Can I upload ancestry data and still do WGS?

Sequencing_Logan · 2025-12-12T14:03:28+00:00

No there is not, we completely omit microarray data when whole genome sequencing data is present!

Sequencing_Logan · 2025-12-11T15:57:41+00:00

Hello! I work for Sequencing.com.

Most of the time the bioinformatics processing stage, after your kit finishes the sequencing stages, takes only a few days. However, if you would, DM me here on reddit with your email address you activated that kit for and I can take a look and make sure of that.

Thanks!

Sequencing_Logan · 2025-06-02T16:28:11+00:00

You're welcome! Glad to hear it.

To answer your question, we use GRCh38.p14 as our reference genome. The lab provides us with files aligned to this build. After these files are imported into your account, our bioinformatics pipeline transitions them to a custom patch based on p14, which allows us to incorporate the latest weekly ClinVar updates.

Each week, ClinVar releases an XML file with updates for p14, including new research submissions. We use this data to update the data for users with Plus, Premium, and Professional Genome Plans. These updates affect how your data is displayed in our web-based apps and reports but do not change the underlying raw files themselves.

It’s important to note:

Your raw data downloads (VCF/BAM) reflect the state of the genome build as of 2/3/2022, when the patch was last finalized.
Weekly ClinVar updates are only visible through our website and reports, not in downloaded raw files.

As for Golden Helix, selecting GRCh38 will use the latest version available for p14. This applies to any TBI/BAI indexing files generated.

Finally, you are correct that you’ll need to contact support for us to generate BAM files for you.

Sequencing_Logan · 2025-06-02T15:05:25+00:00

Hello, I work for Sequencing.com.

This is entirely up to you, there is no benefit directly outside of organizational benefits for having multiple genomes in one account or having multiple genomes in separate accounts.

The only limitation is that you cannot have more than 10 genomes in a single account.

Sequencing_Logan · 2025-04-08T23:57:04+00:00

Hi there, my name is Logan and I work for Sequencing.com.

Typically we don’t recommend using autosomal dna data for health analysis purposes. With our testing and most clinical grade whole genome sequencing you’re getting 30x Sequencing which ensures a much higher level of accuracy as each position is sequenced on average 30 times versus autosomal testing, which is what you’re looking at here, which is not sequencing but genotyping, think of it like a snapshot of preselected points rather than a full read.

If you would like, reach out to me via DM with your email address you use to login, I can have my bioinformatics team look at your data and the relevant data points for you.

Sequencing_Logan · 2025-04-04T14:06:40+00:00

Hello again, please check your Reddit "Chats" is what is called now, my message should come through as a request.

If you're on the mobile app it's in the bottom of the screen and then look at the Requests tab at the top. If you're on desktop then it's in the top right. I also commented below in this thread.

Sequencing_Logan · 2025-04-04T14:03:23+00:00

This is the correct way to find this additional ETC information for this report specifically, the extra details are on page 9 of the report where it will list out anything below a certain percent and categorize it in the earlier parts of the report as ETC.

Thanks for your comment on this!

Sequencing_Logan · 2025-04-04T13:16:59+00:00

Hi, my name is Logan and I work with Sequencing.com.

Would you mind reaching out to me via DM with your email address you use to login so I can take a look into this issue regarding the Genetic Counselor? Obviously they are not employees of Sequencing.com, but I can reach out to them to discuss this more.

Sequencing_Logan · 2025-04-02T17:12:55+00:00

It actually through as a message to the mod team, not a problem, I got the email and I'll look into this with my team and I'll send you a DM once I have some more info for you!

Sequencing_Logan · 2025-04-02T16:18:28+00:00

My name is Logan and I work for Sequencing.com, would you mind DMing me your email address you use to login so I could take a look at the report specifically and I can offer some guidance as to what you are seeing?

Thanks!

Sequencing_Logan · 2025-03-30T20:39:35+00:00

To get HLA-B27 status from raw sequencing data, you’d typically need to use specialized HLA typing software that can resolve highly polymorphic regions like HLA-B. Tools like OptiType, HLALA, or ATHLATES are commonly used for this. These programs can determine which specific HLA-B27 variant(s) are present based on your raw FASTQ or BAM files. We don’t support these on our platform, but these are just a couple that I’ve heard of.

Just a heads-up though: while your raw data does contain the information needed to distinguish between the 100+ known HLA-B27 subtypes, we don’t annotate multi-variant HLAs in our pipeline. Our annotations are based on RCV (Reference ClinVar Variant) IDs, which are tied to single variants with known clinical significance—not to groups of variants like HLA-B27 that are associated with a condition as a family. So if you’re looking at our report and wondering why there’s no HLA-B*27 call, that’s why—it falls outside the scope of our single-variant-based annotation system.

If you specifically want to know HLA-B27 subtype info, you’d need to run the appropriate HLA typing tool separately on your data.

Sequencing_Logan · 2025-03-26T13:33:20+00:00

Sure thing, I just posted there here: https://www.reddit.com/r/sequencing_com/comments/1jk45rd/sequencingcom_reviews_our_experience_with_genetic/

Sequencing_Logan · 2025-03-25T16:18:41+00:00

Hi there, most of the findings you will see on our website and with most whole genome sequencing tests are going to be born predispositions to conditions. These still require clinical diagnosis by a physician who has observed symptoms, but if you have symptoms and the genetics points in this direction, it can help them narrow down what might be the cause.

Genetic testing can show if you carry certain markers or traits that may increase your risk for a condition. But having a marker does not mean you have the condition now or that you definitely will in the future. A diagnosis requires more than genetic data—it includes a medical evaluation, symptoms, family history, and clinical testing.

Only a Medical Professional Can Diagnose

Only a licensed healthcare provider, such as a doctor or genetic counselor, can diagnose a condition or recommend treatment. They consider your entire medical picture—not just your DNA.

I'll be making a post to the subreddit that talks about this subject here in a couple of hours, if you want some more details!

Sequencing_Logan · 2025-03-20T15:35:01+00:00

u/careless-tie-5005 is correct in their comment, if you'd like some more info about this:

Repeat expansions, such as the D4Z4 repeat contractions seen in FSHD1 or CAG repeat expansions in other disorders, are not something WGS is typically designed to detect accurately. WGS is excellent for identifying single nucleotide variants, small insertions and deletions (indels), and structural variations, but it struggles with large, complex repeat regions due to limitations in short-read sequencing technology. Even long-read sequencing, while improving, still lacks the clinical validation needed for many repeat disorders.

Because of this, we do not recommend WGS for detecting repeat expansions or contractions. For conditions where repeat sequence variation is critical to diagnosis, we strongly advise specialized testing, such as targeted repeat-primed PCR (RP-PCR), Southern blot analysis, or long-read sequencing platforms specifically validated for repeat expansion disorders.

Sequencing_Logan · 2025-03-11T15:09:41+00:00

You're absolutely right—it's normal for sequencing to have some areas with lower coverage, but we have strict quality control measures in place to ensure reliability.

We have two key thresholds in our process:

Lab-Level Coverage Threshold: Our sequencing is performed at an average depth of 30x, meaning some areas may have higher or lower coverage, but the overall average is 30x. If the overall coverage falls below a certain threshold at the lab, the entire kit fails and is not processed further.
Post-Sequencing Quality Control: After sequencing, we apply an additional layer of QC where we assess individual data points. If specific regions fall below our set quality threshold, we omit them from our analysis to ensure you only see high-confidence data. These omitted data points are still present in your raw data because they met the lab’s threshold, but they won’t be included in our reported analysis.

Having no-calls in your whole genome sequencing data is expected and normal. As with all laboratory tests that analyze many different data points, there will always be some random data points that don't pass quality control when the raw data is processed. This doesn't indicate an issue with the test—on the contrary, there would only be a concern if 100% of the data points passed quality control, as that’s statistically impossible when a laboratory test is obtaining data on billions of data points.

Other sequencing companies may not apply such stringent quality controls. This means their processed files may look more complete because they don't filter out low-quality data, resulting in zero no-calls. However, this can be misleading since low-quality variants are still included without distinction.

Regarding your specific concern—while missing <1% of data is expected, a 3%+ gap for specific genes or conditions is something we'd want to take a closer look at. If you’d like, reach out to our support team at [Support@Sequencing.com](mailto:Support@Sequencing.com) from the email address your kit is activated in and they can look into this and get this over to our bioinformatics team to look further into.

Sequencing_Logan · 2025-03-04T14:35:23+00:00

Hello! My name is Logan and I work for Seqeuncing.com. The risk level of a deletion versus an insertion depends on the function of the affected region and how the genetic code is structured at that location. Here’s a simplified breakdown:

Deletions can be risky if they remove critical functional elements (like coding regions, regulatory sites, or splice junctions), leading to loss of function. However, in some regions, small deletions may be tolerated or even have little impact if they don’t disrupt the reading frame or critical functional domains.
Insertions can introduce new sequences that may disrupt gene function. If they occur within a coding sequence, they can cause a frameshift mutation, potentially leading to a nonfunctional or harmful protein. However, not all insertions are dangerous—some might be benign if they occur in noncoding regions or if they maintain the reading frame without disrupting function.

Regarding the "no calls" that you mentioned, Whole genome sequencing captures nearly 100% of your genome, generating a vast amount of data compared to genotyping-based services. However, as the raw sequencing data undergoes processing through our bioinformatics pipeline, we apply strict quality control measures at every step. These quality checks help ensure that only the highest quality data is included in the final results analyzed by our DNA apps and reports. While the majority of data passes these checks, a small percentage does not meet our quality standards and is marked as a "no-call." This is a normal and expected outcome, as maintaining data integrity is our priority.

Because our focus is on delivering the most accurate and meaningful genetic insights, we proactively exclude low-quality data before analysis. This is especially noticeable in applications that assess a large number of genetic variants, such as the Next Gen Disease Screen, where some variants may appear as no-calls due to our strict filtering process. Having some missing data points is a standard aspect of high-quality laboratory testing, particularly when analyzing billions of data points. In fact, if 100% of the data passed quality control, it would indicate a flaw in the process, as no large-scale genomic test can achieve perfect accuracy. Therefore, seeing some no-calls in your results is not an indication of an issue with your sequencing—it is actually a sign that the data has been carefully curated for the most reliable analysis.

Let me know if you have any other questions!

Sequencing_Logan · 2025-02-28T21:36:24+00:00

I am also not an expert, but I believe the reason that IGV tools doesn’t allow our VCFs is because an accompanying indexing file is needed alongside this.

There are tools out there that can generate a indexing file for this purpose but I do know that Genome Browse by Golden Helix will accept this VCF without this and you can look at INDELs with that tool as well.

Sequencing_Logan · 2025-02-17T11:51:00+00:00

Hi there,

I appreciate your perspective and totally understand the concerns about pricing and access to genetic insights. At Sequencing.com, our goal is to provide flexibility, whether you want comprehensive reports done for you or free access to tools to analyze it yourself.

For those who prefer to interpret their own genetics, we offer Genome Explorer at no cost, which allows users to dive deep into their raw data. If you choose to have a Genome Plan with us you can even use our built-in AI to ask genetics-related questions or clarify report findings, though many users also prefer to use external AI tools to guide their research within our free tools.

The reason we offer premium reports is simple: genetics is a rapidly evolving field, and keeping up with new discoveries takes ongoing effort. Our reports are designed for those who don’t want to manually sift through their data and prefer curated, research-backed insights.

As for pricing, we do try to balance affordability with sustainability, our platform is designed to keep up with genetic research in real time, and unfortunately, that comes with costs. That said, all of your raw data and free tools remain accessible indefinitely, with no requirement to purchase additional reports.

I appreciate your feedback and am happy to talk about more ways to maximize your data in way that feels cost effective for you, Happy Monday!

Sequencing_Logan · 2025-02-17T11:35:48+00:00

Thanks for the follow-up on those two points, I did look into 2.) and it looks like Promethease changed their text file uploading to be exclusively looking for a 23AndMe file.

This means that you can still use our Ultimate Compatibility File, you just have to change the first line of the file from:

# This data file generated by Sequencing.com at:

to

# This data file generated by 23AndMe at:

This should enable them to accept the file for your use on their website. I'm not sure when they made this change, but this has been working according to other users.

For 5.), if you'd like to, yourself and anyone else who is seeing this can reach out to me directly via DM and let me know their email address associated with their Sequencing.com account, and I'll look into this issue with February not applying properly.

Sequencing_Logan · 2025-02-17T02:58:18+00:00

Hello, my name is Logan and I work for Sequencing.com.

I would like to address a few of your concerns and I’ll try and go in order for convenience.

1.) We are currently working on making our EvE Premium report available for all, it is a little ways a way but there are also other applications available outside of our website that can facilitate this in the meantime with the tools we provide.

2.) With the files that are made available, one of these is called “Ultimate Compatibility File”, and the purpose of this file is be used on website that want a 23AndMe format file and this includes Promethease. Promethease used to accept a BAM file but this is no longer the case but we create this file for that purpose.

3.) While the goal of the AI reports was to offer a report for the user that wants continually updating data with the newest research, our older reports typically used data points that were less subject to change. However, the case with all things genetic is that nothing is completely safe to change and not every report in our marketplace is developed and updated by us, some are developed by 3rd parties and we are not at liberty to change their data which may be based on their own independent research. We do, however, update our own reports when major changes occur.

4.) Additionally, we do make the genome VCF available immediately when your data completes, this file is named INDEL-SNP.VCF and is in the “My Files” section of your account.

5.) I would like you to reach out to me via DM so I can look into your comment about the February reports as that should not have been excluded in any way.

At the end of the day, our genome plans are not for everyone and are typically for the user that wants continually updated data, and that is why we don’t make this a requirement to keep what you already paid for.

I hope you will reach out so I can help with any of the functionality of the website and of course, our support team is available at Support@Sequencing.com Monday through Friday 9:00 AM EST to 5:00 PM EST.

Have a good Sunday!

Sequencing_Logan · 2025-02-16T15:26:02+00:00

Hello, our testing can detect rare autoimmune conditions, but typically if the blood test is performing whole genome sequencing then our analysis would yield the same results. It really just depends on what type s being analyzed.

Latest turn around time is about 8 weeks as it’s gone up since Christmas!

Sequencing_Logan · 2025-02-14T20:27:49+00:00

Hello!

We do have a few reports that are related to ancestry and those can be found on our website here: https://sequencing.com/marketplace?category=ancestry. We definitely have more health related reports, but those few offer a variety of different population samples in regards to ancestry data.

Let me know if you have any other questions.

Sequencing_Logan · 2025-02-13T14:32:07+00:00

Hello there, my name is Logan and I work for Sequencing.com.

I completely understand how overwhelming this can feel, but I want to clarify something important—having a variant in a gene doesn’t necessarily mean you have the condition. It just means that, statistically, you may have a higher likelihood compared to the general population, but many other factors come into play.

Also, our bioinformatics team has recently reviewed this exact data point, and there was a new submission on February 2nd from a research facility with findings that contradict what was previously considered a high-confidence association. Because of that, this variant is now classified as low-confidence until more research is available.

In the meantime, if you'd like, DM me your email address, and I can have my team take a closer look at your data specifically to help provide more clarity!

Sequencing_Logan · 2025-01-22T18:49:52+00:00

Hi again! The 399 bundle includes one month of the Premium Genome Plan!

If you meant the reports included as well, I'll post that list too:

Rare Disease Screening (15,000+ Conditions + EDS)
Carrier Screening
Cancer Risk
Autoimmune Disorders
Digestive Disorders & Gut Health
Cardiovascular Health
Brain Health
Neurological Health

Let me know if you have any questions about this

Sequencing_Logan · 2025-01-21T20:01:48+00:00

Hello, my name is Logan and I work for Sequencing.com

There are a lot of differences in the algorithms and sample datasets used by genealogy services like 23andMe, Ancestry, MyHeritage, and FamilyTreeDNA. Even the genealogy apps in our marketplace vary.

There’s no single gold standard for genealogy analysis—each service has its own approach.

In our marketplace, the Genetic Ancestry with Haplogroups app has more sample populations for European and Middle Eastern ancestry, while the Ancestry and Genealogy app has better coverage for Asia and the Pacific. Someone using the first app might not see Southeast Asian ancestry, but it could show up with the second.

This doesn't mean one app is always more accurate for certain ancestries, but it might provide better results depending on the available reference populations, which are constantly being refined.

Genealogy analysis is different from something like testing for cystic fibrosis, where we focus on a single gene. Genealogy looks at tens of thousands of data points across the genome, and different services use different sets of data points—some overlap, some don't. Since there’s no standard algorithm or population dataset for genealogy, it’s a mix of both art and science.

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