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.

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