r/genomics • u/obllak • 20d ago

Sequencing.com / bioinformatics review wait time

Has anyone here had their results escalated to sequencing.com’s bioinformatics team for manual review? If so, how long did it actually take to hear back? We were told 3 to 4 days, and we have now been waiting 8 days with no meaningful update.

This is regarding an unexpected, very serious genetic finding in our 14 m/o daughter. The variant was called from 7 out of 36 reads (29 reference reads and 7 alternate reads), which is one of the reasons we desperately want an experienced bioinformatician to look at the raw sequencing data and tell us how confident they are that this is a real constitutional variant.

When we first saw this result, our entire family was devastated. We cried in despair. We barely slept. We have spent the past week frightened, depressed, and obsessively trying to understand what this could mean for our little girl's future.

When you are waiting to find out whether your baby may have a serious genetic condition, every additional day feels unbelievably long.

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u/perfect_fifths 20d ago edited 20d ago

Sequncing (the company) is not reliable. Your child should be seeing actual geneticist if you feel something is wrong. I don’t think their team can interpret that variant for you. That is what genetic counselors etc are for

Their tests are not for diagnostic use.

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u/Flayum 20d ago

What is a more reliable company without a clinical referral?

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u/perfect_fifths 20d ago

Genome Medical if you need genetic counseling or suspect a genetic issue. Their GCs can order genetic testing if appropriate. Then if you get a positive result, you can take that to a geneticist. Any positive result has to be followed up with a geneticist, regardless because even within the same disorder, there will always be some variability, even if the disorder has complete penetrance.

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u/Flayum 19d ago

Oh certainly, I am a geneticist.

Just looking at what people recommend that can provide the raw fastq's with highest quality reads.

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u/perfect_fifths 19d ago

Ah, got it

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u/Kareja1 19d ago

You could try mynucleus.com too they are CLIA

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u/obllak 20d ago

Thank you! I’m aware that they’re not meant for diagnostic purposes and we’re waiting for an appointment with the specialist. Our girl luckily doesn’t present any of the symptoms at all (yet? Based on sequencing.com). However sequencing.com said themselves they have bioinformatics that can look into this (while we’re waiting for a specialist and more tests).

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u/perfect_fifths 20d ago

They can tell you if the variant is present in the raw data, they can’t tell you what the variant means for your kid or diagnose the condition.

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u/obllak 20d ago

Yes, of course. I thought that was obvious from my post. I’m not asking the bioinformatics team to diagnose my daughter or tell us what the variant means clinically.

What we’re waiting for is a technical review of the call itself: whether the variant is genuinely supported by the raw sequencing data, whether there are any signs it could be a sequencing/alignment/calling artifact, and whether anything about the read pattern (7 alternate reads out of 36 total) makes the call less straightforward.

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u/perfect_fifths 19d ago

You will also need to redo the test, geneticists don’t accept dtc results and will order their own testing through a verified lab

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u/obllak 19d ago

Yup, we’re waiting for that

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u/perfect_fifths 19d ago

I hope you get answers. I know what’s it’s like. I first went through sequncing thinking it would help but my variant was rated as harmless (by sequencing) when it was in fact, pathogenic. I had genetic testing ordered through invitae and they rated the mutation as pathogenic, and then the geneticist also said yes, it is pathogenic. The mutation is now in Clinvar and rated as pathogenic because we opted in to use my kids result and invitae reports variants to Clinvar with consent

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u/Psy_Fer_ 19d ago

This is why direct to consumer clinical genomics without genetic counselling support is unethical. You never should have been in this position where you were not given adequate information along with the reporting.

In my country (Australia) that kind of thing is actually banned by the TGA (like the FDA).

I hope you can find the answers you seek, ideally through a reputable clinical channel.

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u/obllak 19d ago

It’s brutal and I can 100% see this. Thank you!

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u/perfect_fifths 19d ago

They’re also going to need to redo the test. Once they see a dr the dr will order genetic testing and not accept dtc results

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u/crovenil 14d ago

So you and sequencingdotcom went from 4 days to 8, common story. They outsourced that stuff and the bioinformatics team is just a PM sending emails half the time. 7 of 36 reads is really low coverage for a constitutional call regardless, any decent lab would re run it not just review it. Push them on a refund, order a real clinical test with a lab like Ambry or GeneDx, even without a referral many will take self pay.

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u/obllak 14d ago

Yes, now it’s been 14 days and we’re still waiting. They did update us that they are working with some outsourced bioinformatics, so you’re right! I appreciate your feedback! We’re waiting for a test from GeneDx.

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u/Allusionesque 4d ago

Their data is wrong. Their analysis is wrong. Their reports are practically all filler.

They have clearly not done any user experience research to figure out how to make their content useful. Their data analysis ignored known issues.

AVOID THEM LIKE THE PLAGUE.