Takafumi Ojima

Research Associate, Dep. Genome Informatics in @UTokyo_News_en, PhD @osaka_univ_e, MD @tohoku_univ_med , Interested in WGS🧬 & PGS🎯

[Takafumi Ojima @TakaOjima]

🧬Our PRS paper is out on @NatureGenet 🎯
We evaluated the impact of sample stratification👫 by trait on polygenic prediction🧬🎯 using #BMI and #diabetes ‼️
Huge thanks to all contributors and biobank participants.
https://t.co/h6Cltj2vEf

[YukinoriOkada @okada_yukinori]

Please check our platform talk at #ESHG2026🎉
"Cross-population GWAS highlight polygenetic and cellular contrasts distinctly between dilated and hypertrophic cardiomyopathies"🫀🧬 by Yosuke Ogawa (Award candidate🎖️).
Session C24.2, 17:15, Sunday 14 June.
#GWAS #HCM #DCM #PGS #PRS

[Emil Uffelmann @euffelmann]

🧬 FUMA v2.0.0 is out, updated by Tanya Phung @ CTG Lab

New FLAMES module (effector gene prioritization), new QTLs Analysis module, and expanded xQTL datasets in SNP2GENE

https://t.co/OdppeXx9s4

[YukinoriOkada @okada_yukinori]

Japanese GWAS of #myasthenia #gravis (MG) identified a functional #TERT variant stratifying MG disease subtypes & treatment responses via allele-specific expression (ASE) effects in immature lymphocytes of thymoma. @NatureComms #HLA #GWAS #singlecell
https://t.co/LlGV7UK8Cf

[Go SATO @Go_Sato_UT]

🧬Y chromosome is clinically relevant.🤸‍♂️
We show that both Y haplogroups and mosaic loss of Y (LOY) shape complex traits such as T2D risk @NatureMedicine.
Single-cell analyses reveal cell type-specific LOY accumulation across tissues and disease contexts.
https://t.co/9j0b2b7Bpq

[Shinichi Namba @NambaShinichi]

Just out in @Nature🚀
GWAS treats genetic effects as fixed —but they’re not always.

Using large biobanks, we map gene–environment interactions and show how dynamic genetic effects enable environment-aware polygenic prediction and drug discovery.
https://t.co/Aju4sqy15t

[Takafumi Ojima @TakaOjima]

I will talk about recent topics of polygenic risk score at tomorrow's JSHG symposium @JSHGofficialPR 🧬
Looking forward to the other great talks as well. @akiyama_mst @Ryo_epidemiol

#JSHG #日本人類遺伝学会

[Takafumi Ojima @TakaOjima]

日本人類遺伝学会でポリジェニックスコア(PGS/PRS)について講演します🧬

そもそもPRSとは何か？
臨床への導入状況は？
どうすれば予測を向上できるか？
高PRSだと効きにくい薬とは？
PRSによる胚選択の問題とは？
動物ゲノム研究は人間にどう役立つか？

明日朝のシンポジウムでお待ちしております!!

[藤井亮輔 🦒 Ryosuke Fujii (Ryo) @Ryo_epidemiol]

今週末、第70回日本人類遺伝学会のシンポジウム12「精密医療を創る多因子疾患のゲノム解析」で講演します🧬

メンデルランダム化解析の violating assumption の事例や triangulation の重要性 、それ以外の因果推論の手法についてもお話しします！

@JSHGofficialPR @okada_yukinori @akiyama_mst

[Masato Akiyama @akiyama_mst]

明日は、@okada_yukinori先生と座長を務める日本人類遺伝学会のシンポジウムで、視覚障害の原因疾患の遺伝要因に関する講演を行います。
今年も眼科系学会では多くの講演をしましたが、眼科医でない方に届けることに価値を感じています。
他の演者の先生(@TakaOjima @Ryo_epidemiol )の発表も楽しみ！

[Takafumi Ojima @TakaOjima]

Having wonderful time at 2025 East Asia Biobank Symposium🧬
Grateful to share our biobank research in Japan and gain valuable insights from other biobanks.
Looking forward to advancing our collaborations🤝

[Marios Georgakis @MariosGeorgakis]

The largest GWAS for Alzheimer's disease is now out

👉109,479 cases, 74,141 proxy cases, 2,131,799 controls, 499,708 proxy controls
👉improved SNP-based heritability: 5% in previous studies --> 19%
👉127 loci, 48 novel with enrichment in microglia & neurons

[Emil Uffelmann @euffelmann]

🚨 The preprint for our GWAS of Alzheimer’s disease (AD) is out

Preprint: https://t.co/fbZDUj3c0F

🧵

[YukinoriOkada @okada_yukinori]

Our Platforms & Finalists #ASHG2025🎉🧬
@qsonehara SV & RV psoriasis risk by WGS: CERCAM as novel risk gene
Sugahara K. East Asian GWAS of serum immunoglobulin & subclass for humoral immunity
@Go_Sato_UT Male genetic regulation of germline & somatic Y chr variation shape T2D risk

[Xihao Li @xihaoli]

We’re excited to share our latest publication in
@CellGenomics: “Streamlining Large-Scale Genomic Data Management: Insights from the UK Biobank Whole-Genome Sequencing Data”. Sincerely thanks to @drarwood, @muzizimumu1, @XihongLin, Yuxin Yuan, Gareth Hawkes, Robin Beaumont, Michael Weedon, all collaborators and study participants from the @uk_biobank Program.

We highlight the annotated Genomic Data Structure (aGDS) format, the vcf2agds toolkit, and the STAARpipeline, which together:
• Seamlessly integrate genotypes + functional annotations in an all-in-one compact file for downstream analyses 🗃️
• Reduce UKB 500k WGS storage from 1473.85 TiB (GraphTyper pVCF, #23374) to 1.10 TiB (aGDS); and from 17.87 TiB (ML-Corrected DRAGEN pVCF, #24311) to 1.65 TiB (aGDS) 🗄️
• Enable scalable, functionally informed WGS association analyses across coding & noncoding genome 🧬
• Empower open-source, RAP-integrated genomic analyses for hundreds of thousands of samples ☁️

Applying STAARpipeline to the UKB 500k WGS data for total cholesterol, we identified 480 genome-wide significant rare variant associations, including 200 coding and 280 noncoding functional categories. These signals encompass lipid biology mainstays (e.g., PCSK9, APOB, NPC1L1, LDLR, APOE) and regulatory variants mapped to promoter, enhancer, and UTR regions, demonstrating the power of biobank-scale WGS for genomic discovery.

All tools are open source and freely available:
🔗 vcf2agds toolkit: https://t.co/9hFl9Ux5h1
🔗 STAARpipeline: https://t.co/occB9MbYG5
🔗 See the paper for complete links to software repos: https://t.co/vEkKRi9MwI

[Pradeep Natarajan @pnatarajanmd]

Building on the legacy of many, I'm incredibly excited that we have successfully translated our polygenic risk scores into a validated clinical assay @MassGenBrigham @broadinstitute, orderable by any clinician in the US today.
🧬To order: https://t.co/pivEDisCZR
🧬Announcement: https://t.co/V3GJaa4SHf

The CVD PRS panel is already expanding, and panels in other disease areas are in development. Single sequencing for multiple disease areas.
Methods:
https://t.co/YkPzcgSC8A @CellGenomics
https://t.co/hezzuwNTvZ @NatureComms

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[Takafumi Ojima @TakaOjima]

I will talk about our paper at today’s highlight track session of #iibmp2025

本日のバイオインフォマティクス学会(iibmp2025)のハイライトトラックセッションにて、昨年の筆頭論文を紹介させていただきます。皆様よろしくお願いします。
#iibmp2025

[Takafumi Ojima @TakaOjima]

🧬Our PRS paper is out on @NatureGenet 🎯
We evaluated the impact of sample stratification👫 by trait on polygenic prediction🧬🎯 using #BMI and #diabetes ‼️
Huge thanks to all contributors and biobank participants.
https://t.co/h6Cltj2vEf

[Kyuto Sonehara @qsonehara]

Excited to share our whole-genome sequencing study on psoriasis out in @CellGenomics!
Looking into rare and structural variants highlighted the disease genetics that conventional GWASs have overlooked.
https://t.co/o7IDlhVX3I

[UK Biobank @uk_biobank]

✅ Published in @Nature today, the paper describing the initial whole-genome sequencing analysis of 500,000 UK Biobank participants.

https://t.co/QmyovKXEy1

[Go SATO @Go_Sato_UT]

Our new paper in Nature Genetics!!
Single-cell deconvolution of various somatic mutations including mCAs, loss of Y, and mt-heteroplasmy.
https://t.co/2D2QHmUjps

[Ryuya Edahiro @RyuyaEdahiro]

Our Japanese multi-omic immune cell atlas is out in @NatureGenet!
We projected omics layers — from germline/somatic mutations to metagenomics — into single-cell space to uncover dynamic immune regulation.

https://t.co/H5BRqlxi0M