Fumitaka Inoue

Sep 27, 2024 | nature.com | Qingbo Wang |Ho Namkoong |Ryunosuke Saiki |Kyuto Sonehara |Shuhei Azekawa |Yugo Takahashi | +12 more

Correction to: Nature Genetics https://doi.org/10.1038/s41588-024-01896-3, published online 24 September 2024. In the version of the article initially published, there was an error in the x-axis label of Fig. 1a, where in the text now reading “pQTL –log10(P) ≥ x” it originally read “… ≤ x.” In the keys to both graphs in Fig. 7b, the blue dot was listed as “β > 0” and has now been amended to “β < 0.” The symbols are corrected in the HTML and PDF versions of the article.

Sep 24, 2024 | nature.com | Qingbo Wang |Ho Namkoong |Ryunosuke Saiki |Kyuto Sonehara |Shuhei Azekawa |Saori Sakaue | +12 more

AbstractStudying the genetic regulation of protein expression (through protein quantitative trait loci (pQTLs)) offers a deeper understanding of regulatory variants uncharacterized by mRNA expression regulation (expression QTLs (eQTLs)) studies. Here we report cis-eQTL and cis-pQTL statistical fine-mapping from 1,405 genotyped samples with blood mRNA and 2,932 plasma samples of protein expression, as part of the Japan COVID-19 Task Force (JCTF).

Jan 10, 2024 | nature.com | Ning Xie |Fumitaka Inoue |Shaohua Fan |Alfred K Njamnshi |Michael Marks |Nadav Ahituv | +1 more

AbstractSkin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles.

Sep 29, 2023 | biorxiv.org | Jiayi Liu |Tal Ashuach |Fumitaka Inoue |Nadav Ahituv

AbstractThe advent of the perturbation-based massively parallel reporter assays (MPRAs) technique has enabled delineating of the roles of non-coding regulatory elements in orchestrating gene expression. However, computational efforts remain scant to evaluate and establish guidelines for sequence design strategies for perturbation MPRAs. Here, we propose a framework for evaluating and comparing various perturbation strategies for MPRA experiments.