vervet monkey genomics: genome canada and g é nome qu é bec physical map project
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Vervet Monkey Genomics: Genome Canada and G é nome Qu é bec 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. - PowerPoint PPT PresentationTRANSCRIPT
Vervet Monkey Genomics: Genome Canada and GVervet Monkey Genomics: Genome Canada and Géénome Qunome Quéébec Physical Map Projectbec Physical Map Project J.Wasserscheid, K.McKee, A. Badhwar, C.Nagy, V.Forgetta, G.Leveque, K.Dewar (McGill University and Genome Québec Innovation Center)
• 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.
• UCSC Genome Browserlink : view of the alignmentsindicating nature of the alignment and quality of the sequences.
• Coverage is underlinedby overlapping clones.
• Mapping rearrangements :concentrations of discordant clones in the same region hint at how and wherethe genomes have changed
http://www.genomequebec.mcgill.ca/compgen/submit_db/vervet_projectThis work is funded by Genome Canada and Genome Québec.
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 BAClibrary (202752 BAC clones) to generatea physical map based on end-sequencing of vervet BACs (avg. 160kb insert).
Accessing the data• Submission of quality sequences to GSS database once a month• Sequences available on NCBI and on the Vervet Monkey Genomics Website.
Sequencing rate
Quality control of the sequences
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.
Tracking the efficiency of thermocyclersand ABI 3730XL detectors.
• Start date : Sept 2005• As of Nov 2006 : - reads generated : 94670 - reads submitted to GSS : 91914
IntroductionIntroduction
384 well plate
Failed clone (Sp6 and T7 pair) visualized in red
• Sequencing plates :
• Machines :
• Concordance control :
Sequencing & Quality Sequencing & Quality ControlControl
AnalysisAnalysis
ConclusionConclusion
Comparative genomics tools
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.
• Map of the human genome representing the distribution of the vervet clones along the chromosomes.
Comparative mapping
Progress of coverage on human• 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
• Percent coverage
• Number of BACs
• Proportion of BACs per Mb
Distribution of coverage on human
• Statistics per chromosome :
Mapping of BAC endsMapping of BAC ends
• 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 ofgenome rearrangements.
In green : reads passing 400 Q20