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Dragen 2 platform

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The DRAGEN 2 platform is a high-performance computing solution designed for genomic analysis. It provides hardware-accelerated processing of next-generation sequencing data, enabling rapid and efficient bioinformatics workflows.

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DRAGEN (13 citations) DRAGEN Platform (4 citations)

2 protocols using dragen 2 platform

1

Trio Exome Sequencing for Mosaic SNVs

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We analyzed family trio ES data from approximately 15,000 patients enrolled in clinical diagnostic studies. Average depth-of-coverage was ~100x with >70% of reads aligned to target, >95% target base covered at >20x, >85% target base covered at >40x. Since ES data in BG have been pre-processed using a different analytical pipeline than BHCMG cohort, we modified the mosaic SNV candidate selection accordingly. We have used three different data subsets, as presented in Supplementary Figure 1. The first subset of parental mosaic variants was derived from the analysis of 3165 apparent de novo heterozygous SNVs in the probands selected previously in the process of clinical analysis. Second subset consists of approximately 1000 trios for which joint VCF files were generated on the Illumina DRAGEN 2 platform. We focused on unique rare variants that occurred in only one family. We also removed any variants that overlapped segmental duplications. Similar to the approach used for the BHCMG cohort, we required a depth of at least 20 reads in each parent, an evidence of heterozygous state in the proband with a VAF of 0.3-0.7 and 0
Gambin T., Liu Q., Karolak J.A., Grochowski C.M., Xie N.G., Wu L.R., Yan Y.H., Cao Y., Akdemir Z.H., Wilson T.A., Jhangiani S.N., Chen E., Eng C.M., Muzny D., Posey J.E., Yang Y., Zhang D.Y., Shaw C., Liu P., Lupski J.R, & Stankiewicz P. (2020). Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genetics in medicine : official journal of the American College of Medical Genetics, 22(11), 1768-1776.
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2

Trio Exome Sequencing for Mosaic SNVs

Check if the same lab product or an alternative is used in the 5 most similar protocols
We analyzed family trio ES data from approximately 15,000 patients enrolled in clinical diagnostic studies. Average depth-of-coverage was ~100x with >70% of reads aligned to target, >95% target base covered at >20x, >85% target base covered at >40x. Since ES data in BG have been pre-processed using a different analytical pipeline than BHCMG cohort, we modified the mosaic SNV candidate selection accordingly. We have used three different data subsets, as presented in Supplementary Figure 1. The first subset of parental mosaic variants was derived from the analysis of 3165 apparent de novo heterozygous SNVs in the probands selected previously in the process of clinical analysis. Second subset consists of approximately 1000 trios for which joint VCF files were generated on the Illumina DRAGEN 2 platform. We focused on unique rare variants that occurred in only one family. We also removed any variants that overlapped segmental duplications. Similar to the approach used for the BHCMG cohort, we required a depth of at least 20 reads in each parent, an evidence of heterozygous state in the proband with a VAF of 0.3-0.7 and 0
Gambin T., Liu Q., Karolak J.A., Grochowski C.M., Xie N.G., Wu L.R., Yan Y.H., Cao Y., Akdemir Z.H., Wilson T.A., Jhangiani S.N., Chen E., Eng C.M., Muzny D., Posey J.E., Yang Y., Zhang D.Y., Shaw C., Liu P., Lupski J.R, & Stankiewicz P. (2020). Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genetics in medicine : official journal of the American College of Medical Genetics, 22(11), 1768-1776.
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