Germline Variant Identification Pipeline

Raw output was stored in Illumina’s BaseSpace Sequence Hub and data was analyzed using the Germline Pipeline of Illumina’s DRAGEN™ (Dynamic Read Analysis for GENomics) Bio-IT platform v3.7.5 [25 (link), 26 (link)]. In short, after data is demultiplexed, mapped, and aligned (GRCh37), the DRAGEN Germline Pipeline provides a comprehensive analysis, including small variant (SNV and indels < 50 bp), ROH, CNV, and SV calling, as well as repeat expansion detection and genotyping through Illumina Expansion Hunter [27 (link)]. In addition, we used newly developed DRAGEN SMA [28 (link)] and CYP21A2 (DRAGEN v3.9) callers for those specific cases in which the genetic variants located in SMN1/2 or CYP21A2 (n = 19 cases, 34 variants).

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Schobers G., Derks R., den Ouden A., Swinkels H., van Reeuwijk J., Bosgoed E., Lugtenberg D., Sun S.M., Corominas Galbany J., Weiss M., Blok M.J., Olde Keizer R.A., Hofste T., Hellebrekers D., de Leeuw N., Stegmann A., Kamsteeg E.J., Paulussen A.D., Ligtenberg M.J., Bradley X.Z., Peden J., Gutierrez A., Pullen A., Payne T., Gilissen C., van den Wijngaard A., Brunner H.G., Nelen M., Yntema H.G, & Vissers L.E. (2024). Genome sequencing as a generic diagnostic strategy for rare disease. Genome Medicine, 16, 32.

Publication 2024

BaseSpace Sequence Hub Germline Pipeline

Corresponding Organization :

Other organizations : Radboud University Nijmegen, Radboud University Medical Center, Maastricht University, Illumina (United Kingdom)

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Variable analysis

independent variables

Illumina's DRAGEN™ (Dynamic Read Analysis for GENomics) Bio-IT platform v3.7.5 used for data analysis
DRAGEN Germline Pipeline used for comprehensive analysis, including small variant (SNV and indels < 50 bp), ROH, CNV, and SV calling, as well as repeat expansion detection and genotyping through Illumina Expansion Hunter
DRAGEN SMA and CYP21A2 (DRAGEN v3.9) callers used for specific cases with genetic variants located in SMN1/2 or CYP21A2 (n = 19 cases, 34 variants)

dependent variables

Small variants (SNV and indels < 50 bp)
ROH (Runs of Homozygosity)
CNV (Copy Number Variations)
SV (Structural Variations)
Repeat expansions
Genetic variants in SMN1/2 and CYP21A2 (n = 19 cases, 34 variants)

control variables

Genome build used for alignment (GRCh37)

Annotations

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