Abstract

Please come along the monthly campus Single Cell Seminar series. All are welcome, including colleagues from Cambridge (though email me so we can book them in as a visitor with security). This month we have two exciting talks, please join us C302 from 3.00 – 4.00pm THIS FRIDAY (19th October)

1) Matthew Young (Behjati group): “Using single cell transcriptomic signatures to understand tumour bulk RNA -seq”

2) Chris Laumer (Marioni/Birney groups): “Detecting germline mutations in single gametes by preserving molecular identity during amplification”

Chris’s abstract: Geneticists study the generation and transmission of new genetic variation by comparing deeply resequenced genomes of parents and offspring; variants found in offspring but neither parent are mutations. However, this pedigree sequencing design is limited by family size, and might mask variation in the germline mutation process within and between individuals. Single cell genomics could provide an alternative approach, allowing mutations to be discovered in large samples of gametes from a single individual. However, this field is limited by the enzymatic pre-amplification process typically used, which breaks the link between sequencing read and molecule of origin, allowing false positive mutations and undetectable allelic dropouts to predominate. Here, we present efforts to overcome these challenges through a novel protocol that capitalizes on the concept of unique molecular identity. The method uses restriction enzymes to fragment the naked genome of a lysed single cell, ligates adapters with double-stranded molecular barcodes to each fragment, and then linearly amplifies the DNA from both strands independently, all in succession without intermediate clean-up steps. Sequencing reads generated from such libraries are by design unambiguously assignable to their original molecule of origin, therefore permitting sequencing and amplification errors to be corrected by forming a computational consensus of duplicate reads, and also allowing counting of molecules captured, facilitating detection of allelic and strand dropouts. It can also be modified to produce reduced representation libraries, permitting the pooling of many cells on a single sequencing lane. We are applying this method to sequence single gametes from a hermaphroditic marine invertebrate model, Ciona intestinalis, which has a small genome (~160 Mbp), and from which gametes and embryos can be easily obtained and manipulated. Our data will test the hypothesis that individual gametes can serve as reasonable proxies for successfully developed offspring in studying germline mutations.