Research Applications

the most accurate and comprehensive

research services available

Research Applications 2016-12-06T14:02:20+00:00

Research Applications

The most accurate and comprehensive solution for a wide variety of study types and study areas.

Case Control Studies

For customers studying large groups of patients with a shared disease phenotype, phenotypic trait, tumor, or drug response profile, we offer services for sequencing, alignment, variant calling, annotation, and analysis for identifying biomedically relevant variants. In situations where controls are not available from the customer, we provide access to an extensive Personalis library of genome controls. We also provide leading edge analytics for determining variant, gene, disease, and pathway enrichment that are powered by a high-quality manually-curated disease-to-variant database, enabling interpretation and annotation of potentially causative variants in both exonic and non-exonic regions.

Proband, Family, and Extended Pedigree Studies

For customers interested in identifying potentially causative variants underlying a disease or trait, known or suspected to follow a Mendelian pattern of inheritance, we offer services for sequencing, alignment, variant calling and inheritance analysis. Our flexible approach enables analysis of phenotypes observed either sporadically or segregating in a family under a variety of inheritance models: de novo dominant, inherited dominant, recessive (homozygous, compound heterozygous), and X-linked. Flexibility with respect to family structure enables us to undertake studies with the following designs: proband only, trios, quartets, and larger extended pedigrees, as well as multi-family designs. We leverage ethnicity-specific reference sequences and unique linkage and IBD inference algorithms to capitalize on the information that can be obtained from the available samples, maximizing the chance of success. Our extensive phenotype-driven database enables generation of comprehensive candidate gene lists that are cross-referenced against candidate variants emerging from the data. Pre- and post-analysis review by clinical specialists guides both our analysis and interpretation.

Research Clinical Implementation of Pharmacogenomics

For customers interested in evaluating the efficacy and impact of pharmacogenomics in clinical situations, under a research protocol, we offer services to interrogate the “pharmacogenome”. Personalis uses its ACE technology, in combination with its proprietary and comprehensive pharmacogenomics database, to query the set of genes for which there is published evidence of impact on drug response. These include high-evidence associations between genetic variations and drug response, including warfarin, clopidogrel, simvastatin, thiopurines, codeine, abacavir and allopurinol, as well as medium- and low-evidence associations for hundreds of other drugs that may be of interest for advancing understanding of their role or impact on clinical care. Personalis pharmacogenomics capabilities allow the accurate measurement of not only common variations, but also the assessment of rare variation in key regions of the exome, and key splice-site and regulatory regions. Personalis can produce focused panels of genes of interest, including specialty-specific panels as well as easy-to-read reports describing the likely genetic influence on drug response.

Genome Analysis of Drug Trial Outliers

For customers engaged in drug development, we offer services to identify relevant variants that may explain unexpected drug responses in study subjects as part of a Phase I, II, III or post-market investigation. Personalis can combine its ACE technology with its proprietary and comprehensive pharmacogenomics database to identify and interpret sequence variation in key regions that may explain unexpected toxicity, dosing or efficacy effects. These studies may include small cohorts in an exploratory phase aimed at determining pharmacogenomic influences on response, or large case-control cohorts in which compelling statistical evidence is required. The Personalis analysis includes interrogation of documented Phase I and Phase II metabolic enzymes, transporters, as well as commonly assayed genes involved in toxicity and side effects (e.g. long QT syndrome, adrenergic, dopaminergic, and cholinergic pathways). In addition, Personalis can work with customers to interrogate specific genes known or suspected to be important for the therapy in question, in order to assess the role of genetic variation in explaining unexpected drug responses.

Cancer Research Studies


For customers studying inherited predisposition to cancer, we offer services for sequencing, alignment, variant calling, annotation, and analysis for identifying biomedically relevant variants.

Tumor / Normal Pairs

Personalis also supports sequencing of tumor / normal sample-pairs, including tumor samples from FFPE blocks. Our standard exome coverage for tumor samples is 16 Gb of raw data (passing filter), for every sample. This provides very high average coverage in order to maximize the chance of capturing driver mutations which may only be present in a small fraction of tumor-sample cells. We recommend ACE sequencing in order to surpass the accuracy and content of traditional approaches. Data analysis can be customized to meet specific customer needs.


Personalis® ACE Services for Research Selector

Research Areas
Features DiscoveryResearch ClinicalResearch CancerResearch
Optimized for Cost-effective variant discovery in large-scale studies Maximum variant detection for every sample Acccurate and comprehensive analysis of cancer samples with enhanced coverage of over 1,400 cancer genes
Output (Gigabase


3.5, 5, 6 Gb – average output per samples 8, 12, 16 Gb – minimum output guarantee 8, 16 Gb – minimum output guarantee
Example study types Screening, case control, longitudinal, pedigree Clinical research, FFPE sequencing, and low input DNA studies Tumor only / tumor pairs
Minimum sample committment YES – increments of 24 for fewer than 96 samples NO NO
Analysis included FASTQ, QC, and performance summaries FASTQ, QC, and performance summaries FASTQ, QC, and performance summaries
Additional analysis and annotation Aligned BAM, VCF, and VAR file with more than 40 public and proprietary databases Aligned BAM, VCF, and VAR file with more than 40 public and proprietary databases Cancer-specific analysis and annotation including somatic VAR, VCF, and annotation including COSMIC and Cancer Gene Census