Biology subjects

Khan, Z. M.

Publications and source records attributed to Khan, Z. M..

3 recordsLinked to original sources

bioRxiv2026

Genetic and Epigenetic Landscape of Self-Identified Hispanics/Latino in All Of Us

Human genetic studies still underrepresent many populations, limiting discovery and interpretation of medically relevant variation. Extensive admixture in self-identified Hispanic/Latino populations increases the need for representative reference data and ancestry-aware interpretation of medically relevant variation. We used long-read sequencing to analyze genetic variation, ancestry, and DNA methylation in 1,490 self-identified Hispanic/Latino participants from the All of Us Research Program. We identified 10 million novel variants and more than 100 candidate phenotype associations, with fine-mapping prioritizing structural variants over nearby single-nucleotide variants in more than half. We linked 3,329 tandem repeats to DNA methylation, resolved widespread allele-specific methylation, and identified ancestry-linked regulation across paralogous genes. These results reveal previously inaccessible genetic and regulatory variation and show the value of long-read sequencing for diverse populations.

genetics↗

bioRxiv2026

COGNITIVE DETERIORATION IS REVERSED BY AN INSULIN-LIKE GROWTH FACTOR 1 SENSITIZER IN A MOUSE MODEL OF ALZHEIMER DISEASE

Previous observations in preclinical and clinical studies indicate a beneficial effect of insulin-like growth factor 1 (IGF-1) in different neurological illnesses, including Alzheimers disease (AD). AD is the most important neurodegenerative disease in the world and despite previous intensive research and the recent approval of putative disease-modifying therapies, available treatments provide only modest clinical benefit and do not halt disease progression. Consequently, there remains a pressing need to develop novel therapeutic strategies for AD. Since resistance to IGF-1 may be involved in development of AD, as it regulates cognition and amyloid {beta} (A{beta}) metabolism, we recently developed a small molecule IGF-1 sensitizer, AIK3a305, that crosses the blood brain barrier (BBB) and exerts modulatory actions in the brain. Using a mouse model of familial AD, the APP/PS1 mouse, we administered them AIK3a305 for 3 months. Treatment started at 12 months of age, when the disease is already well established, and cognitive deterioration readily measurable. One month after starting daily intraperitoneal injections of AIK3a305, mice showed normal cognitive performance in the Y maze, a measure of working memory that enables daily life activities. After 3 months, cognition remained fully preserved, mood-associated disturbances such as anxiety, were corrected, and brain A{beta} levels significantly ameliorated. AIK3a305 may therefore be a promising novel therapeutic strategy for AD patients.

neuroscience↗

bioRxiv2021

Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

The repetitive nature and complexity of multiple medically important genes make them intractable to accurate analysis, despite the maturity of short-read sequencing, resulting in a gap in clinical applications of genome sequencing. The Genome in a Bottle Consortium has provided benchmark variant sets, but these excluded some medically relevant genes due to their repetitiveness or polymorphic complexity. In this study, we characterize 273 of these 395 challenging autosomal genes that have multiple implications for medical sequencing. This extended, curated benchmark reports over 17,000 SNVs, 3,600 INDELs, and 200 SVs each for GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically important genes including CBS, CRYAA, and KCNE1. Our proposed solution improves variant recall in these genes from 8% to 100%. This benchmark will significantly improve the comprehensive characterization of these medically relevant genes and guide new method development.

genomics↗