Vervet Monkey Genomics: Genome Canada and G Vervet Monkey Genomics: Genome Canada and G é é nome Qu nome Qu é é bec Physical Map Project 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) • 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 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 http://www.genomequebec.mcgill.ca/compgen/submit_db/vervet_projec This 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 BAC library (202752 BAC clones) to generate a 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. racking the efficiency of thermocyclers nd ABI 3730XL detectors. • Start date : Sept 2005 • As of Nov 2006 : - reads generated : 94670 - reads submitted to GSS : 91914 Introduction Introduction 384 well plate Failed clone (Sp6 and T7 pair) visualized in red • Sequencing plates : • Machines : • Concordance control : Sequencing & Quality Sequencing & Quality Control Control Analysis Analysis Conclusion Conclusion 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 ends Mapping 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 of genome rearrangements. In green : reads passing 400 Q20

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 Presentation

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Page 1: Vervet Monkey Genomics: Genome Canada and G é nome Qu é bec Physical Map Project

• 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