Sahin Naqvi

May 29, 2024 | biorxiv.org | Sahin Naqvi |Seungsoo Kim |Saman Tabatabaee |Anusri Pampari

AbstractDeep learning approaches have made significant advances in predicting cell type-specific chromatin patterns from the identity and arrangement of transcription factor (TF) binding motifs. However, most models have been applied in unperturbed contexts, precluding a predictive understanding of how chromatin state responds to TF perturbation.

Nov 15, 2023 | nature.com | Seppe Goovaerts |Meng Yuan |Sahin Naqvi |Paul A. Romitti |Mary L. Marazita |John R. Shaffer | +2 more

AbstractThe cranial vault in humans is highly variable, clinically relevant, and heritable, yet its genetic architecture remains poorly understood. Here, we conduct a joint multi-ancestry and admixed multivariate genome-wide association study on 3D cranial vault shape extracted from magnetic resonance images of 6772 children from the ABCD study cohort yielding 30 genome-wide significant loci.

Oct 19, 2023 | nature.com | Hakhamanesh Mostafavi |Jeffrey P. Spence |Sahin Naqvi

AbstractMost signals in genome-wide association studies (GWAS) of complex traits implicate noncoding genetic variants with putative gene regulatory effects. However, currently identified regulatory variants, notably expression quantitative trait loci (eQTLs), explain only a small fraction of GWAS signals. Here, we show that GWAS and cis-eQTL hits are systematically different: eQTLs cluster strongly near transcription start sites, whereas GWAS hits do not.

May 29, 2023 | biorxiv.org | Seungsoo Kim |Ekaterina Morgunova |Sahin Naqvi |Maram Bader

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Apr 6, 2023 | nature.com | Sahin Naqvi |Richard A. Spritz |Ophir Klein |Benedikt Hallgrímsson |Peter Claes |Jon Pritchard

AbstractTranscriptional regulation exhibits extensive robustness, but human genetics indicates sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, largely lacking so far.