Whole-Genome Sequencing of QBB Cohort

The WGS data of the QBB study participants was provided by the Qatar Genome Project (QGP) [46 (link)]. Details of WGS and quality control measures have been described previously [47 (link)]. Briefly, genomic DNA from peripheral blood samples was extracted using Qiagen MIDI kit (Qiagen, Hilden, Germany), following the manufacturer’s protocol and using the automated QIASymphony SP instrument (Qiagen). DNA integrity was evaluated using Caliper Labchip GXII (Perkin Elmer, Waltham, MA, USA) Genomic DNA assay and was quantified using the Quant-iT dsDNA Assay (Invitrogen, Waltham, MA, USA). Whole-genome libraries were prepared using Illumina TruSeq DNA Nano kit (Illumina, San Diego, CA, USA). HiSeq X Ten (Illumina) was used to sequence genomic libraries to achieve a minimum average coverage of 30×. Library construction and sequencing was performed at Sidra Clinical Genomics Laboratory Sequencing Facility (Sidra Medicine, Doha, Qatar). The generated files were subjected to quality control using FastQC (v0.11.2) and reads were aligned to the CRCh38 reference genome. Quality control on mapped reads was performed using Picard (v1.117). A combined variant call file (gVCF) was generated for all study subjects, which contained all genetic variations detected in the QBB study participants.