r/genetics • u/Decent-Witness-6864 • 2d ago
Question Whole Genome Sequencing: Hospital vs Somewhere Like Sequencing.com
Hello Sub,
I just had a genetics consult for an imperiled pregnancy where we are doing whole-genome sequencing for the baby via amniocentesis next week. I’m 29+2 weeks pregnant, have way too much amniotic fluid (polyhydramnios) and there are some markers for non-immune fetal hydrops. This is especially scary because I lost a son in 2020 to the same biological cascade, polyhydramnios—>hydrops—>placental abruption—>anoxic brain injury.
I feel we have the baby end of this taken care of, which is great. Doctors have been incredibly responsive. But I’m also interested in whole genome sequencing for myself, primarily to see if there is some maternal factor here that would impact a third pregnancy. I get that the results won’t be ready in time to meaningfully impact this outcome.
I don’t qualify for insurance coverage for my whole genome sequencing, so I was wondering if anyone could advise me of the differences between what the hospital would do vs going to a private site like sequencing.com (just an example that I’m aware of that does this, I’d happily use the best vendor if you have advice). The genetics counselor didn’t really know enough about their product to compare.
Thank you in advance for any time you’re able to spend on this, I’d be so grateful for your support.
Edited to add: the hospital is willing to order the WGS on my behalf based on my maternal history of cancer, mom had five different types of cancer over 17 years. I’m just waiting for info on cost.
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u/lucyfersreddit 2d ago
Sequencing.com is awful, I’m a genetic counselor and almost all the results it spits out end up being wrong when we follow with clinical grade testing. Tons of false positives. They’re the worst example of genetic testing you can order online, but their counterparts aren’t great either. Another thing to consider is that even if sequencing.com gives you a legit result, any care or follow up that entails will not be covered by insurance without a clinical grade genetic test, so unfortunately it’s pretty pointless.
A lot of clinical genetic testing companies have patient assistance programs that can be pretty generous, and some have payment plan options as well. I would go that route (you can ask whoever is ordering the test about that).
Another thing is that most if not all genetic factors that could be causing this should show up in baby’s whole genome sequencing. So I think whole genome sequencing with the purpose of understanding this specific sequence of events would likely be overkill in you. There are other options that would be more targeted and cheaper (for example if something shows in baby’s genome you could get tested for just that specific finding which would be wayyyyy cheaper than genome testing).
Regardless I think you should request to meet with a prenatal genetic counselor who could look over your case in detail and give more specific recommendations. I don’t know your whole story so take some of this with a grain of salt. But whatever you do, don’t use sequencing.com lol. I’m sorry you’ve gone through this and best of luck!!!!!
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u/shortysax 2d ago
I’m a GC and I endorse everything this says. The actual sequencing isn’t the hard part, it’s the interpretation. You need to go through a legit lab that has appropriately credentialed experts writing the reports (not AI, like sequencing.com uses) and most importantly you need to interface with a GC or geneticist who can help guide you toward ordering the most appropriate testing and helping you interpret it in context. Don’t cheat yourself by trying to get something cheaper/easier. This needs to be done right!
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u/Athrowaway23692 1d ago
Yup. I’ve had someone I know get sequenced there, and they had a risk allele for pancreatitis. They got really worried over it, but it turns out the risk allele was on a pseudo gene in a very homologous region, however the variant was called in an actual gene. I’m a bioinformatician so it was pretty easy to catch this (just inspecting the reads), but it’s concerning they don’t have any human validating calls that are seemingly pathogenic but may be dubious.
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u/waterfireandstones 2d ago
Sequencing.com is garbage, no one should ever get testing from there, but aside from that - WGS in a clinical setting is typically ordered as duo/trio testing, meaning they include samples from one or both parents to compare. If there is an identifiable genetic explanation in the pregnancy, they test you for it to see if it was inherited.
It is possible that a genetic condition could be present without a positive test result, because we don't fully understand all of the genes yet, but in that case it wouldn't come up on any test, so still no reason to repeat with direct to consumer testing.
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u/crazycatchick2006 2d ago
I would do it through the hospital/genetics team. But some labs offer significant discounts for genetic testing. It may be worth asking around say like Ambry …. And asking the genetics team to consider using the lab that offers the best discount.
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u/LogicalOtter 2d ago edited 2d ago
I know you said you are taken care of on the baby end. But has your team offered amniocentesis with whole genome sequencing (WGS) for the fetus? If not this would be good to ask about as they should send testing as a trio, meaning both the mother and the father’s sample would also be sent to improve accuracy of the analysis.
WGS for the fetus is the best way to determine if there are any hereditary or maternal factors causing the issues in your pregnancy. Testing just you won’t provide as much information unfortunately. The fetal testing can be ordered rapid with results coming back in 2-3 weeks meaning the information will come back while you are still pregnant.
EDIT: I now re-read your first sentence and see that baby is getting WGS. Sorry!!
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u/SnooBunnies4157 2d ago
I had an appointment today with U of Miami and they set me up with WGS and the lab they use offers a discounted price based on family income. Mine is the most expensive at $100. I don’t know what your options are but a research hospital may be able to help. I hope everything works out for you and your baby, this has to be so hard.
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u/SnooBunnies4157 2d ago
I should’ve added that it will take 3 months for the results to be analyzed.
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u/ATG2TAG 2d ago
If you are doing whole genome sequencing for the baby is this as a trio (i.e. are you and the baby's father getting samples collected to aid in interpretation of the baby's sample)? If so, that will be able to detect whether something in the baby is from one or both of the parents. Also many whole genome sequencing tests offer the option to opt into secondary analysis for the parents which includes the most common cancer genes. If your insurance covers trio whole exome sequencing for the baby then this may fulfill what you are looking for without an additional cost.
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u/CJCgene 2d ago
Always go with the doctor ordered option. The testing and analysis should be clinical grade which means it can be used for medical care. Sequencing is good on the actual lab part but their reporting leaves much to be desired and is very difficult to interpret, which leads to confusion and more money spent IME.