The UCSC Repeat Browser allows discovery and visualization of evolutionary conflict across repeat families, bioRxiv, 2018-09-28

ABSTRACTBackgroundNearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of these sequences play important biological roles. However repeat elements pose several unique challenges to current bioinformatic analyses and visualization tools, as short repeat sequences can map to multiple genomic loci resulting in their misclassification and misinterpretation. In fact, sequence data mapping to repeat elements are often discarded from analysis pipelines. Therefore, there is a continued need for standardized tools and techniques to interpret genomic data of repeats.ResultsWe present the UCSC Repeat Browser, which consists of a complete set of human repeat reference sequences derived from the gold standard repeat database RepeatMasker. The UCSC Repeat Browser contains mapped annotations from the human genome to these references, and presents all of them as a comprehensive interface to facilitate work with repetitive elements. Furthermore, it provides processed tracks of multiple publicly available datasets of biological interest to the repeat community, including ChIP-SEQ datasets for KRAB Zinc Finger Proteins (KZNFs) – a family of proteins known to bind and repress certain classes of repeats. Here we show how the UCSC Repeat Browser in combination with these datasets, as well as RepeatMasker annotations in several non-human primates, can be used to trace the independent trajectories of species-specific evolutionary conflicts.ConclusionsThe UCSC Repeat Browser allows easy and intuitive visualization of genomic data on consensus repeat elements, circumventing the problem of multi-mapping, in which sequencing reads of repeat elements map to multiple locations on the human genome. By developing a reference consensus, multiple datasets and annotation tracks can easily be overlaid to reveal complex evolutionary histories of repeats in a single interactive window. Specifically, we use this approach to retrace the history of several primate specific LINE-1 families across apes, and discover several species-specific routes of evolution that correlate with the emergence and binding of KZNFs.

biorxiv genomics 0-100-users 2018

Cohort Profile East London Genes & Health (ELGH), a community based population genomics and health study of British-Bangladeshi and British-Pakistani people., bioRxiv, 2018-09-27

Cohort profile in a nutshell East London Genes & Health (ELGH) is a large scale, community genomics and health study (to date >34,000 volunteers; target 100,000 volunteers). ELGH was set up in 2015 to gain deeper understanding of health and disease, and underlying genetic influences, in British-Bangladeshi and British-Pakistani people living in east London. ELGH prioritises studies in areas important to, and identified by, the community it represents. Current priorities include cardiometabolic diseases and mental illness, these being of notably high prevalence and severity. However studies in any scientific area are possible, subject to community advisory group and ethical approval. ELGH combines health data science (using linked UK National Health Service (NHS) electronic health record data) with exome sequencing and SNP array genotyping to elucidate the genetic influence on health and disease, including the contribution from high rates of parental relatedness on rare genetic variation and homozygosity (autozygosity), in two understudied ethnic groups. Linkage to longitudinal health record data enables both retrospective and prospective analyses. Through Stage 2 studies, ELGH offers researchers the opportunity to undertake recall-by-genotype andor recall-by-phenotype studies on volunteers. Sub-cohort, trial-within-cohort, and other study designs are possible. ELGH is a fully collaborative, open access resource, open to academic and life sciences industry scientific research partners.

biorxiv genomics 0-100-users 2018

 

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