title: Ghana Breast Health Study
design: Initial DNA input was normalized to be within the range of 25–52.5ng in 50μL of TE buffer (10mM Tris HCl 1mM EDTA, pH 8.0) according to picoGreen quantification. Library preparation was performed using a commercially available kit provided by KAPA Biosystems (KAPA HyperPrep Kit with Library Amplification product KK8504) and IDT's duplex UMI adapters. Unique 8-base dual index sequences embedded within the p5 and p7 primers (purchased from IDT) were added during PCR. Enzymatic clean-ups were performed using Beckman Coultier AMPure XP beads with elution volumes reduced to 30µL to maximize library concentration.Library quantification was performed using the Invitrogen Quant-It broad range dsDNA quantification assay kit (Thermo Scientific Catalog: Q33130) with a 1:200 PicoGreen dilution. Following quantification, each library was normalized to a concentration of 35ng/µL, using Tris-HCl, 10mM, pH 8.0.In preparation for the sequencing of the ultra-low pass libraries (ULP), approximately, 4µL of the normalized library was transferred into a new receptacle and further normalized to a concentration of 2ng/µL using Tris-HCl, 10mM, pH 8.0. Following normalization, up to 95 ultra-low pass WGS samples were pooled together using equivolume pooling. The pool was quantified via qPCR and normalized to the appropriate concentration to proceed to sequencing.