Scalable inference and analysis of ancestral recombination graphs in large data sets including modern and ancient genomes
For our next talk, in the BDI/CHG (gen)omics Seminar series, we will be hearing from Professor Pier Palamara, Associate Professor of Statistical and Population Genomics, Department of Statistics; Group Leader, Centre for Human Genetics and Zoi Tsangalidou, DPhil student, Department of Statistics. We’re delighted to host Pier and Zoi in what promises to be a great talk!

Date: Tuesday 29 October
Time: 9:30 – 10:30
Location: BDI OxPop Seminar Room 0

Talk title: Scalable inference and analysis of ancestral recombination graphs in large data sets including modern and ancient genomes

Abstract: Ancestral recombination graphs (ARGs) can be used to compactly represent and efficiently analyze the evolutionary history of a set of genomes. We developed a scalable algorithm to infer ARGs, called Threads that can be applied to hundreds of thousands of genotyped, imputed, or sequenced genomes. We also developed approaches to use these inferred ARGs for genotype imputation, complex trait analysis, and studying the ancestry of modern and ancient individuals. We applied Threads to 487,409 UK Biobank individuals and used the inferred ARG to impute genotyped data from a reference of up to ~200,000 exome-sequenced samples, observing accuracy improvements (r²) of up to ~10% for ultra-rare variants (MAC ≤ 10). We developed a scalable variance-component association algorithm, called ARG-RHE, and applied it to a UK Biobank ARG inferred using SNP array data, detecting more gene-trait associations compared to testing only genotype data imputed from ~65,000 sequenced haplotypes. Finally, we developed an approach to analyze the ancestry composition of modern and ancient DNA samples by threading unphased ancient genomes onto an existing ARG. We applied this approach to 487,409 UK Biobank samples and ~5,000 imputed ancient samples from the Allen Ancient DNA resource, spanning the past 4,000 years. We observed increased recent shared ancestry between Viking samples and UK Biobank participants from northern and southern England, compared to those from Scotland and Wales. Roman and Iron Age samples were most closely related to regions of Wales and Scotland, complementing areas associated with Saxon migrations into the UK. We analyzed the distribution of haplotype sharing along the genome, which may reflect the action of recent natural selection, observing several genomic regions with increased shared ancestry between modern and ancient groups.

Bio: Zoi Tsangalidou is a DPhil candidate in the Department of Statistics interested in developing statistical and machine learning methods for population genetics leveraging ancient DNA data.
Pier Palamara is an Associate Professor of Statistical and Population Genomics in the Department of Statistics and a group leader at the Centre for Human Genetics.
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As a reminder, the (gen)omics seminar series runs every other Tuesday morning and is intended to increase interaction between individuals working in genomics across Oxford. We encourage in-person attendance where possible. There is time for discussion over, tea, coffee and pastries after the talks.

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Date: 29 October 2024, 9:30
Venue: Big Data Institute, Old Road Campus OX3 7LF
Venue Details: Seminar Room 0
Speaker: Prof Pier Palamara (University of Oxford)
Organising department: Big Data Institute (NDPH)
Organisers: Nicola Whiffin (University of Oxford), Duncan Palmer (University of Oxford)
Organiser contact email address: sumeeta.maheshwari@ndph.ox.ac.uk
Host: Sumeeta Maheshwari (University of Oxford)
Part of: BDI/CHG Genomics Seminar Series
Booking required?: Not required
Audience: Members of the University only
Editor: Sumeeta Maheshwari