Genome Explorer – Sequencing Support

What data can be viewed with Genome Explorer?

Genome Explorer enables you to explorer all formats and types of genetic data without having to download anything to your computer. This includes the ability to view data from whole genome sequencing, exome sequencing and genotyping (DNA microarrays).

If you've taken a DNA test or had your genome sequenced, you can explore your data with Genome Explorer. This includes DNA data files provided by any genetic testing laboratory as well as genetic test providers such as 23andMe, Ancestry.com, MyHeritage, Genes for Good, FamilyTreeDNA, Dante Labs, Nebula Genomics and Full Genomes.

Genome Explorer is accessible using any browser on any device including tablets and phones.

Do I have to convert my data into a specific format before using Genome Explorer?

Genome Explorer is already compatible with the format that your genetic data is already in. You do not have to modify or convert your DNA data file in any way.

Sequencing.com's unique Universal Data Compatibility technology enables all genetic data formats to be fully compatible with all DNA analysis apps including Genome Explorer.

Will I be able to understand the genetic data that appears in Genome Explorer and Genome Explorer Plus?

Genome Explorer and Genome Explorer Plus are designed for people who are comfortable interpreting their own raw genetic data. Interpreting your own data can become technical at times so it isn't for everyone.

If you find the data difficult to understand or simply want to learn actionable information about your genes, there are a wide range of apps in the marketplace in the Wellness, Nutrition, Fitness, and similar categories. These apps are designed to provide clear solutions for optimizing wellness and lifestyle.

I'm female but my Genome Explorer shows a Y chromosome. Why is there a Y chromosome?

The image of chromosomes at the top of your Genome Explorer is the same image for everyone. It shows all of the chromosomes that can exist for a human and is not related to your specific DNA data.

The image of the Y chromosome (as well as the image of all other chromosomes) appears the same in everyone's Genome Explorer, including for all males and for all females.

If you are female, this doesn't mean you have a Y chromosome. You can explore this further by clicking on the image of the Y chromosome. For females, the column 'Your Data' will show all dashes "-", which means no data was detected. Having no data detected on the Y chromosome is consistent with there being no Y chromosome.

How can I ask questions and get help for understanding my data? Is there anyone I can ask?

Yes, assistance is available from a certified genetic counselor. To speak with a genetic counselor, please use the Genetic Counseling app.

What's the difference between Genome Explorer and Genome Explorer Plus?

For information about Genome Explorer Plus, please click on the 'Genome Explorer Plus' tab on this page.

Why are genes or genetic variants missing?

When viewing any version of Genome Explorer, only the raw data contained within your genetic data file will be displayed. If a gene wasn't tested for, data on that gene won't be displayed.

This doesn't mean you don't have that gene! Instead, it means your DNA test didn't provide results for that gene.

This occurs because some types of DNA tests only test a part of your genome instead of your whole genome. Tests performed by the following test providers only test a part of you genome: Ancestry.com, 23andMe, MyHeritage, FamilyTreeDNA and similar companies.

Testing your entire genome, which means sequencing all of your genetic data, is called 'Whole Genome Sequencing'. Only whole genome sequencing will provide data on all of your genes. Learn more and compare genome sequencing services.

Why is there missing data for some genetic variants?

If information appears to be missing from a row then this means the information doesn't exist for that specific variant.

For example, a variant may exist within a gene and therefore the 'Gene' column will be blank. Another variant may not have any known condition associated with it and therefore the 'Condition', 'Interpretation, 'Review Status' and 'References' columns will be blank.

My data is from Sequencing.com's Ultimate Genome Sequencing service but when I search for a rsid, I can't find it. Shouldn't all rsid's be found in my whole genome?

If a rsid, such as rs74956615, is not detected then this means the chromosomal position for that rsid (the position within the genome) is located with a 'homozygous reference block.'

A block is two or more consecutive positions within the genome that are all homozygous reference. Homozygous reference means your result at that position is the same as the reference genome.

Some blocks can be ten of thousands or even hundreds of thousands of positions in length. When a rsid exists within a block, it won't be detected by searching for that rsid. Instead, please try searching by 'Position', which for rs74956615 is 10317045. You can determine the position of a rsid using the dbSNP database for rs74956615.

When searching the Position column for 10317045, the result should be the block that contains this position, which should list the start position, the end position, and the first letter of the sequence. We don't list the entire sequence of the block as it could be enormous in size.

Checking dbSNP for rs74956615 shows that the reference genome has a 'T' at position 10317045 on chromosome 19, so your result for rs74956615 will be TT.

When I search for a gene, why do the results show a different gene?

Most gene names have aliases (also known as synonyms). For example, the BRCA1 gene is also known as BRCC1, BROVCA1, FANCS, PNCA4, PSCP and RNF53. Each of those names is an alias for the same gene. This can get pretty confusing!

Genome Explorer takes this into consideration and makes it easy to search using any alias. Simply search for any alias the gene is known by and Genome Explorer will always know what gene you are referring to.

For example, if you search for FANCS, Genome Explorer will know this is the same as the BRCA1 gene. The search results will show all of your data that's associated with the BRCA1 gene.

It's also important to point out that if you search for FANCS, the results will not show 'FANCS' in the Gene column. Instead, BRCA1 will appear. This is because BRCA1 is the most widely used name for this gene. (The most widely used gene name is also known as the HGNC Approved Gene Symbol.)

So if you search for a gene and a different gene name appears, it's because each name is an alias for the same gene. You can verify gene aliases at HGNC's GeneNames.org.

Why does Genome Explorer show data that I can't find in my data file?

Some data files may not contain a rsid (also known as a rs#) for a variant. Instead, the file may identify the variant simply by it's chromosomal coordinate or the file may use an alternative identification system. Genome Explorer is very advanced and if a data file does not include a rsid for a variant, Genome Explorer will try to add this information.

For example, 23andMe files identify some variants by an i# instead of a rsid. While the i# is an ID system used only by 23andMe, the rsid is the ID used by all scientists throughout the world. Because the rsid is universally recognized as the standard nomenclature for variant identification, Genome Explorer will always try to indicate the rsid for a variant even if the original data file doesn't include the rsid.

While Genome Explorer always tries to assign a rsid to a variant, sometimes this is not possible. For example, a rsid may not appear for a variant because a rsid has not yet been established for that specific variant.

If I see a disease listed, does it mean I'm at risk for that disease?

When you see a condition (disease, trait, medication reaction, etc. ) in Genome Explorer Plus, it doesn't mean you have an increased risk for that condition.

When a condition appears in Genome Explorer, it means that the genetic variant listed in that row has been associated in scientific research with that condition. Whether your genetic data indicates that you are at risk of that condition will depend upon the interpretation of your raw genetic data. Your raw genetic data is located in the 'Genotype' column.

Example:

If variant rs123 is associated with Cystic Fibrosis, anytime data contain genetic testing results for rs123, even if the results indicate no-risk, Genome Explorer will include rs123 and will show that this variant is associated with the condition 'Cystic Fibrosis.'
On a technical level, if rs123 has reference allele C and alternative allele T then this means that Cystic Fibrosis risk is likely associated with the "T" allele. If the genetic testing results shown in the 'Genotype' column is 'CC' then there is no risk of Cystic Fibrosis due to variant rs123. But if the Genotype column is 'CT' or 'TT' then there may be a risk of Cystic Fibrosis.

Get help understanding your genetic data: Use the Genetic Counseling app to speak with a genetic counselor.

The word 'Pathogenic' appears in the 'Interpretation' column of my Genome Explorer. Does this mean I'm at risk for the condition?

Genome Explorer does not perform any analysis about whether you do or do not have a risk for a condition. Because of this, Genome Explorer will not state that you are or are not at risk for any condition. Only the apps in the 'Health' category of the App Market provide analysis as to whether you are likely to be at increased risk of a condition.

When it appears in Genome Explorer, the term 'Pathogenic' is determined only by the variant, not by your genetic data. Everyone's Genome Explorer that lists that same variant will always show the same data in the interpretation column.

For example, if person A and person B both take 23andMe's DNA test and then they both use Genome Explorer to explore their DNA data, they will have the same list of genetic variants (because 23andMe performs the same test for everyone). While the results for each genetic variant will be unique between person A and person B, the list of variants will be exactly the same.

Since person A and person B will have the same list of variants, they will also have the same information in the 'Interpretation' column of their Genome Explorer. This is because the information in the Interpretation column is associated with the variant.

If 'Pathogenic' appears in the Interpretation column, this is because researchers have identified the variant as being associated with the condition. This is why the term 'Pathogenic' is used. The term Pathogenic does not mean that you have the variant or that this variant is harmful to your health.

The word 'Interpretation' and all the terms in that column such as 'Pathogenic' are official terms obtained directly from the NIH's ClinVar database. Please see the table at the end of this section for more information about the meaning of the terms in the Interpretation column.

Have a question about your DNA data? Use the Genetic Counseling app to get answers.

Why is my SV (Structural Variations) VCF incompatible?

SVs are very complex genetic variations. Sequencing.com is compatible with the most modern way of representing SVs in a VCF file. If your SV file is not compatible with Genome Explorer, it is most likely because your the file was produced using an alternative data structure.

For example, we've identified SV VCFs generated by Dante Labs with 'WGZ' in the filename, such as *.wgz.sv.vcf.gz, use an alternative data structure to represent SVs. Because of this, most SV files with WGZ in the filename was incompatible with Genome Explorer.

Why does my data sometimes reload when I access Genome Explorer again?

Sequencing.com's Bioinformatics Team releases updates to Genome Explorer on a weekly basis. Some of these updates require the genetic data from your file to 'reload' in your Genome Explorer. This helps ensure you always benefit from the most up-to-date version of Genome Explorer.

Reloading of data in your Genome Explorer is both free and fully automated. It will occur only if there has been an update since the last time you accessed your file's data using your Genome Explorer.

Definitions of the values in the 'Interpretation' column.

Interpretation Value	Additional Information
Benign	As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Likely benign	As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Uncertain significance	As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Likely pathogenic	As recommended by ACMG/AMP for variants interpreted for Mendelian disorders.
Pathogenic	As recommended by ACMG/AMP for variants interpreted for Mendelian disorders. Variants that have low penetrance may be submitted as "Pathogenic"; please also include information about the penetrance in a "Comment on clinical significance
drug response	A general term for a variant that affects a drug response, not a disease. We anticipate adding more specific drug response terms based on a recommendation by CPIC.
association	For variants identified in a GWAS study and further interpreted for their clinical significance.
risk factor	For variants that are interpreted not to cause a disorder but to increase the risk.
protective	For variants that decrease the risk of a disorder, including infections.
Affects	For variants that cause a non-disease phenotype, such as lactose intolerance.
conflicting data from submitters	Only for submissions from a consortium, where groups within the consortium have conflicting intepretations of a variant but provide a single submission to ClinVar.
other	If ClinVar does not have the appropriate term for your submission, we ask that you submit "other" as clinical significance and contact us to discuss if there are other terms we should add.
not provided	For submissions without an interpretation of clinical significance. The primary goal of ClinVar annotations within Genome Explorer Plus is to archive reports of the clinical significance of variants. Therefore submissions with a clinical significance of "not provided" should be limited to: "literature only" submissions that report a publication about the variant, without interpreting the clinical significance "research" submissions that provide functional significance (e.g. undetectable protein level) but no interpretation of clinical significance "clinical testing" or "phenotyping only" submissions from clinics or physicians that provide additional information about individuals with the variant, such as observed phenotypes, but do not interpret the clinical significance

Searching Genome Explorer - Best Practices

As for genome explorer when searching by a position the first search field should be "Chromosome" and should be the chromosome # and the second search field should be the position.

As an example to search for TNXB we set the search to Position and enter the position as 6:32115334. The number 6 is the chromosome and 32115334 is the position on chromosome.

An improved Genome Explorer v3 is set to launch within a few months, I happy to extend and offer to be a betta tester.

Reference: Clinvar, GeneCard, dbSNP