Lorne Genome 2024

The Bovine Long Read Consortium aims to use long read sequencing of cattle at population scale to characterise structural variation of the genome. This pilot study used sequences from 41 animals from two breeds, including two trios at 45X. The trios were scaled back to lower read depths. SV recall and precision was lower at 10-15X versus 45X, however this may be an acceptable compromise for population scale studies to spread costs over large numbers of animals. However, if the purpose is to discover a deleterious mendelian mutation, closer to 45X is preferred. SNP and INDEL were called from various read depths and compared to a filtered set of high-quality calls from short read sequences. At each read depth the recall and precision of SNP was considerably higher than INDEL. At 10X, SNP recall was 0.86 and 0.99 at 45X. The precision for SNP and particularly INDEL suggested that long-read variant calls include a relatively high, but likely overestimated proportion of false positives. After merging and joint SV calling across all animals, levels of sporadic missing genotypes was less than 5% per animal (most 10-25X). A total of 76,572 SVs were detected across all samples, one third of which were segregating in one breed. Using variant effect predictor annotations, a much higher proportion of SV compared to SNP had high impact effects. Insertions and deletions tended to be smaller and duplications larger. Insertions and deletions more often segregated across both breeds, while inversions were more often breed specific. Few duplications were detected but they were slightly more likely to be breed specific. The results highlight that it would be beneficial to build a large reference population to understand the structural variation, to impute these SV into large phenotyped populations and to explore the impact of SVs on traits of interest.

Through the combination of long reads and native inference of CpG methylation, Oxford Nanopore Technologies sequencing platforms offer a method to explore genomic imprinting with unprecedented ease and comprehension. Imprinted genes, whose expression is confined to either the paternal or maternal allele, are enriched for critical roles in promoting and regulating foetal growth and development. Their allele-specific expression serves to balance resource allocation between the mother and the developing foetus. As the placenta forms the interface between mother and foetus, this temporary organ of pregnancy is a highly relevant place to study genomic imprinting. In this talk I will present our work surveying the placental genome with nanopore sequencing, discovering hundreds of novel loci which differ in their methylation, expression, or both between the maternal and paternal alleles, a subset of which are likely to be novel imprinted genes. Nanopore data allows us to study the allele-specific regulation of highly repetitive loci that have been technically infeasible to approach via previous methods. The technical aspects of using nanopore sequence data presented here can be applied to study allele-specific effects in any tissue or organism.