The Beginning of BCM-HGSC
The Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) was established in 1996 when the National Human Genome Research Institute (NHGRI) designated Baylor College of Medicine as one of six pilot programs for the final phases of the Human Genome Project (HGP). Then in 1999, the Center was chosen as one of three sites from the pilot program to complete the HGP.
In June 2000, scientists triumphantly announced they had deciphered the human genome, the blueprint for human life. This announcement did not mark the end of the project. In a sense, it was only the beginning.
In April 2003, the human genome project consortium announced the completion of Phase II of the HGP, which involved producing a complete, high-quality human DNA reference. Completion of this stage was a large-scale endeavor for the BCM-HGSC. The center was responsible for determining the DNA sequence of chromosomes 3, 12, and part of X. These sequences represent about 10 percent of the human genome.
Current Research Focus of BCM-HGSC
Genomics in Medicine
The field of genomics is now in a new phase of exploring individual DNA sequence variation and its association with human diseases. A major focus of the BCM-HGSC is the deciphering of the genetic architecture of common complex diseases. These include cardiovascular disease (CVD), neurodegeneration and cancer predisposition – all major causes of adult death with strong heritable components. Understanding the genetic architecture of these disorders is the key to identifying gene changes that directly cause the diseases in order to direct therapeutic strategies. This pathway from ”bench to bedside” is the foundation of the new national initiative in Precision Medicine.
In direct response to this new era, the BCM-HGSC has launched the HGSC Clinical Lab (HGSC-CL), which has a complete infrastructure to support large-scale sequencing and genomics projects. With its sophisticated informatics core and pipeline and state-of-the-art technology development core, the CAP accredited/CLIA certified HGSC-CL can deliver clinical test grade data for returning results to diagnosing physicians.
Integrating Other Omics
Most contemporary genomic studies have achieved adequate power by increasing the size of the discovery sample to tens or hundreds of thousands of individuals. An alternative approach for detecting novel genes with variants of functional effect is to measure phenotypes that more immediately reflect gene function. By focusing on proximal measures of cellular, physiologic and metabolic processes, the BCM-HGSC optimizes the size of a gene’s effect relative to corresponding risk factor level or disease endpoint. For this reason, in addition to studing genetic datasets, the BCM-HGSC places great emphasis on integrating other omic data into genetic analyses.
In support of this effort, the BCM-HGSC routinely generates RNA-Seq data to look at expression patterns across samples and time points. Additionally, the BCM-HGSC regularly evaluates metabolomic and methylation profiles across samples. The BCM-HGSC also works in close partnership with the Alkek Center for Metagenomics and Microbiome Research (CMMR) to assess how the microbiome impacts human health.
Developing new technologies and applications is a major objective for the BCM-HGSC. These development steps, which produce laboratory innovations and enhancement to analyses, are made possible by a dedicated R&D team. The BCM-HGSC regularly serves as a beta test site for new technologies and provides feedback to companies on performance of new technologies. This arrangement allows the BCM-HGSC to have early access to the latest improvements available.
Today the BCM-HGSC employs more than 180 staff and occupies more than 36,000 square feet on the top three floors of the Margaret M. and Albert B. Alkek Building. The BCM-HGSC is located on the southwest edge of downtown Houston, the fourth largest city in the U.S., in the Texas Medical Center, the world’s largest medical complex.
The major activity of the BCM-HGSC is high-throughput DNA sequence generation and the accompanying analysis. The center currently operates multiple sequencing platforms (Illumina, Pacific Biosciences, Oxford Nanopore, and Sanger). The sequence data generated by these machines is analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI) or cloud partners for secure data sharing. This ensures that the worldwide research community has timely access to the data.
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BCM-HGSC Minority Diversity Initiative
In 2003, the BCM-HGSC, with the support of the NHGRI, launched a program to increase minority representation in the genomic sciences. Minorities underrepresented in the genomic sciences are defined as African American, Hispanic American, Native American, and Pacific Islander (non-Asian).
The BCM-HGSC Minority Diversity Initiative aims to encourage minority students to pursue a career in the genomic sciences and to address the historical underrepresentation of minorities in the field. We have had great success since the initial launch of our program, and many of the students who have participated are already moving toward graduate degrees in this field.
Our diversity initiative actively collaborates with colleges in the local academic community, including Prairie View A&M University, Jarvis Christian College, the University of Houston, Texas A&M University-Corpus Christi, and University of Texas at El Paso.