arXiv subjects

Charleston W. K. Chiang

Publications and source records attributed to Charleston W. K. Chiang.

4 recordsLinked to original sources

arXiv2025

Challenges and Recommendations in Establishing National Human Diversity Genomic Projects

Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant challenge for advancing biomedical discovery and accessible health solutions worldwide. Establishing a national genomic project is not a one-size-fits-all endeavor, as each country presents distinct challenges and opportunities. We identify challenges in the way of obtaining and publishing data from Whole Genome Sequencing (WGS) of people in various countries, discuss the progress made by some in their efforts to study their genetic diversity, and assess the most common issues. We recognize that a successful national genome database requires addressing several major issues, including the variable awareness of the recent developments in genomics among government officials, healthcare administrators, and policymakers, the absence of regulations, and ethical considerations, the challenges in securing funding, establishing legal frameworks, and building the necessary infrastructure. By assembling a diverse team of experts across 19 countries, we aim to provide a balanced approach in our recommendations to establish national projects. Our study acknowledges and addresses major intricacies and nuances specific to various settings and regions while presenting diverse opinions of scientists from both high-resource and low-resource countries contributing to a more inclusive and globally relevant framework for advancing genomic research and its applications.

q-bio.OT↗

arXiv2020

The opportunities and challenges of integrating population histories into genetic studies of diverse populations: a motivating example from Native Hawaiians

There is an urgent and well-recognized need to extend genetic studies to diverse populations, but several obstacles continue to be prohibitive, including (but not limited to) the difficulty of recruiting individuals from diverse populations in large numbers and the lack of representation in available genomic references. These obstacles notwithstanding, studying multiple diverse populations would provide informative, population-specific insights. Using Native Hawaiians as an example of an understudied population with a unique evolutionary history, I will argue that by developing key genomic resources and integrating evolutionary thinking into genetic epidemiology, we will have the opportunity to efficiently advance our knowledge of the genetic risk factors, ameliorate health disparity, and improve healthcare in this underserved population.

q-bio.PE↗

arXiv2018

Keck OSIRIS AO LIRG Analysis: Feedback in the Nuclei of Luminous Infrared Galaxies

The role of feedback in triggering or quenching star formation and hence driving galaxy evolution can be directly studied with high resolution integral field observations. The manifestation of feedback in shocks is particularly important to examine in galaxy mergers, where violent interactions of gas takes place in the interstellar medium during the course of the galactic collision. As part of our effort to systematically study the local population of luminous infrared galaxies within the Great Observatories All-Sky LIRG Survey, we undertook the Keck OSIRIS AO LIRG Analysis observing campaign to study the gas dynamics in the inner kiloparsec regions of these systems at spatial scales of a few 10s of parsecs. With high-resolution near-infrared adaptive optics-assisted integral-field observations taken with OSIRIS on the Keck Telescopes, we employ near-infrared diagnostics such as Brg and the ro-vibrationally excited H2 lines to quantify the nuclear star formation rate and identify feedback associated with shocked molecular gas seen in 21 nearby luminous infrared galaxies. Shocked molecular gas is preferentially found in the ultraluminous infrared systems, but may also be triggered at a lower luminosity, earlier merging stage. On circumnuclear scales, AGN have a strong effect on heating the surrounding molecular gas, though their coupling is not simply driven by AGN strength but rather is complicated by orientation, dust shielding, density, and other factors. We find that the nuclear star formation correlates with merger class and diminishing projected nuclear separations. These trends are largely consistent with the picture of merger-induced starbursts within the center of galaxy mergers.

astro-ph.GA↗

arXiv2015

Conflation of short identity-by-descent segments bias their inferred length distribution

Identity-by-descent (IBD) is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to contain an IBD segment if they share a segment that is inherited from a recent shared common ancestor without intervening recombination. Long IBD segments (> 1cM) can be efficiently detected by a number of algorithms using high-density SNP array data from a population sample. However, these approaches detect IBD based on contiguous segments of identity-by-state, and such segments may exist due to the conflation of smaller, nearby IBD segments. We quantified this effect using coalescent simulations, finding that nearly 40% of inferred segments 1-2cM long are results of conflations of two or more shorter segments, under demographic scenarios typical for modern humans. This biases the inferred IBD segment length distribution, and so can affect downstream inferences. We observed this conflation effect universally across different IBD detection programs and human demographic histories, and found inference of segments longer than 2cM to be much more reliable (less than 5% conflation rate). As an example of how this can negatively affect downstream analyses, we present and analyze a novel estimator of the de novo mutation rate using IBD segments, and demonstrate that the biased length distribution of the IBD segments due to conflation can lead to inflated estimates if the conflation is not modeled. Understanding the conflation effect in detail will make its correction in future methods more tractable.

q-bio.PE↗