Research Activities
Over the next five years, I and my colleagues at the GSC will be involved in the design, evaluation and implementation of novel genomics approaches to research problems fundamentally important in health and disease. My personal research program, which is designed to complement those of others at the GSC, will utilize state-of-the-art genomics approaches to focus primarily on (1) identification and analysis of genome variation in health and disease models and (2) expression genomics, in which DNA sequencing and micro-array approaches will be used to identify, clone and sequence differentially expressed transcripts, including alternatively spliced transcripts produced from the same locus but encoding different proteins. Specific examples of projects in both of my two selected areas of emphasis are provided below to illustrate the approaches I will use to study mental retardation, cancers, and embryonic stem cell lines. Much of work is collaborative, and so involves researchers with biological and disease expertise complementary to my own expertise in genomics.
Genome Variation Project I: Improved diagnoses and evaluation of mental retardation
Dr. Jan Friedman of UBC, and I co-lead a project funded by Genome Canada and by the Canada Foundation for Innovation to identify and analyze “copy number variants” (“CNVs”, which we define as losses or amplifications of genomic material) in the genomes of children with idiopathic mental retardation. The purpose of this project is to evaluate high-resolution genomic array technologies as an alternative to conventional cytogenetic analysis (the current standard of clinical care) for the identification of constitutional chromosomal abnormalities in individuals with idiopathic mental retardation. Such technologies have been successfully applied in numerous studies of cancers, but our study is among the first to apply genomic arrays to the study of mental retardation.
Genome Variation Project II: High resolution analysis of follicular lymphoma genomes
I, along with Drs. Joe Connors and Randy Gascoyne, lead the project “High resolution analysis of follicular lymphoma genomes”, which has been approved for funding in the latest Genome Canada competition and has started in early 2006. Co-funding for this project is provided by a National Cancer Institute of Canada Program Project Grant to Drs. Connor, Gascoyne, Horsman, and I, all of whom are the BC Cancer Agency. The primary aims of the effort are to reconstruct entire tumor genomes in sequence-ready clones, and use the clones to identify and sequence genome rearrangements. This high-resolution, novel approach will contribute to a fundamental undestanding of the genetic alterations that underlie neoplastic progression. In this project, we will (1) produce BAC fingerprint whole-genome maps of at least 24 follicular lymphoma genomes, (2) identify recurrent genome rearrangements in these genomes, and (3) sequence Bacterial Artificial Chromosome (BAC) clones bearing such rearrangements. We will apply genomics technologies including BAC library construction, BAC fingerprinting, genomic arrays, BAC end sequencing and BAC shotgun sequencing to identify and sequence genome regions rearranged in lymphoma. We are particularly interested in identifying and sequencing rearrangements correlated with progression from follicular lymphoma to diffuse large B cell lymphoma.
Gene Expression Project I: Identification and characterization of differentially expressed alternatively spliced transcripts in cancer models and embryonic stem cells.
A major challenge in decoding the information content of the human genome is presented by the process of alternatively splicing (AS), which can produce from a single locus different transcripts with different combinations of exons and regualtory sequences. Many if not most of the ~25,000 human genes produce alternative transcripts and this has contributed to estimates of more that 100,000 proteins encoded by these loci. We hypothesize that AS is an important mechanism for encoding a diversity of functions at a single genomic locus and that this diversity is realized in part through alterations in protein-protein interactions or sub-cellular location. Until recently it was not possible to measure the prevalence of AS or detect comprehensively the transcripts produced by it. With the availability of high-density micro-arrays, populated by hundreds of thousands of oligonucleotide probes, these limitations have in large part been addressed. The implications of this technical development and the application of it to study AS in the context of cancers are substantial, for up until this time measurements of gene expression relied largely on the detection of a single transcript for each gene. We speculate that by applying to cancer models micro-arrays designed to detect AS, we will discover novel protein-coding exon combinations that may reveal candidates for development of new therapies including vaccines.
Gene Expression Project II: Analysis of transcripts uniquely expressed in human embryonic stem cell lines
We have an ongoing interest in identifying novel genes that may play a role in the maintenance of pluripotentiality and in self-renewal. Accordingly, in collaboration with Dr. Connie Eaves, and with funding from the National Cancer Institute (USA), we recently conducted a study in which we characterized the human embryonic stem cell (ESC) transcriptome by generating and analyzing 2.5 million LongSAGE tags representing nine human ESC lines (www.transcriptomes.org). We also initiated a project to clone novel transcripts identified by LongSAGE tags, using a high throughput pipeline already in place as part of our involvement in the NIH-sponsored Mammalian Gene Collection Consortium. This effort has the potential to contribute significantly to an understanding of the unique repertoire of genes expressed in the stem cell compartment, and how these may function to regulate self-renewal.
Significant Research Contributions
My most significant contributions to genome science are listed below. Publications have been organized into six groups of technically or scientifically related topic areas.
I. Science, 2009 Apr 24;324(5926):522-528; Genome Biol, 2007 Oct 22;8(10):R224; Science, 2007 Apr 13;316(5822):222-234; Science, 2006 Nov 10;314(5801):941-952; Science, 2006 Sep 15;313(5793):1596-1604; Genome Res, 2006 Jun;16(6):768-775; Science, 2006 Sep 15; 313 (5793):1596-1604. Proc Natl Acad Sci USA, 2005 Dec 20;102(51):18526-18531; Science, 2005 Jul 15;309(5733):436-442; Nature, 2005 Apr 7;434(7034):724-731; Science, 2005 Feb 25;307(5713):1321-1324; Nature, 2004 Apr 1;428(6982):493-521; Nature, 2003 Jul 10;424(6945):157-164; Nature, 2002 Aug 15;418 (6899):743-750; Nature Genet, 2001Oct;29(2):133-134; Genome Res, 2001 Feb;11(2):274-280; Nature, 2001 Feb 15;409(6822):934-941; Nature, 2001 Feb 15; 409(6822):860-921.Genome Res, 1997;7:1072-1084.
These selected publications describe large-scale high throughput DNA sequencing conducted via a hierarchical map-based approach. The papers published in the Feb. 15, 2001 issue of Nature, titled "The Human Genome", describe the construction and use of the human genome map to fuel human genome sequencing. My contribution was to devise and then implement the approaches that led to the construction and use of the map, which served as the centralized coordinating resource for the sequencing effort. I also led map construction efforts in support of the sequencing of the mouse, rat, bovine, and other genomes, as described in these papers.
II. Nature, 2000 Dec 14;408(6814):796-815; Nature, 2000;408:823-826; Cell, 2000;100:377-386; Nature, 1999; 402:769-776; Science, 1999;286:2468-2474; Nature Genet, 1999;22:265-270; Nature Genet, 1999;22:271-275.
The series of papers describes the mapping and sequencing of the Arabidopsis thaliana genome. A. thaliana is an important model plant used widely to address issues relevant to plant developmental genetics. I was a key member of the Cold Spring Harbor Sequencing Consortium, focused on first leading the effort to map the A. thaliana genome and subsequently coordinating aspects of the whole genome sequencing activity.
III. Emerg Infect Dis, 2004 Dec;10(12):2192-2195; Science, 2003 May;300(5624):1399-1404.
The EID publication describes the sequencing of Avian flu genomes isolated from human patients during an Avian flu outbreak. The Science publication describes the rapid generation of the complete and accurate sequence of the SARS-associated coronavirus. The Genome Sciences Centre generated and end-sequenced cDNAs, and then assembled these sequences into the final ~29 kilobase genome sequence. The entire effort took about six days, demonstrating that genome sequencing of a new viral pathogen could be considered a legitimate part of a "rapid response" to an emerging infectious disease. The Science paper has been cited more than 900 times.
Marco Marra's Complete Publications List including selected links to full text articles.