https://tanigawalab.org/tags/computational-genomics/Computational GenomicsHugo Blox Builder (https://hugoblox.com)enTue, 01 Jul 2025 00:00:00 +0000https://tanigawalab.org/media/logo_hu_6ec5cb994dd998e6.pnghttps://tanigawalab.org/tags/computational-genomics/https://tanigawalab.org/research/disease-heterogeneity/Tue, 01 Jul 2025 00:00:00 +0000https://tanigawalab.org/research/disease-heterogeneity/<p>Diagnosis for the same disease affects individuals differently. However, we don’t know how best to represent biologically meaningful axes of variation within a disease, beyond the standard case vs. control comparison or proxy measure of severity. We combine human genetics, causal inference, and modern AI to address this challenge.</p> <ul> <li>Decomposition of genetic associations across many phenotypes</li> <li>Causal representation learning from pleiotropic associations</li> <li>Assessing the biological bases of disease subtypes</li> </ul> <h2 id="representative-studies">Representative studies</h2> <div class="not-prose research-publication-cards"> <div class="container px-8 mx-auto xl:px-5 pt-0 pb-2 max-w-screen-xl"> <div class="grid gap-10 md:grid-cols-2 lg:grid-cols-3 lg:gap-10"> <div class="group bg-white/90 dark:bg-zinc-900/90 backdrop-blur-sm rounded-2xl ring-1 ring-zinc-900/5 dark:ring-white/10 shadow-lg overflow-hidden transition-all duration-300 ease-out hover:shadow-xl hover:shadow-blue-500/10 hover:-translate-y-2 focus-within:ring-2 focus-within:ring-blue-500/50" role="article" aria-labelledby="card-title-a650e4193e33852896b21ba917b05324"> <div class="relative overflow-hidden aspect-[16/9] bg-gradient-to-br from-zinc-100 to-zinc-200 dark:from-zinc-800 dark:to-zinc-900"> <a href="https://tanigawalab.org/publications/2019/degas/" class="block"> <img class="w-full h-full transition-transform duration-500 ease-out group-hover:scale-105 object-fill" srcset="https://tanigawalab.org/publications/2019/degas/featured_hu_298ed8f352d934f3.webp 400w, https://tanigawalab.org/publications/2019/degas/featured_hu_88e32a69be907a6f.webp 600w, https://tanigawalab.org/publications/2019/degas/featured_hu_a1582a459169185b.webp 800w, https://tanigawalab.org/publications/2019/degas/featured_hu_e1affe50ddf0acd2.webp 800w" sizes="(max-width: 768px) 100vw, (max-width: 1200px) 50vw, 33vw" src="https://tanigawalab.org/publications/2019/degas/featured_hu_298ed8f352d934f3.webp" width="800" height="450" loading="lazy" decoding="async" fetchpriority="high" style="position: absolute; height: 100%; width: 100%; inset: 0px; color: transparent;" alt="Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology featured image"> </a> <div class="absolute inset-0 pointer-events-none bg-gradient-to-t from-black/10 via-transparent to-transparent opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> </div> <div class="p-8 space-y-4"> <div class="flex flex-wrap gap-2"> <a href="https://tanigawalab.org/tags/uk-biobank/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> UK Biobank </span> </a> <a href="https://tanigawalab.org/tags/latent-components/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Latent Components </span> </a> <a href="https://tanigawalab.org/tags/obesity/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Obesity </span> </a> <span class="inline-block px-2 py-1 text-gray-500 dark:text-gray-400 text-xs"> +1 more </span> </div> <h3 id="card-title-a650e4193e33852896b21ba917b05324" class="text-xl font-bold tracking-tight text-zinc-900 dark:text-zinc-100 group-hover:text-blue-600 dark:group-hover:text-blue-400 transition-colors duration-200 leading-tight"> <a href="https://tanigawalab.org/publications/2019/degas/" class="hover:underline"> Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology </a> </h3> <p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> We developed DeGAs to decompose shared genetic associations across 2,138 UK Biobank phenotypes and identify their underlying pleiotropic structure. </p> <div class="pt-3 border-t border-zinc-100 dark:border-zinc-800"> <div class="flex items-center gap-3 text-xs text-zinc-500 dark:text-zinc-500 flex-wrap mb-3"> <div class="flex items-center gap-2 min-w-0"> <div class="relative h-6 w-6 flex-shrink-0"> <img alt="avatar" class="rounded-full object-cover" src="https://tanigawalab.org/authors/yosuke-tanigawa/avatar_hu_e4b15cd8591d702.webp" width="24" height="24" loading="lazy" decoding="async" /> </div> <span class="truncate max-w-[9rem] text-sm">Yosuke Tanigawa, Ph.D.</span> </div> <span class="opacity-40">•</span> <time class="hidden sm:inline whitespace-nowrap" datetime="2019-12-31"> Dec 31, 2019 </time> <span class="hidden sm:inline opacity-40">•</span> <span class="hidden sm:inline whitespace-nowrap">1 min read</span> </div> <div class="pt-2 border-t border-zinc-200/50 dark:border-zinc-700/50"> <a href="https://tanigawalab.org/publications/2019/degas/" class="inline-flex items-center gap-2 text-primary-600 dark:text-primary-400 hover:text-primary-700 dark:hover:text-primary-300 font-medium text-sm transition-all duration-300 group/link"> <span>Read more</span> <svg class="w-4 h-4 transition-transform group-hover/link:translate-x-1" fill="none" stroke="currentColor" viewBox="0 0 24 24" aria-hidden="true"> <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M17 8l4 4m0 0l-4 4m4-4H3"/> </svg> </a> </div> </div> </div> </div> <div class="group bg-white/90 dark:bg-zinc-900/90 backdrop-blur-sm rounded-2xl ring-1 ring-zinc-900/5 dark:ring-white/10 shadow-lg overflow-hidden transition-all duration-300 ease-out hover:shadow-xl hover:shadow-blue-500/10 hover:-translate-y-2 focus-within:ring-2 focus-within:ring-blue-500/50" role="article" aria-labelledby="card-title-357785520e0fce8f6507fb29f9ddc5cf"> <div class="relative overflow-hidden aspect-[16/9] bg-gradient-to-br from-zinc-100 to-zinc-200 dark:from-zinc-800 dark:to-zinc-900"> <a href="https://tanigawalab.org/publications/2021/dprs/" class="block"> <img class="w-full h-full transition-transform duration-500 ease-out group-hover:scale-105 object-fill" srcset="https://tanigawalab.org/publications/2021/dprs/featured_hu_cfe45e0f970bf14d.webp 400w, https://tanigawalab.org/publications/2021/dprs/featured_hu_1d8eb57d67dde97f.webp 600w, https://tanigawalab.org/publications/2021/dprs/featured_hu_5806cde0f8130698.webp 800w, https://tanigawalab.org/publications/2021/dprs/featured_hu_b900259490964ef1.webp 800w" sizes="(max-width: 768px) 100vw, (max-width: 1200px) 50vw, 33vw" src="https://tanigawalab.org/publications/2021/dprs/featured_hu_cfe45e0f970bf14d.webp" width="800" height="450" loading="lazy" decoding="async" style="position: absolute; height: 100%; width: 100%; inset: 0px; color: transparent;" alt="Polygenic risk modeling with latent trait-related genetic components featured image"> </a> <div class="absolute inset-0 pointer-events-none bg-gradient-to-t from-black/10 via-transparent to-transparent opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> </div> <div class="p-8 space-y-4"> <div class="flex flex-wrap gap-2"> <a href="https://tanigawalab.org/tags/polygenic-scores/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Polygenic Scores </span> </a> <a href="https://tanigawalab.org/tags/latent-components/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Latent Components </span> </a> <a href="https://tanigawalab.org/tags/disease-heterogeneity/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Disease Heterogeneity </span> </a> </div> <h3 id="card-title-357785520e0fce8f6507fb29f9ddc5cf" class="text-xl font-bold tracking-tight text-zinc-900 dark:text-zinc-100 group-hover:text-blue-600 dark:group-hover:text-blue-400 transition-colors duration-200 leading-tight"> <a href="https://tanigawalab.org/publications/2021/dprs/" class="hover:underline"> Polygenic risk modeling with latent trait-related genetic components </a> </h3> <p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> Polygenic risk score (PRS) has been proposed for disease risk prediction with potential clinical relevance for some traits, but its personalized interpretation is generally … </p> <div class="pt-3 border-t border-zinc-100 dark:border-zinc-800"> <div class="flex items-center gap-3 text-xs text-zinc-500 dark:text-zinc-500 flex-wrap mb-3"> <time class="hidden sm:inline whitespace-nowrap" datetime="2021-02-08"> Feb 8, 2021 </time> <span class="hidden sm:inline opacity-40">•</span> <span class="hidden sm:inline whitespace-nowrap">1 min read</span> </div> <div class="pt-2 border-t border-zinc-200/50 dark:border-zinc-700/50"> <a href="https://tanigawalab.org/publications/2021/dprs/" class="inline-flex items-center gap-2 text-primary-600 dark:text-primary-400 hover:text-primary-700 dark:hover:text-primary-300 font-medium text-sm transition-all duration-300 group/link"> <span>Read more</span> <svg class="w-4 h-4 transition-transform group-hover/link:translate-x-1" fill="none" stroke="currentColor" viewBox="0 0 24 24" aria-hidden="true"> <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M17 8l4 4m0 0l-4 4m4-4H3"/> </svg> </a> </div> </div> </div> </div> <div class="group bg-white/90 dark:bg-zinc-900/90 backdrop-blur-sm rounded-2xl ring-1 ring-zinc-900/5 dark:ring-white/10 shadow-lg overflow-hidden transition-all duration-300 ease-out hover:shadow-xl hover:shadow-blue-500/10 hover:-translate-y-2 focus-within:ring-2 focus-within:ring-blue-500/50" role="article" aria-labelledby="card-title-25754c58734bea9449eac92e150166c6"> <div class="relative overflow-hidden aspect-[16/9] bg-gradient-to-br from-zinc-100 to-zinc-200 dark:from-zinc-800 dark:to-zinc-900"> <a href="https://tanigawalab.org/publications/2021/degas-bbj/" class="block"> <img class="w-full h-full transition-transform duration-500 ease-out group-hover:scale-105 object-fill" srcset="https://tanigawalab.org/publications/2021/degas-bbj/featured_hu_3a1bfe30b78adaa7.webp 400w, https://tanigawalab.org/publications/2021/degas-bbj/featured_hu_62bfe907569a84e9.webp 600w, https://tanigawalab.org/publications/2021/degas-bbj/featured_hu_bc51a9d9e9559d55.webp 800w, https://tanigawalab.org/publications/2021/degas-bbj/featured_hu_55c26ebfa9be13b6.webp 800w" sizes="(max-width: 768px) 100vw, (max-width: 1200px) 50vw, 33vw" src="https://tanigawalab.org/publications/2021/degas-bbj/featured_hu_3a1bfe30b78adaa7.webp" width="800" height="450" loading="lazy" decoding="async" style="position: absolute; height: 100%; width: 100%; inset: 0px; color: transparent;" alt="A cross-population atlas of genetic associations for 220 human phenotypes featured image"> </a> <div class="absolute inset-0 pointer-events-none bg-gradient-to-t from-black/10 via-transparent to-transparent opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> </div> <div class="p-8 space-y-4"> <div class="flex flex-wrap gap-2"> <a href="https://tanigawalab.org/tags/uk-biobank/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> UK Biobank </span> </a> <a href="https://tanigawalab.org/tags/phenotyping/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Phenotyping </span> </a> <a href="https://tanigawalab.org/tags/latent-components/"> <span class="inline-block px-2 py-1 bg-gray-100 dark:bg-gray-700 text-gray-700 dark:text-gray-300 text-xs rounded"> Latent Components </span> </a> <span class="inline-block px-2 py-1 text-gray-500 dark:text-gray-400 text-xs"> +1 more </span> </div> <h3 id="card-title-25754c58734bea9449eac92e150166c6" class="text-xl font-bold tracking-tight text-zinc-900 dark:text-zinc-100 group-hover:text-blue-600 dark:group-hover:text-blue-400 transition-colors duration-200 leading-tight"> <a href="https://tanigawalab.org/publications/2021/degas-bbj/" class="hover:underline"> A cross-population atlas of genetic associations for 220 human phenotypes </a> </h3> <p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> Using a set of GWAS summary statistics of diseases characterized from both European (UK Biobank and FinnGen) and East Asian (Biobank Japan) populations, we dissected latent DeGAs … </p> <div class="pt-3 border-t border-zinc-100 dark:border-zinc-800"> <div class="flex items-center gap-3 text-xs text-zinc-500 dark:text-zinc-500 flex-wrap mb-3"> <time class="hidden sm:inline whitespace-nowrap" datetime="2021-09-30"> Sep 30, 2021 </time> <span class="hidden sm:inline opacity-40">•</span> <span class="hidden sm:inline whitespace-nowrap">1 min read</span> </div> <div class="pt-2 border-t border-zinc-200/50 dark:border-zinc-700/50"> <a href="https://tanigawalab.org/publications/2021/degas-bbj/" class="inline-flex items-center gap-2 text-primary-600 dark:text-primary-400 hover:text-primary-700 dark:hover:text-primary-300 font-medium text-sm transition-all duration-300 group/link"> <span>Read more</span> <svg class="w-4 h-4 transition-transform group-hover/link:translate-x-1" fill="none" stroke="currentColor" viewBox="0 0 24 24" aria-hidden="true"> <path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M17 8l4 4m0 0l-4 4m4-4H3"/> </svg> </a> </div> </div> </div> </div> </div> </div> </div>