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Germline Genetics at Scale

Germline variant calling plays a crucial role in unlocking the mysteries encoded within our DNA and helps us understand the unique genetic variations passed down from generation to generation.

Beyond the exploration of heritage, germline variant calling plays a pivotal role in understanding the causes of hereditary diseases. By identifying genetic markers associated with conditions like cystic fibrosis or certain cancers, we gain valuable tools for predicting and preventing health challenges that may affect not only ourselves but also our descendants. The utility of germline variants relies on accurate sequencing quality, which the UG 100 delivers on.

  • Advanced machine learning algorithms that are part of the ecosystem that comes with the UG 100
  • Accurate SNP (F1 > 99.5%) and Indel (F1 > 99%) variant calls
  • High accuracy copy number variant calls
  • At only $100/genome, gain more insights from larger and better powered studies
  • Applications include Clinical genomics, population studies, shallow WGS
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SNP and INDEL variant calling

Sequencing of 7 Genome in a Bottle (GIAB) samples shows high accuracy for SNP and INDEL variant calling evaluated over the Ultima Genomics High Confidence Region (UG-HCR), determined using GIAB v4.2.1 ground truth and high confidence regions. The UG-HCR data sets contain >99% of the GIAB v4.2.1 HCR.


Download our newest GIAB dataset

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CNV calling

Using samples from the NIGMS human genetic cell repository and clinical samples, data from the UG 100 has 97% precision and 99% recall compared to the 1K genome project‡.


Read our germline WGS app note

‡CNV calling was performed on a defined UGCNV-HCR, which excludes regions of low mappability, low coverage, high coverage variability, telomeres, centromeres, and regions with empirically defined noisy CNV calls. In total, these excluded regions cover 175,212,713 bp (5.5% out of the ungapped human genome).

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Table: Counts and length of CNVs identified in the cohort

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Figure: Recall and Precision values of the UG 100 callset showed high concordance with those values of the 1kGP callset.

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Figure: IGV snapshot for NA06802 coverage data with corresponding CNV detection. known germline CNVs are marked with red rectangles: heterozygous deletion (copy number=1) in chr6 and heterozygous duplication (copy number=3) in chr16.

Partnerships

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Explore IDT's xGen™ for Ultima Genomics® product line including adapters, primers, and blocking oligos to expand the scale of your experiments.

Order xGen™ for Ultima Genomics®

Explore our GitHub repository containing our WDL-format pipelines for calling short and copy-number variants and instructions for running on AWS HealthOmics Ready2Run.

Check out our AWS Ready2Run solution

Resources

White Paper

Learn how we perform variant calling analysis using a UG-adapted version of DeepVariant

Read White Paper

Application Notes

Learn how WGS on the UG 100™ sequencing platform achieves high accuracy for germline variant calling

Read our germline WGS app note

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