Crowdfunded whole-genome sequencing of the celebrity cat Lil BUB identifies causal mutations for her osteopetrosis and polydactyly, bioRxiv, 2019-02-23
Rare diseases and their underlying molecular causes are often poorly studied, posing challenges for patient diagnosis and prognosis. The development of next-generation sequencing and its decreasing costs promises to alleviate such issues by supplying personal genomic information at a moderate price. Here, we used crowdfunding as an alternative funding source to sequence the genome of Lil BUB, a celebrity cat affected by rare disease phenotypes characterized by supernumerary digits, osteopetrosis and dwarfism, all phenotypic traits that also occur in human patients. We discovered that Lil BUB is affected by two distinct mutations a heterozygous mutation in the limb enhancer of the Sonic hedgehog gene, previously associated with polydactyly in Hemingway cats; and a novel homozygous frameshift deletion affecting the TNFRSF11A (RANK) gene, which has been linked to osteopetrosis in humans. We communicated the progress of this project to a large online audience, detailing the 'inner workings' of personalized whole genome sequencing with the aim of improving genetic literacy. Our results highlight the importance of genomic analysis in the identification of disease-causing mutations and support crowdfunding as a means to fund low-budget projects and as a platform for scientific communication.
biorxiv genetics 200-500-users 2019The effect of environmental enrichment on behavioral variability depends on genotype, behavior, and type of enrichment, bioRxiv, 2019-02-22
Non-genetic individuality in behavior, also termed intragenotypic variability, has been observed across many different organisms. A potential cause of intragenotypic variability is sensitivity to minute environmental differences during development, even as major environmental parameters are kept constant. Animal enrichment paradigms often include the addition of environmental diversity, whether in the form of social interaction, novel objects, or exploratory opportunities. Enrichment could plausibly affect intragenotypic variability in opposing ways it could cause an increase in variability due to the increase in microenvironmental variation, or a decrease in variability due to elimination of aberrant behavior as animals are taken out of impoverished laboratory conditions. In order to test our hypothesis, we assayed five isogenic Drosophila melanogaster lines raised in control and mild enrichment conditions, and one isogenic line under both mild and intense enrichment conditions. We compared the mean and variability of six behavioral metrics between our enriched fly populations and the laboratory housing control. We found that enrichment often caused a small increase in variability across most of our behaviors, but that the ultimate effect of enrichment on both behavioral means and variabilities was highly dependent on genotype and its interaction with the particular enrichment treatment. Our results support previous work on enrichment that presents a highly variable picture of its effects on both behavior and physiology.
biorxiv genetics 100-200-users 2019Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation, bioRxiv, 2019-02-17
AbstractThe number of de novo mutations (DNMs) found in an offspring’s genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, with estimates ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that approximately 3% of DNMs originated following primordial germ cell specification (PGCS) in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that the rate of germline mutation accumulation varies among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of de novo mutations in humans.Data and code availability. Code used for statistical analysis and figure generation has been deposited on GitHub as a collection of annotated Jupyter Notebooks <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsgithub.comquinlan-labceph-dnm-manuscript>httpsgithub.comquinlan-labceph-dnm-manuscript<jatsext-link>. Data files containing high-confidence de novo mutations, as well as the gonosomal and post-primordial germ cell specification (PGCS) mosaic mutations, are included with these Notebooks. To mitigate compatibility issues, we have also made all notebooks available in a Binder environment, accessible at the above GitHub repository.
biorxiv genetics 0-100-users 2019