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Structural Brain Defects Program Core

In addition to the three Cores, a number of collaborative agreements have been established to support this project.

Project I

Project I has obtained an agreement from several local or statewide institutions In support of this project:

  1. Rady Children's Hospital has agreed to provide bioinformatics support to Identify SBD patients appropriate for study, in both retrospective and prospective fashions, as well as support for patient consenting and phlebotomy. These will be identified from inpatient and outpatient records as well as from the network of newborn nurseries (the largest in San Diego).
  2. Kaiser Permanente Southern California has agreed to provide bioinformatic support to identify SBD patients from their entire patient population of over 3 million individuals in Southern California, using database personnel at a rate of $50/hr.
  3. The California Birth Defects Monitoring Program (CBDMP), which maintains Guthrie newborn bloodspot cards on nearly all Infants born In California since 1986, has agreed to search their entire database of medical records (updated with birth defects noted by 1 year of age), consisting of 10-15 million individuals, and provide blood spots for our study at a cost of $24/ea. For these nominal fees, we will be able to take advantage of these exciting and extremely diverse resources of SBD patients.

Project II

Project II has obtained agreements from:

  1. Professor Bruce Beutler at The Sripps Research Institute, who oversees the Mutagenetix ENU mouse mutagenesis project, to provide all founder lines with SBDs. This is an Invaluable resource, built upon a decade of experience with mutagenesis and phenotyping.
  2. The Director of the Dorris Neuroscience Center at TSRI, Dr. Mueller, to take advantage of a vast array of promoter- specific tetracycline-regulated Cre lines.

Project III

Project III has obtained agreements from:

  1. Dr. Cecelia Moens at the Fred Hutchins Cancer Center at University of Washington to identify zebrafish lines with mutations In specific SBD genes. Although this Is already a free service, the contribution of these germline mutant lines, and the ability to help prioritize their generation, will be Important validation for the planned morpholino experiments.
  2. Dr. Herwig Baier has agreed to provide a vast array of neural specific GAL4 driver lines as well as UAS reporter lines Including, UAS:mGFP and UAS:Kaeda . The combination of these tools will permit the detailed cell morphologic and migration analysis of specific neural cell subtypes and photoconvertlon of specific neural cell subpopulations from green to red, allowing for cell lineage and time-lapse studies during zebrafish neuronal development.

Core 8 has obtained agreements from Agilent, Inc, to provide both the beta-version (next generation) of whole exome library reagents for human, as well as the as-yet-unreleased versions for both mouse and zebrafish.

These collaborative agreements between well-known and critical partners will help ensure the success of the individual components as well as the overall goals of the program.


Core A

Core A: Administrative and Organizational 

This Administrative Core (Core A) will have two major functions. First, it will provide administrative support and intellectual enrichment for the investigators in this program. Due to the fact that the Program includes 5 senior investigators from two institutions (UC San Diego and the Scripps Research Institute) belonging to several departments: Pediatrics, Medicine, Neuroscience (School of Medicine at UCSD), Computer Science (UCSD) and the Scripps Research Institute.

Additionally, three different species will be used for this work (Human, Mouse, Zebrafish) and work accomplished at four different campuses (UCSD School of Medicine, UCSD Cancer Center, UCSD Computer Sciences, Scripps Research Institute). Because of this and the multi- disciplinary nature of the Program, a central administrative core is essential. The Core will work closely with the administration of the two major institutions, as well as administrators, business managers, and scientists in each department involved.

The Administrative Core will assist individual investigators in budgeting and will coordinate travel, purchasing, meetings and seminars.

The second function of the Administrative Core is to provide and encourage intellectual collaboration between members of the Program Project, faculty within the University (who are not members of this Program Project), and outside consultants. The Core will achieve these objectives in two ways:

  1. We will have a monthly two-hour seminar for all investigators in this Program. Research progress will be presented by one of the Program's investigators during each seminar. This will average about 10-12 seminars per year and about 2-3 per Project/year. We will also have the Directors of Cores B and C present new data generation and analytical techniques, especially in the rapidly moving field of genomics and bioinformatics.
  2. The Program Project plans to have outside experts visit each year as consultants, at least one of the Project groups. The role of the consultant will be to work directly with his/her host, to advise regarding their progress, to suggest possible new directions for both the individual Projects and potentially the overall Program.

In addition, we propose also to have a mid-term whole day symposium during which we invite consultants whose work is on some aspects of the research of each Project. During these workshops, each of the PIs presents their progress over the preceding 2 years and the outside experts are asked to critically evaluate the progress of each project.

Leader: Joseph G. Gleeson M.D.
Professor of Neurosciences and Pediatrics
UC San Diego
Dr. Gleeson's Lab Website

Core B

Core B: High-Throughput Sequencing Genomics

The amazing advances brought fonward by the completion of the Human Genome Project, new sequencing technologies and new methodologies to extract specific fragments of genomic DNA (gDNA), have now made it possible to sequence the "exome" in an individual patient in a relatively short time-frame (whole exome sequencing, WES). The Core PI and Co-PI  are thoroughly expert in the design and implementation of next-generation sequencing (NGS) experiments, and will establish and operate the NGS Core B to generate WES data across each of the proposed Projects, involving human, mouse and zebrafish.

It has long been appreciated that the vast majority of alleles with strong effect are located in the exome, which constitutes just 1% of most vertebrate genomes. The methodologies to capture and sequence the exome in humans was the first to emerge and is transforming the way scientists approach genetic disease. Methodologies to capture and sequence the mouse and zebrafish exomes will be available shortly. In this Core, we will bring these technologies to bear on structural brain diseases (SBDs) across the evolutionary spectrum. We have been successful at generating WES data that produces 95% target bases at >10X coverage. For dominant disease, the ability to systematically identify heterozygous variants is limited by this coverage, but for recessive disease, this hurdle is easily overcome. Because recessive disease due to homozygous mutations in humans, mouse and zebrafish is the focus of this application, we will be extraordinarily well-powered to identify causative mutations in these species using this approach.

An important aspect of Core B is the close ties that will develop not just to the Scientific Projects but also with Core C (Bioinformatics Core) and Core A (Administrative Core). Core C will develop and utilize new software that is specifically devised for identifying homozygous potentially deleterious sequence variants (PDSVs) in the data from Core B. Core A will support the technological infrastructure of both Core B and Core C. Projects I, II and III will be well-positioned to uncover new mechanisms of SBDs, and translate these into new discoveries about underlying mechanisms.

Director: Kelly Frazer, Ph.D.
Co-Director: Olivier Harismendy, PhD
Division of Genome Information Sciences
Department of Pediatrics
UC San Diego

Core C

Core C: Bioinformatics Genomics

Bioinformatics is the application of statistics and computer science to the field of molecular biology. It has emerged as a field unto itself, as the datasets that are generated by modern biomedical researchers easily exceeds what can be directiy analyzed. Core C will work with the data generated from massive parallel sequencing from human, mouse and zebrafish, to extract variants that are potential to cause disease.

The PIs of Cores A, B and C have worked together extensively in the past, and have an established track record of productivity in the area of next generation sequencing (NGS) data analysis. Dr. Bafna has worked broadly in bioinformatics and genomics in the development computational methodologies employing novel algorithms and statistical techniques for NGS datasets. We envision that the WES data generated from Core B will be delivered to Core C for extraction of the potentially deleterious sequence variants (PDSVs), which will be delivered back to each of the Projects for segregation analysis and further validation. This will be accomplished by developing the four key pipelines of Core C:

  1. WES data tracking and storage pipeline
  2. WES data analysis pipeline
  3. Mutation identification pipeline
  4. Comparative genomics pipeline

The analysis of WES datasets is presented in this application as a series of filters that is applied to the primary sequence to extract all relevant variants, and then apply a heuristic ranking strategy to detect the PDSVs mostly likely associated with the phenotype. The output of this FILTER and PRIORITIZE programs are then reported as both SNPs and INDELs in a ranked fashion, for later validation and segregation testing. Further analysis will help uncover the contribution of these genes to common disease as well as genome- wide gene-gene interactions using other software we have developed. We are also well-positioned to take full advantage of the 3^" generation DNA sequencers, and are excited that UCSD will serve as one of the national HHMI PacBio Sequencing Centers. These tools, together with the outstanding and unique human and animal resources, will make for a powerful combination to investigate new causes of structural brain disorders.

Leader: Vineet Bafna, PhD
Professor, Computer Science and Engineering
UC San Diego
Dr. Bafna's Research Website