Germline pipeline

Manufactured by Illumina

Sourced in United States

The Germline Pipeline is a lab equipment product from Illumina designed for the analysis of genetic data. It is capable of processing and analyzing DNA samples to identify germline genetic variations. The core function of the Germline Pipeline is to perform high-throughput sequencing and data analysis for the detection of inherited genetic changes.

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Lab products found in correlation

Basespace sequence hub, by Illumina (1 mentions)

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DRAGEN Bio-IT Platform Germline Pipeline v3.0.7 (7 citations) Illumina pipelines (6 citations) DRAGEN Germline Pipeline (5 citations) DRAGEN Germline Pipeline v3.2.8 (3 citations) DRAGEN Bio-IT Platform Germline Pipeline (3 citations)

2 protocols using germline pipeline

Whole-Genome Sequencing Data Analysis

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Reads in the FASTQ files were aligned to the standard human genome reference (GRCh37) using Illumina’s Dynamic Read Analysis dor GENNomics (DRAGEN) Genomic Pipeline. Resultant BAM files were position-sorted and duplicate reads marked. Single-sample genomic variant call files (gVCF) were generated by the DRAGEN Germline Pipeline, and joint calling of all samples in the study cohort was performed by DRAGEN Joint Genotyping (Illumina, CA, USA).

Alkhamis F.A., Alabdali M.M., Alsulaiman A.A., Alamri A.S., Alali R., Akhtar M.S., Alsalman S.A., Cyrus C., Albakr A.I., Alduhalan A.S., Gandla D., Al-Romaih K., Abouelhoda M., Loza B.L., Keating B, & Al-Ali A.K. (2023). Whole‐exome sequencing analyses in a Saudi Ischemic Stroke Cohort reveal association signals, and shows polygenic risk scores are related to Modified Rankin Scale Risk. Functional & Integrative Genomics, 23(2), 102.

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Germline Variant Identification Pipeline

Cited 3 times

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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).

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.

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