The pharmacogenomic landscape of an Indigenous Australian population

Background: Population genomic studies of individuals of Indigenous ancestry have been extremely limited comprising <0.5% of participants in international genetic databases and genome-wide association studies, contributing to a "genomic gap" that limits their access to personalised medicine. While Indigenous Australians face a high burden of chronic disease and associated medication exposure, corresponding genomic and drug safety datasets are sorely lacking.Methods: To address this, we conducted a pharmacogenomic study of almost 500 individuals from a founder Indigenous Tiwi population. Whole genome sequencing was performed using short-read Illumina Novaseq6000 technology. We characterised the pharmacogenomics (PGx) landscape of this population by analysing sequencing results and associated pharmacological treatment data.Results: We observed that every individual in the cohort carry at least one actionable genotype and 77% of them carry at least three clinically actionable genotypes across 19 pharmacogenes. Overall, 41% of the Tiwi cohort were predicted to exhibit impaired CYP2D6 metabolism, with this frequency being much higher than that for other global populations. Over half of the population predicted an impaired CYP2C9, CYP2C19, and CYP2B6 metabolism with implications for the processing of commonly used analgesics, statins, anticoagulants, antiretrovirals, antidepressants, and antipsychotics. Moreover, we identified 31 potentially actionable novel variants within Very Important Pharmacogenes (VIPs), five of which were common among the Tiwi. We further detected important clinical implications for the drugs involved with cancer pharmacogenomics such as thiopurines and tamoxifen, immunosuppressants like tacrolimus and certain antivirals used in the hepatitis C treatment due to potential differences in their metabolic processing.Conclusion: The pharmacogenomic profiles generated in our study demonstrate the utility of pre-emptive PGx testing and have the potential to help guide the development and application of precision therapeutic strategies tailored to Tiwi Indigenous patients. Our research provides valuable insights on pre-emptive PGx testing and the feasibility of its use in ancestrally diverse populations, emphasizing the need for increased diversity and inclusivity in PGx investigations.Personalised Therapeutic

High-energy physics with particles carrying non-zero orbital angular momentum

Thanks to progress in optics in the past two decades, it is possible to create photons carrying well-defined non-zero orbital angular momentum (OAM). Boosting these photons into high-energy range preserving their OAM seems feasible. Intermediate energy electrons with OAM have also been produced recently. One can, therefore, view OAM as a new degree of freedom in high-energy collisions and ask what novel insights into particles' structure and interactions it can bring. Here we discuss generic features of scattering processes involving particles with OAM in the initial state. We show that they make it possible to perform a Fourier analysis of a plane wave cross section with respect to the azimuthal angles of the initial particles, and to probe the autocorrelation function of the amplitude, a quantity inaccessible in plane wave collisions.Comment: 7 pages, 1 figure, talk given at the workshop "30 years of strong interactions", Spa, Belgium, 6-8 April 201

The landscape of genomic structural variation in Indigenous Australians

Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50  b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.Andre L. M. Reis, Melissa Rapadas, Jillian M. Hammond, Hasindu Gamaarachchi, Igor Stevanovski, Meutia Ayuputeri Kumaheri, Sanjog R. Chintalaphani, Duminda S. B. Dissanayake, Owen M. Siggs, Alex W. Hewitt, Bastien Llamas, Alex Brown, Gareth Baynam, Graham J. Mann, Brendan J. McMorran, Simon Easteal, Azure Hermes, Misty R. Jenkins, The National Centre for Indigenous Genomics, Hardip R. Patel, Ira W. Deveso

Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20

To identify multiple sclerosis (MS) susceptibility loci, we conducted a genome-wide association study (GWAS) in 1,618 cases and used shared data for 3,413 controls. We performed replication in an independent set of 2,256 cases and 2,310 controls, for a total of 3,874 cases and 5,723 controls. We identified risk-associated SNPs on chromosome 12q13–14 (rs703842, P = 5.4 times 10-11; rs10876994, P = 2.7 times 10-10; rs12368653, P = 1.0 times 10-7) and upstream of CD40 on chromosome 20q13 (rs6074022, P = 1.3 times 10-7; rs1569723, P = 2.9 times 10-7). Both loci are also associated with other autoimmune diseases1, 2, 3, 4, 5. We also replicated several known MS associations (HLA-DR15, P = 7.0 times 10-184; CD58, P = 9.6 times 10-8; EVI5-RPL5, P = 2.5 times 10-6; IL2RA, P = 7.4 times 10-6; CLEC16A, P = 1.1 times 10-4; IL7R, P = 1.3 times 10-3; TYK2, P = 3.5 times 10-3) and observed a statistical interaction between SNPs in EVI5-RPL5 and HLA-DR15 (P = 0.001)

Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20

To identify multiple sclerosis (MS) susceptibility loci, we conducted a genome-wide association study (GWAS) in 1,618 cases and used shared data for 3,413 controls. We performed replication in an independent set of 2,256 cases and 2,310 controls, for a total of 3,874 cases and 5,723 controls. We identified risk-associated SNPs on chromosome 12q13–14 (rs703842, P = 5.4 times 10⁻¹¹; rs10876994, P = 2.7 times 10⁻¹⁰; rs12368653, P = 1.0 times 10⁻⁷) and upstream of CD40 on chromosome 20q13 (rs6074022, P = 1.3 times 10⁻⁷; rs1569723, P = 2.9 times 10⁻⁷). Both loci are also associated with other autoimmune diseases. We also replicated several known MS associations (HLA-DR15, P = 7.0 times 10⁻¹⁸⁴; CD58, P = 9.6 times 10⁻⁸; EVI5-RPL5, P = 2.5 times 10⁻⁶; IL2RA, P = 7.4 times 10⁻⁶; CLEC16A, P = 1.1 times 10⁻⁴; IL7R, P = 1.3 times 10⁻³; TYK2, P = 3.5 times 10⁻³) and observed a statistical interaction between SNPs in EVI5-RPL5 and HLA-DR15 (P = 0.001)