Whole Genome Sequencing and Genotyping Reprocessing

Previous to this study, 106 individuals from the cohort had their genomes sequenced to high coverage (TruSeq Nano libraries sequenced on HiSeqX) and 1293 individuals were genotyped using Illumina Infinium CoreExome arrays (v1.0–1.3) [34 (link)]. We reprocessed the 106 whole genomes to obtain joint variant calls as detailed below. For the array data, GRCh37 genotype calls were lifted over to GRCh38, resulting in 471,499 genotyped positions on autosomes which were then further imputed into the 1000 Genomes mapped onto GRCh38 reference panel [49 (link)] using Beagle v5.1 [30 (link)] (beagle.27Apr20.b81.jar).

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Emde A.K., Phipps-Green A., Cadzow M., Gallagher C.S., Major T.J., Merriman M.E., Topless R.K., Takei R., Dalbeth N., Murphy R., Stamp L.K., de Zoysa J., Wilcox P.L., Fox K., Wasik K.A., Merriman T.R, & Castel S.E. (2021). Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations. BMC Genomics, 22, 666.

Publication 2021

Infinium CoreExome arrays

Genomes Joint

Corresponding Organization :

Other organizations : University of Otago, University of Auckland, University of California, San Diego, University of Alabama at Birmingham

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Variable analysis

independent variables

Genome sequencing method (TruSeq Nano libraries sequenced on HiSeqX)
Genotyping method (Illumina Infinium CoreExome arrays (v1.0–1.3))

dependent variables

Variant calls from whole genome sequencing data
Genotype calls from array data

control variables

GRCh37 genotype calls lifted over to GRCh38
Imputation into the 1000 Genomes mapped onto GRCh38 reference panel using Beagle v5.1

controls

No positive or negative controls were explicitly mentioned in the provided information.

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