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Alex @alexpellancheng.bsky.social · Aug 14

We believe that these sorts of innovation will greatly serve the at large genomics community. More innovation = more options for scientists = more discoveries. Super exciting. Let's gooooooo!

Alex @alexpellancheng.bsky.social · Aug 14

Massive team effort. A huge thank you to the Ultima Genomics team, our clinical collaborators and sequencing team @nygenome.org
Look at the author list, it's huge! Takes a village. Super proud of trainees Aaron, Sam and Sri

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Alex @alexpellancheng.bsky.social · Aug 14

Patient vignettes in lung cancer patients also show concordance with scans. A huge thank you to our collaborators Drs Altorki and Saxena

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Alex @alexpellancheng.bsky.social · Aug 14

We looked at patients with urothelial cancer, and found strong correlation between tumor-informed and tumor naive measurements. Great collaboration with Dr Bishoy Faltas

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Alex @alexpellancheng.bsky.social · Aug 14

But what if you don't have the tumor? DOESN'T MATTER. ppmSeq is so error robust that you don't need tumor sequencing to detect ctDNA. Hello, new era of tumor-naive patient monitoring.

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Alex @alexpellancheng.bsky.social · Aug 14

Application 1: tumor-informed ctDNA detection. ppmSeq is perfectly suited for this. We sequence the tumor, and mine for mutations in the blood with ppmSeq. This enabled part per TEN MILLION ctDNA detection. PAR PER 10M. Insanity.

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Alex @alexpellancheng.bsky.social · Aug 14

ppmSeq is a broad DNA sequencing method. The applications are endless. We looked at 2:

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Alex @alexpellancheng.bsky.social · Aug 14

Error rate analysis in sperm gDNA (🙏 Gilad Evrony) and cell-free DNA shows comparable error rates to duplex technologies.

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Alex @alexpellancheng.bsky.social · Aug 14

Initial benchmarking shows massive scalability of ppmSeq, ~40-60% of our reads encode dsDNA molecules. The more you sequence, the more get dsDNA
CRAZY STAT: ppmSeq is a PCR-FREE method that works with ONE NANOGRAM of input. ONE!!!

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Alex @alexpellancheng.bsky.social · Aug 14

You can ID Watson and Crick strands using a mismatched adapter, and single-stranded artifacts cause a conflicting sequencing signal > this is naturally encoded as a low-quality base. You then just filter out the error!

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Alex @alexpellancheng.bsky.social · Aug 14

Turns out you can achieve this with PCR-free library prep, some (extremely) clever adapter design, and denaturation-free clonal amplification.

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Alex @alexpellancheng.bsky.social · Aug 14

What if we encode double stranded DNA into a single sequencing read? One read = one dsDNA molecule

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Alex @alexpellancheng.bsky.social · Aug 14

Beautiful works from amazing scientists seeks to address this. See work from Hoang (BotSeqS), Abasbal (NanoSeq) and Bae (CODEC) with bottlenecking and concatenation strategies. We took a different approach.

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Alex @alexpellancheng.bsky.social · Aug 14

State of the art error corrected sequencing methods incorporate some form of duplex sequencing, when both strands of a molecule are read to correct for error

This is ultra accurate, but also inefficient. You need to sequence a lot of reads to get modest amounts of duplexes

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Alex @alexpellancheng.bsky.social · Aug 14

Highly accurate sequencing OR high throughput? We refuse to choose.

Introducing ppmSeq, a method built to deliver both. Our latest from the @landau.bsky.social lab with Ultima Genomics
👀👀👀

See ⬇️ for a primer on the next frontier of genomics
www.biorxiv.org/content/10.1...

Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules

Distinguishing real biological variation in the form of single-nucleotide variants (SNVs) from errors is a major challenge for genome sequencing technologies. This is particularly true in settings whe...

www.biorxiv.org

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Alex @alexpellancheng.bsky.social · Apr 11

Thank you! An abbr version is in the Methods section (past the references, Cell-free DNA library preparation header). E-mail me if you’d like a step-by-step protocol!

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Alex @alexpellancheng.bsky.social · Apr 11

And that's it for now! A huge thank you to the patients and funders. This was a huge collaboration and this project simply does not happen without strong support from @nicorobine.bsky.social @gmboland.bsky.social @jeddwolchok.bsky.social @nygenome.org and a ton more

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Alex @alexpellancheng.bsky.social · Apr 11

Not only that can we resolve multiple signatures, we highlight many instances of patients with very little ctDNA, but appreciable SBS31. Interesting implications that highlight our ability to comprehensively monitor patients for ctDNA and chemo genotoxicity

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Alex @alexpellancheng.bsky.social · Apr 11

In @landau.bsky.social 's words ... "Amazing! So, what's next?"

Let's look at detecting multiple signatures. Can we resolve signatures from patients APOBEC3A (SBS2 + SBS13) AND platinum chemotherapy mutations (SBS31)
Phenomenal collaboration with Bishoy Faltas 🙏🙏🙏

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Alex @alexpellancheng.bsky.social · Apr 11

Mutational signature fitting allowed for PLASMA-ONLY ctDNA detection! No more need for tumor sequencing!!

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Alex @alexpellancheng.bsky.social · Apr 11

We leverage this ultra-clean data to perform single molecule mutation calling, allows us to match melanoma patient plasma signatures to UV radiation signatures

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Alex @alexpellancheng.bsky.social · Apr 11

We developed error corrected WGS for the
Ultima Genomics platform, and measured error rates in the part per ten million range

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Alex @alexpellancheng.bsky.social · Apr 11

Cost effective sequencing for tumor-informed ctDNA detection will let you sequencer deeper, or sequence more samples.. but can we develop tools that are only sustainable with cheaper sequencing?

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Alex @alexpellancheng.bsky.social · Apr 11

We evaluated the error modes of different sequencers and challenged our ability to detect ctDNA with part-per-million dillutions ... it can be done with deep sequencing :)
Huge MRD implications (amongst others 🤫😉)

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Alex @alexpellancheng.bsky.social · Apr 11

Routine WGS would have been insanity in 2020 💰💰💰But today? Prices can be as low as 0$ per GB.
www.genengnews.com/topics/omics...

Ultima Genomics Gives Away Sequencing for Free. Literally.

Ultima Genomics announces that it will provide three trillion DNA sequencing reads free of charge to researchers across the United States and Canada.

www.genengnews.com

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