaneously using standard hard filtering parameters or variant quality score recalibration according to GATK Best Practices recommendations^{17 (link),18} . WGS was performed with a minimum median coverage of 30X.