Overview of HGSC Sequencing Projects
 

Human sequencing

The Human Genome Project is the largest biological project ever undertaken. The project goals are to:

• Identify variations in the human genetic code that cause disease
• Determine how individual genes play a role in health and disease
• Analyze the genetic codes of model organisms to help find human genes
• Develop efficient technology to sequence DNA
• Develop methods to collect, analyze, and store genomic information to make the human DNA sequence available to the scientific community and the public
• Train scientists for genomic research and analysis
• Examine and propose solutions regarding ethical, legal, and social implications of genomic research

The results are anticipated to change the way we understand disease and the various life processes involved in human existence. We are living in the most exciting time in medicine. In June 2000, scientists triumphantly announced they had deciphered the human genome, the blueprint for human life. This announcement did not mark the end, but in a sense, only the beginning. In April, 2003, scientists announced the completion of Phase II of the project which involved producing a complete, high quality human DNA reference. The project is now in Phase III, and this involves exploring individual DNA sequence variation and its association with human phenotypes, through targeted re-sequencing.

Rat sequencing

The HGSC has coordinated the collaborative sequencing of the rat (Rattus norvegicus). This rodent is important as a model organism for cardiovascular and psychological research. The rat, the third mammalian genome available, allows comparative sequence analysis for greater understanding of functional elements in a mammalian genome. The assembled genomic sequence was published in 2004, and will be updated periodically as new information becomes available.

CCS sequencing

The Baylor College of Medicine Human Genome Sequencing Center's (Baylor HGSC) Concatenation cDNA Sequencing (CCS) program is focused on sequencing full-length cDNA clones and ESTs from human, mouse, and rat as well as from progenitor stem cells and human disease models.

Drosophila sequencing

The Drosophila Genome Project at the HGSC has initiated sequencing of the second Drosophila species: Drosophila pseudoobscura. Comparison of this species assembly with the recently completed sequence of Drosophila melanogaster is expected to offer important further insights into the biology of this historic model for experimental genetics.

The Baylor HGSC finished Drosophila melanogaster chromosomes 3L and X in collaboration with the Berkeley Drosophila Genome Project. Funding for the Drosophila Genome Project is provided by the NIH.

Dictyostelium sequencing

Sequencing the 34 million bases of the social amoeba Dictyostelium discoideum is an international collaboration between European and American centers. At Baylor, the effort is shared between the lab of Adam Kuspa and the HGSC with funding from the National Institutes of Health, through the National Institute for Child Health and Human Development.

Rhesus macaque sequencing

This project is a collaborative effort between BCM HGSC, JCV JTC, and WUSTL GSC. The aim of this project is to produce a comparative genome sequence of the rhesus macaque (rhesus monkey, Macaca mulatta). This sequence comparison will highlight features of human DNA.

Honey Bee sequencing

The HGSC is currently sequencing the honey bee, Apis mellifera. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social instincts and behavioral traits.

Sea Urchin genome project

The sea urchin has been an important model system for many years in the study of basic biology, particularly in developmental biology. The sea urchin occupies an important evolutionary position with respect to vertebrates and humans. There is a large body of information about gene expression in the sea urchin and there are a number of genomic resources available, making the sea urchin an ideal organism for learning how pathways of genes and proteins regulate growth and development, with potentially profound implications for understanding human biology.

Chimpanzee genomic analysis

The Human Genome Sequencing Center has sequenced some of the genome of the chimpanzee, Pan troglodytes.

Bovine sequencing

The Human Genome Sequencing Center is working to sequence and annotate the genome of the cow, Bos taurus.

Orangutan sequencing

The BCM HGSC is working in collaboration with WUSTL GSC to sequence the Orangutan (Pongo pygmaeus). The sequence of this great ape is expected to provide insights into human biology when compared to human and other primate sequences.

Wallaby sequencing

The HGSC is sequencing the genome of the tammar wallaby (Macropus eugenii) as part of the Tammar Wallaby Genome Sequencing Consortium, a collaboration between the HGSC and the Australian Genome Research Facility Ltd. (AGRF). The goal of the project is to produce a two-fold coverage draft sequence by whole genome shotgun sequencing. The project will expand existing wallaby genetic resources and explore the unique biological features of this marsupial, centered on reproduction, fertility, seasonal breeding, pregnancy, lactation, sex determination and differentiation.

Marmoset sequencing

The HGSC is sequencing the genome of the white-tufted-ear Marmoset (Callithrix jacchus). The Marmoset Genome Sequencing Consortium is a collaboration between the Baylor College of Medicine Human Genome Sequencing Center and the Genome Sequencing Center at Washington University, St. Louis. The goal of the project is to produce a seven-fold WGS shotgun assembly, using small insert plasmids as well as large insert clone ends from BACs and Fosmids. There will be finishing and BAC sequencing components of the project to investigate interesting regions for human diseases and to highlight primate evolution.

Nasonia sequencing

The HGSC is sequencing three species of parasitic wasp: Nasonia vitripennis, Nasonia giraulti, and Nasonia longicornis. Nasonia is a genus containing these three parasitic wasps whose hosts include house flies and other filth flies. It is a genetic model for all parasitic wasps which are used in the biological control of insect pests. Because of its usable haploid genetics, Nasonia is a facile model for discovering the genes behind complex traits. Nasonia will be the second representative of the Hymenoptera to be sequenced at the HGSC. N. vitripennis has been sequenced using a WGS strategy with a six-fold sequence coverage, whereas N. giraulti and N. longicornis are being sampled at single-fold sequence coverage, and will be aligned to the N. vitripennis assembly to identify and localize sequence markers necessary for mapping quantitative traits to individual gene loci.

Pea aphid sequencing

The HGSC is sequencing the pea aphid Acyrthosiphon pisum. The pea aphid displays both sexual and asexual reproduction, and it is a model for bacterial endosymbiosis and developmental plasticity. It is also an important agricultural pest, and a study of how resistance to insecticides and host plant defenses evolves and may be overcome. The sequencing strain was provided by David Stern's laboratory at Princeton University. The 525Mb genome is being sequenced using a whole genome shotgun strategy to a six-fold sequence coverage.

The Human Genome Sequencing Center has several microbial genome projects that are in progress, have been completed, or are funded but not yet underway.

Genomic sequencing of cancer genes in collaboration with David Nelson in Baylor's Department of Molecular and Human Genetics.

CCS and EST (Expressed Sequence Tags) sequencing of pediatric leukemias and other cancer genes in collaboration with Judy Margolin (BCM-Pediatrics), Claudio Schneider (C.I., Trieste, IT), and Dieter Greunert (UCSF).