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Vervet Monkey Genomics Physical Map Project Results

Explore the collaborative Vervet Monkey Physical Map Project's success in mapping BAC ends for comparative genomics. Access sequences aligning on human, chimpanzee, or rhesus genomes and track sequencing progress and quality control.

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Vervet Monkey Genomics Physical Map Project Results

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  1. Vervet Monkey Genomics: Genome Canada and Génome Québec Physical Map Project J.Wasserscheid, K.McKee, A. Badhwar, C.Nagy, V.Forgetta, G.Leveque, K.Dewar (McGill University and Genome Québec Innovation Center) Conclusion Mapping of BAC ends Introduction Analysis The Vervet Monkey Physical Map Project is a collaborative project between UCLA and the McGill University and Genome Québec Innovation Center. Our contribution is to use the vervet BAC library (202752 BAC clones) to generate a physical map based on end-sequencing of vervet BACs (avg. 160kb insert). Comparative mapping Comparative genomics tools • Every end sequence is aligned by BLAT to the genome • assemblies of human, chimpanzee and rhesus. By analyzing • how the two ends of each BAC align, we can infer regions of • genome co linearity versus regions indicating different types of • genome rearrangements. • Vervet-vs-human / vervet-vs-rhesus fetching software available online. • Goal : accessing all vervet sequences aligning on a region of interest on either one of those two species. Progress of coverage on human Sequencing & Quality Control • Mapping success : a high percentage (76%) of clones having • 2 ends that map allows us to infer co linearity or discordance. • Goal on human : 8X coverage • Visualization of coverage on human • chromosomes • UCSC Genome Browser • link : view of the alignments • indicating nature of the • alignment and quality of • the sequences. • Coverage is underlined • by overlapping clones. • Mapping rearrangements : • concentrations of discordant • clones in the same region • hint at how and where • the genomes have changed Sequencing rate • Start date : Sept 2005 • As of Nov 2006 : • - reads generated : 94670 • - reads submitted to GSS : 91914 • Statistics per chromosome : Quality control of the sequences • Sequencing plates : • Percent coverage 384 well plate • Number of BACs In green : reads passing 400 Q20 Accessing the data • Proportion of BACs per Mb • Submission of quality sequences to GSS • database once a month • Sequences available on NCBI and on the Vervet Monkey Genomics Website. Failed clone (Sp6 and T7 pair) visualized in red Distribution of coverage on human • Machines : Tracking the efficiency of thermocyclers and ABI 3730XL detectors. • Map of the human genome • representing the distribution of • the vervet clones along • the chromosomes. • We have developed a comprehensive web resource that: • Stores, processes and manages BAC-end sequencing data • Ensures sequence quality • Automatically prepares GSS submissions • Generates a human-vervet comparative BAC-end map • Provides comparative analysis tools. • Concordance control : Paired end sequences concordance test : pass or fail depending on the positions and orientation on human. This test ensures we have maintained the correct naming of samples. http://www.genomequebec.mcgill.ca/compgen/submit_db/vervet_project This work is funded by Genome Canada and Genome Québec.

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