A powerful platform for population-scale genomic research

Helix’s genomics research platform, supported by our proprietary Exome+® assay, CLIA / CAP next-generation sequencing lab, and proprietary bioinformatics tools, enables genomic research at a scale and depth not previously possible. Learn more from our latest research findings and white papers.


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The Exome+ assay: Enabling clinical results
and powering research with one assay

Helix's proprietary Exome+ assay is a panel-grade clinical exome enhanced by ~300,000 informative non-coding regions. Due to its custom design and proprietary bioinformatics solutions, the Exome+ assay provides the benefits of a targeted panel, the breadth of a microarray, and the completeness of an exome—all from one sample and one assay.


Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts

In this paper, we demonstrate the superiority of exome sequencing data (as compared to microarray data) in researching the trait-level effects of rare variants. Using an analytical method that groups together multiple rare variants based on their co-occurrence within a gene—referred to as a gene-based collapsing analysis—we analyzed 4,264 phenotypes in 49,960 exome-sequenced individuals from the UK Biobank. We also performed replication as well as meta-analyses with 1,934 phenotypes in 21,866 members of the Healthy Nevada Project (HNP) cohort.

Our results show that 88% of the significant gene-trait associations were weakened when singleton variants—variants that appeared only once in our cohort—were excluded. Further, when variants were considered individually, 84% of genes with a significant association appeared to have no significantly associated variants. This means that the majority of the identified associations could not have been found using traditional array-based methods.

The Impact

This is the first analysis to leverage rare variant discovery and PheWAS in two large exome cohorts across thousands of medical record phenotypes to demonstrate novel biomarker discoveries. Our data show the importance of considering unique and rare variants in gene-phenotype studies. We also highlighted how the Exome+ assay can be used to discover novel genetic insights that would otherwise be missed using array-based methods.

Read the full article on Nature.com

Conceptual diagram depicting gene-based collapsing analysis

Research tools

UK Biobank Exome Rare Variant Analysis

The UK Biobank released the whole exome sequences of 50,000 volunteers, each of whom has been measured for thousands of traits (phenotypes) and donated their information to the research community. This dashboard provides anyone who is interested in our research the ability to deep-dive into the research results to better understand the findings.


Helix Mitochondrial database (HelixMTdb)

The HelixMTdb database reflects aggregated and de-identified mitochondrial DNA variants observed in individuals sequenced at Helix. These individuals have not been sequenced based on the presence or absence of any medical phenotype (i.e. there are no inclusion or exclusion criteria in the registration process based on any medical phenotype). The full database, HelixMTdb, can be downloaded here. Please use the appropriate citation when using the HelixMTdb. 

Download the HelixMTdb

*Panel-grade: defined as a ~100% call rate across every base within clinically relevant panels (offering equivalent or superior quality to clinical panels in the market)

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