Alex
@alexpellancheng.bsky.social
ohhhmics | Associate Professor at ETSmtl & CRCHUM | 🐶🧬☕️ 🐥
https://pellanchenglab.github.io/#join
https://pellanchenglab.github.io/#join
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!
August 14, 2025 at 5:41 PM
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!
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
Look at the author list, it's huge! Takes a village. Super proud of trainees Aaron, Sam and Sri
August 14, 2025 at 5:41 PM
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
Look at the author list, it's huge! Takes a village. Super proud of trainees Aaron, Sam and Sri
Patient vignettes in lung cancer patients also show concordance with scans. A huge thank you to our collaborators Drs Altorki and Saxena
August 14, 2025 at 5:41 PM
Patient vignettes in lung cancer patients also show concordance with scans. A huge thank you to our collaborators Drs Altorki and Saxena
We looked at patients with urothelial cancer, and found strong correlation between tumor-informed and tumor naive measurements. Great collaboration with Dr Bishoy Faltas
August 14, 2025 at 5:41 PM
We looked at patients with urothelial cancer, and found strong correlation between tumor-informed and tumor naive measurements. Great collaboration with Dr Bishoy Faltas
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.
August 14, 2025 at 5:41 PM
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.
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.
August 14, 2025 at 5:41 PM
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.
ppmSeq is a broad DNA sequencing method. The applications are endless. We looked at 2:
August 14, 2025 at 5:41 PM
ppmSeq is a broad DNA sequencing method. The applications are endless. We looked at 2:
Error rate analysis in sperm gDNA (🙏 Gilad Evrony) and cell-free DNA shows comparable error rates to duplex technologies.
August 14, 2025 at 5:41 PM
Error rate analysis in sperm gDNA (🙏 Gilad Evrony) and cell-free DNA shows comparable error rates to duplex technologies.
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!!!
CRAZY STAT: ppmSeq is a PCR-FREE method that works with ONE NANOGRAM of input. ONE!!!
August 14, 2025 at 5:41 PM
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!!!
CRAZY STAT: ppmSeq is a PCR-FREE method that works with ONE NANOGRAM of input. ONE!!!
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!
August 14, 2025 at 5:41 PM
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!
Turns out you can achieve this with PCR-free library prep, some (extremely) clever adapter design, and denaturation-free clonal amplification.
August 14, 2025 at 5:41 PM
Turns out you can achieve this with PCR-free library prep, some (extremely) clever adapter design, and denaturation-free clonal amplification.
What if we encode double stranded DNA into a single sequencing read? One read = one dsDNA molecule
August 14, 2025 at 5:41 PM
What if we encode double stranded DNA into a single sequencing read? One read = one dsDNA molecule
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.
August 14, 2025 at 5:41 PM
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.
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
This is ultra accurate, but also inefficient. You need to sequence a lot of reads to get modest amounts of duplexes
August 14, 2025 at 5:41 PM
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
This is ultra accurate, but also inefficient. You need to sequence a lot of reads to get modest amounts of duplexes
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!
April 11, 2025 at 9:38 PM
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!
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
April 11, 2025 at 3:53 PM
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
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
April 11, 2025 at 3:53 PM
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
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 🙏🙏🙏
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 🙏🙏🙏
April 11, 2025 at 3:53 PM
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 🙏🙏🙏
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 🙏🙏🙏
Mutational signature fitting allowed for PLASMA-ONLY ctDNA detection! No more need for tumor sequencing!!
April 11, 2025 at 3:53 PM
Mutational signature fitting allowed for PLASMA-ONLY ctDNA detection! No more need for tumor sequencing!!
We leverage this ultra-clean data to perform single molecule mutation calling, allows us to match melanoma patient plasma signatures to UV radiation signatures
April 11, 2025 at 3:53 PM
We leverage this ultra-clean data to perform single molecule mutation calling, allows us to match melanoma patient plasma signatures to UV radiation signatures
We developed error corrected WGS for the
Ultima Genomics platform, and measured error rates in the part per ten million range
Ultima Genomics platform, and measured error rates in the part per ten million range
April 11, 2025 at 3:53 PM
We developed error corrected WGS for the
Ultima Genomics platform, and measured error rates in the part per ten million range
Ultima Genomics platform, and measured error rates in the part per ten million range
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?
April 11, 2025 at 3:53 PM
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?
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 🤫😉)
Huge MRD implications (amongst others 🤫😉)
April 11, 2025 at 3:53 PM
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 🤫😉)
Huge MRD implications (amongst others 🤫😉)
Routine WGS would have been insanity in 2020 💰💰💰But today? Prices can be as low as 0$ per GB.
www.genengnews.com/topics/omics...
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
April 11, 2025 at 3:53 PM
Routine WGS would have been insanity in 2020 💰💰💰But today? Prices can be as low as 0$ per GB.
www.genengnews.com/topics/omics...
www.genengnews.com/topics/omics...