Biostatistician @ University of Wisconsin-Madison. Scientist @ Qiongshi Lu's group. 子曰:“学而不思则罔,思而不学则殆。”

Wisconsin, USA
Joined April 2019
In March 2024, at the age of 35, I was diagnosed with stage IV rectal cancer with a metastasis in my liver. This was a shock: I had no family history, and none of the doctors suspected it. After two years of chemotherapy, radiation, and multiple surgeries, I'm still not cured. Now I'm asking for help to get a personalized cancer vaccine. This is my story so far. Following diagnosis, I was treated with total neoadjuvant therapy at UCLA. I had 6 weeks of radiation and chemotherapy (Xeloda). This was followed by 6 rounds of oxaliplatin infusions and Xeloda. I tolerated this unusually well. During this period, I managed to hike up to over 11,000ft multiple times in the Sierras, and I wrote the main text of a 72 author meta-analysis paper and submitted it to Nature where it is still in review. I showed a good clinical response, and at the end of October I had surgery: I was under for 9 hours, and they cut out a bit of my rectum, 1/3rd of my liver, and gave me a temporary ileostomy. Waking up from this was probably the strangest experience of my life: I felt more machine than man, and I had wild hallucinations form such a large dose of anesthesia. It took a while to feel OK after that surgery. However, I still had the ostomy. I had that reversed at the end of January in another surgery, which took a greater toll on me than I expected. I only just started to feel OK again and I got bad news: I got a positive circulating tumor DNA test (ctDNA), the signatera test from natera. Unfortunately, the ctDNA carried on rising, and in July 2025 a new lesion appeared in a lymph node near my liver (periportal). I was treated with irinotecan and panitumumab infusions, which showed a good response, followed by live MRI guided SBRT radiation treatment to the lesion. However, after finishing this treatment, the ctDNA remained positive and began rising again. I restarted irinotecan and panitumumab infusions, which brought ctDNA back to negative (signatera), although it remained positive on the more sensitive Personalis assay. During this period I had begun to develop stomach pain and digestive symptoms. Then I collapsed vomiting blood while out in Santa Monica and was rushed to the ER. They found out I had a duodenal ulcer that had bled. I had some blood transfused, and I was sent home to complete an intensive course of antibiotics for H. Pylori infection. However, after about a week, I started to get very weak. I collapsed again and went back to the ER in an ambulance. They found my hemoglobin was 5g/dL, a dangerously low level (normal is over 13.5). Multiple blood transfusions didn't bring it up and I collapsed again in the night after passing a large amount of blood. They took me to intensive care and performed an emergency endoscopy where they clipped and sprayed the ulcer. Thankfully this worked and I was discharged after another 3 nights in hospital. Unsurprisingly, nearly bleeding to death wasn't good for me, and my ctDNA began to spike rapidly. I had a PET-CT and it revealed 3 new disease sites in abdominal lymph nodes. I restarted irinotecan and panitumumab infusions after barely recovering from the ulcer incident. This showed an excellent response, with the sites resolving on imaging, although ctDNA remained positive. I've now started bot/bal immunotherapy, a not yet approved immunotherapy treatment that is the first of its kind to show strong results in my kind of cancer, micro-satellite stable colorectal cancer. This was possible thanks to a donation from an anonymous benefactor and supporter of free and open inquiry in science. Hopefully this treatment will be effective, but it is unlikely to be enough on its own to prevent future disease recurrence. I am asking for help to get a personalized neoantigen cancer vaccine, which could substantially increase my chances of surviving this deadly disease that is likely incurable under standard care. While cancer vaccines have shown promising results, they are not yet approved, meaning one has to pay for the design, manufacture, and administration of the vaccine. The total cost of which is $104,133, beyond my means or those of my family. Any help would be greatly appreciated! I've started a GoFundMe here: gofundme.com/f/cancer-vaccin…. Please donate and share with anyone who might be interested in helping. I've carried on working throughout this period and I'm still running a research group in statistical genetics at UCLA. I'm hoping to continue making contributions to science for as long as I can, hopefully longer with your help.
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Wow! Need a LoF variant list in AllofUs. Filter the giant variant annotation table? Hours of waiting! Ended up copying and pasting data browser results to DeepSeek and in 10 seconds I got a clean tab-separated file! Cool!
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update: The filter function on data browser does not give accurate results: some categories and some variants meet the criteria are missing. Guess we have to use VAT for more serious work.
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Yuchang Wu retweeted
Our new PRS paper is out! We introduce a method to create regularized ensemble PRS on GWAS sumstats. Individual-level data is no longer needed for sophisticated ensemble learning @ZijieZhao1996 @stphn_drn Paper📰:biorxiv.org/content/10.1101/… Software🧑‍💻:github.com/qlu-lab/PUMAS
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One score to rule them all: regularized ensemble polygenic risk prediction with GWAS summary statistics biorxiv.org/cgi/content/shor… #biorxiv_genetic
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pain in using cloud computing: took 1 day 10 hours and 44 minutes to finish some analysis using AllofUs data, and I accidentally deleted the "environment" and all the results are gone forever ... 😭😭😭
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#ASHG24 Interested in how to reliably use AI/ML to accelerate genetic discovery? Stop by poster 4151 this afternoon to chat!
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Yuchang Wu retweeted
Four presentations from us this year, covering very diverse topics. Stop by and say hi🍷#ASHG24 #ASHG2024 1) Genetic effect heterogeneity @yy_stat 2) Genetics of partner choice @S5b6bY284u9qqoa 3) Perturb-seq/GWAS data integration @stphn_drn 4) ML-assisted GWAS @Jiacheng_Miao
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Thrilled to see this published on Nature Genetics! We found weird results using AD GWAX in another project and discovered that the bias is actually a very serious issue in the AD field. This underscores the importance of data quality. Larger is not always better!
Our paper on misleading biases in AD GWAS-by-proxy is published @NatureGenet. We identify the source of biases and explore strategies to reduce them @yy_stat @SunZhongxuan Paper📰: doi.org/10.1038/s41588-024-0… Software🧑‍💻: github.com/qlu-lab/GSUB Sumstats⬇️: qlu-lab.org/data.html
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While we didn't explore it in this paper, another tool (POP-GWAS) from our lab (xitter.cf/Q_StatGen/status/18407…) may offer a better solution when dealing with phenotypes with biases. --- also check it out!
POP-GWAS led by @Jiacheng_Miao is published today in @NatureGenet. This work showcases modern data science leveraging the power of machine learning while maintaining statistical validity. It also provides a GWAS solution when the outcome is ML-predicted nature.com/articles/s41588-0…
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Yuchang Wu retweeted
Our paper on misleading biases in AD GWAS-by-proxy is published @NatureGenet. We identify the source of biases and explore strategies to reduce them @yy_stat @SunZhongxuan Paper📰: doi.org/10.1038/s41588-024-0… Software🧑‍💻: github.com/qlu-lab/GSUB Sumstats⬇️: qlu-lab.org/data.html
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At Stanford for the IGSS conference. Interesting talks, lovely weather, and beautiful campus! I think I like this place.
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New preprint from my group led by @yy_stat @SunZhongxuan. Almost every recent Alzheimer's GWAS combines clinical AD diagnosis and proxy phenotypes based on parental health survey. We report major limitations in the current practices of GWAS-by-proxy (GWAX) biorxiv.org/content/10.1101/…
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You'll want to check out @Jiacheng_Miao's new paper if your work involves gene-environment interaction. This is our best GxE work so far. We introduce a statistical framework named PIGEON to reimagine how GxE studies could and should unfold. biorxiv.org/content/10.1101/…
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Preprinted in time for #ASHG2022! Happy to share @ZijieZhao1996's new work. We present PUMA-CUBS which advances PRS benchmarking & optimization. We can now fine-tune any PRS models and even do ensemble learning to combine models using GWAS sumstats alone! biorxiv.org/content/10.1101/…
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#ASHG2022 poster alert (Thursday afternoon; Board No.3383): It's well-known that autism has strong environmental contributions (e.g. autism susceptible genes are preferentially expressed in developing brain thus intrauterine environment from the mother is critical), however,
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many genetic studies on autism pretend that E does not exist. In this poster, we proposed a unique study design to quantify the contribution of maternal genotype to child's ASD risk in addition to child's genotype. Come and let's discuss more details if you're interested.
Don't know you, but I'm more excited about the posters than the talks. Looking forward to many inspiring conversations and discussions! #ASHG2022 #poster
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Excited to finally throw our hat in the ring. Here is our new method (named X-Wing) for cross-ancestry PRS. A key takeaway is that we now do EVERYTHING with sumstats alone which is a major methodological advance. Work is led by @Jiacheng_Miao & Hanmin. biorxiv.org/content/10.1101/…
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