GeneSavvy Variant Exploration Report

Convert your raw data into actionable information!

Our Variant Exploration Report is included with our GeneSavvy Starter Kit and was built to utilize the specialized data generated by our Genesavvy Starter Kit lab processes. If you do not yet have raw data, or if you have genetic data generated by other genetic testing companies, we highly encourage you to order the GeneSavvy Starter Kit so you can take full advantage of our functional genetic tools. However, if you already have raw genetic data files from another genetic testing company, you can still order a GeneSavvy Variant Exploration Report, although it may not contain all the specialized data that requires GeneSavvy’s testing standards.

GeneSavvy Variant
Exploration Report

$125

VIEW SAMPLE REPORTAdd to cart

The Variant Exploration Report information includes:

  • All Genetic Variants found by our Enhanced Human Whole-Exome Sequencing (WES)
  • All Genetic Variants found by our Mitochondrial Whole-Genome Sequencing (mtWGS)
  • Genotyping data and SNPs curated for functional medicine practitioners
  • HLA Subtypes found (Human Leukocyte Antigens)
  • KIR Subtypes found (Killer-cell Immunoglobulin-like Receptors)
  • RCCX gene module information
  • And more***

***We are continuously pioneering new analysis tools to help identify functional genetic patterns between disease associated rare variants, lifestyle changing polymorphisms, real-time protein/enzyme activity, and environmental factors which we use to provide actionable options for vibrant life longevity. Many of these tools can be used to enhance and add information to your GeneSavvy reports without the need for cellecting new saliva samples and re-testing.

Functional data enrichment

Data enrichment is all about creating more actionable insights through associations. We’ve built our own custom enrichment database that is full of clinical actionability for functional health practitioners.
We are constantly adding new information to our databases, providing new insights into gene/variant associations with health-related pathways, cellular & molecular functions, lab biomarkers, interactions with pharmaceuticals, food/nutrients, environmental factors, vitamins/herbs, and MORE. Our roots are in functional medicine, so our enrichment data is geared around terms that functional health practitioners can easily use to guide action.
*Not all genes/variants are currently enriched by our database. Our database will continue to grow as research continues.

Built for functional medicine

Our reports were built with functional medicine practitioners in mind, so the results and terminology used in our reports will be easy to understand and work with in functional clinical settings.

Personalized results

We use genetics to develop more personalized approaches to functional medicine. That’s why we prioritize the less common variants found in each gene, those are the genetic markers that make people different!

Actionable genetic associations

We work hard to include clinically-actionable associations for the results outlined in our reports. Those actionable associations can include further recommended lab testing, treatments, clinical action bullet points, and environmental interactions related to the genes and gene networks.

Battle tested

All of our genetic reporting tools began as custom-built solutions for real-life cases in which we were contracted to help practitioners get better insights into finding the missing pieces keeping their patients from making progress. The custom reports built to break ground for those patients and practitioners have been redesigned to produce the reports we offer to you today.
If you need a custom genetic tool or report built to help assist in a complex health case, please contact us at [email protected]

Treatment modalities combined

Our GeneSavvy advisors, panel curators, and action research experts have come together from many different modalities of the health industry to provide a well-rounded set of genetic data assocations without bias towards one approach or another, its all about providing the best insights for you in all aspects of health! Some of the backgrounds of our experts include:

Medical Doctors
Functional Medicine Practitioners
Naturopathic Doctors
Doctors of Osteopathic Medicine
Chiropractors
Genetic Counselors
Nutritionists and Other Functional Health Professionals.

Turn Around Time

Once you purchase this service, you will receive an email with a link to submit your VCF file. If you do not receive the email within 30 minutes of completing the order, or need help with your VCF file, please contact us at [email protected]

Once your genetic raw data files are uploaded we will start working on your data conversion! You should recieve your GeneSavvy Variant Exploration Report delivered to your email within 1 business day. Our office is open Monday-Friday, so orders placed on Friday may be delivered on Monday. If you do not receive your report within 1 business day, please contact us at [email protected]

This estimate is assuming the VCF file submitted is in the correct format, and without errors. If the VCF file is not in the correct format we will contact you to try to correct the problem. Most problems can be fixed, but may add to the turn-around time.

With a quick upload you can squeeze more info out of the data you already have!

Step 1

Make sure you have a VCF file type.

Your file(s) must be VCF files. It’s not uncommon for raw data from your lab to be divided into more than one file; make sure all of them are VCF files. If you have genetic data in the form of a TXT, BAM, or FASTQ file contact us at [email protected] or (425) 686-0000.

Step 2

Compress the file(s)

Because raw data files can be large, and because there can be more than one file per person, we require you to compress your files before uploading. Most Windows and Mac computers have a built in file compression option on right click. The compressed file will usually have a .zip or .gz extension. If you are submitting data for more than one person (such as in the case of submitting all members of a family) please compress the files for each person separately.

Step 3

Upload

Once you pay for the Variant Exploration Report you will be prompted to upload your file(s). Your upload request email should show up within half an hour. Please check your spam and trash folders. If you don’t receive an upload request email, please contact us at [email protected] or (425) 686-0000.

Step 4

Receive your report

Once your files have been successfully uploaded, your report should be available for you to download within 24 hours. If you don’t receive your report, please contact us at [email protected] or (425) 686-0000.

Lab Testing

This test was designed to sequence the exons and canonical splice sites (+/1,2) of the whole exome including extra coverage genes associated with Medical Disorders and treatment options. GeneSavvy has developed highly advanced protocols to target and extract variants in exonic regions, intronic regions of interest, splice sites, and untranslated gene regions of interest with the following technical specifications:

Mean depth of coverage: 100x
Specificity:>98%
Sensitivity: >94%

Insurance CPT Codes

GeneSavvy currently does not work with any insurance payments. However, we do provide any information we can find to help you self-submit to your insurance for potential reimbursement for our tests or services.

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Database

Our reports are built using our proprietary pipeline combined with manual curation to provide the most valuable and actionable results we can find. We utilise the following databases to build actionable results for you.

Gene/Variant Definitions

  • BUILD: hg19
  • RefSeq
  • UCSC
  • ENSEMBL
  • GENCODE
  • dbSNP
  • Population Frequency
  • 1000 Genomes Project
  • ExAC
  • NHLBI-ESP
  • gnomAD
  • Complete Genomics

Splice Site Predictions

  • dbscSNV

Functional Variant Predictions

  • SIFT
  • PolyPhen2
  • LRT
  • Mutation Taster
  • Mutation Assessor
  • FATHMM
  • PROVEAN
  • MetaSVM
  • MetaLR
  • VEST
  • MitImpact
  • regSNP
  • LoFtool
  • GeneSavvyDB
  • M-CAP
  • CADD
  • GERP++
  • DANN
  • Eigen
  • GenoCanyon
  • fitCons
  • PhyloP
  • SiPhy
  • Revel
  • InterVar
  • RVIS-ESV
  • GDI
  • TMC-SNPDB

What if you don’t have a VCF file?

VCF files contain the list of genetic variants that differ from a reference human genome. They are more popular than raw genetic sequencing files (.bam, .sam, .fastq) because of their smaller size, which makes them easier to work with. Most genetic sequencing labs will provide you with a VCF data file you can use for GeneSavvy’s secondary analysis services such as our Variant Exploration Service or any of our other Health Report Services. It is also possible for us to take certain BAM files but it requires manual work on our part so incurs extra fees. If you have a BAM file, please contact us.

Common File Types for Genetic Sequencing Data other than VCF:

FASTQ
FASTQ files are usually fresh off the sequencing machine! They contain raw
genetic reads that still need to be aligned to a reference genome before they
can be processed. These files generally come in pairs of 2 so you’ll see people
reference these files as “paired FASTQ files”. When FASTQ files are aligned to a
reference genome, it produces a .BAM file.

BAM
BAM files are made from the process of aligning a FASTQ file to a reference
genome. These files are generally very large (several GB) and contain raw
genetic data organized in a way that can really only be understood by
specialized software. One more processing step that groups the raw data and
removes redundancies produces a much smaller VCF file.

TXT
TXT files also usually contain the actual variants found, but they are usually
from a genotyping process instead of sequencing. These are usually common files
used by ancestry genetic testing companies and are not considered diagnostic
grade data. These TXT files also contain variant calls and non-variant calls
used for genotyping and common SNP information.

GeneSavvy Reports
Our Variant Exploration spreadsheet files take the data from VCF or TXT files
and organizes it in a way that makes it easier to explore and utilize with
regards to functional health. Gene names, variant predictions, related health
conditions, rarity, and predicted impact are all included in our reports, plus
much more. This allows you to explore all the functional aspects of thousands of
genetic variants in a much simpler way.

The GeneSavvy Variant Exploration Report is in BETA: Version 0.7, “Ugly Duckling!” Anyone who orders the BETA version now (as a part of the Starter Kit) will receive free upgrades through V1! Offer only available for the current BETA Variant Report version of Starter Kit. Support our BETA and grow your data with us!

Doctors, do you need kits for your office?CONTACT US