And the winner is…

In November 2017 we announced a genomics challenge to fund a research project on innovative uses of low-pass sequencing — the technology behind Gencove. We were very excited with the overwhelming response we received and the variety of projects sent to us. After hours of debating the internal committee decided that the decision was too difficult. There were simply too many interesting proposals! In the end, we selected two winners: Gyaneshwer Chaubey from Banaras Hindu University, India and Cristian Capelli from University of Oxford, UK.

Gyaneshwer Chaubey, together with Gencove, will sequence the genomes of Indian Parsi minority. He suspects that the 57K Parsi population is very homogenous due to the custom of endogamy, which suggests a limited numbers of founders. Gyaneshwer is not only interested in describing the distinct Parsi founders (genomic history, admixture pattern), but he also wants to design a genetic screening panel for common diseases prevalent among the Parsis. Gencove’s low-pass sequencing of several hundred individuals will enable identifying common genetic variants, which can be associated with an extensive Parsi phenotype database.

Gyaneshwer Chaubey processing DNA samples

Cristian Capelli wants to understand how the human saliva microbiome changes across space, culture and the host’s genetic make-up. In order to investigate the role of diet and environment Cristian, together with Gencove, will sequence DNA from the saliva of individuals belonging to Southern African populations. They all share a common genetic background but have different subsistence strategies (agriculturalist or pastoralists) or live in different regions (Namibia and Lesotho in two different ecological zones, highlands and lowlands). The gut microbiome has been shown to differ across geographically close groups exploring different diets. Cristian will test if saliva microbial communities are similarly influenced by variation in diet. The use of whole genome sequence data will offer the opportunity to compare affinities and differences between groups in both their microbial taxonomic composition and their metabolic profile.

Cristian Capelli and his group collect samples in Namibia

Both projects take advantage of the unique features of Gencove’s low-pass sequencing technology — the ability to discover new variants in the Parsi population and the presence of sequencing reads from the mouth microbiome for the Southern African project.

Needles to say, both researchers will make their data available to the scientific community.

There were some other fantastic projects sent to us. Many researches wanted to use low-pass sequencing to study the genetics of a disease and we had several submissions about exploring the connection between the mouth microbiome, mitochondria, genome, and the environment. There were also several projects focused on studying the genomics of understudied populations with future diagnostic applications. One submission suggested using low-pass sequencing to assess copy number variation in tumors. As for the non-human studies, identifying optimal yeast strains for biofuel production was our absolute favorite.

Facilitating this type of research is exactly why we started Gencove!

As with any giveaway there were also submissions that were straight sci-fi but we congratulate you on the imagination! After tweaking some details, some of those might qualify for re-submission to our next challenge.