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Archive - Mar 11, 2010

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First Whole Genome Sequencing of Entire Family

Collaborating institutions, including the Institute for Systems Biology (ISB), Complete Genomics, the University of Washington, and the University of Utah, have sequenced and analyzed the first whole genomes of a human family of four. The authors said that the benefits of sequencing an entire family include lowering DNA sequencing error rates, identifying rare genetic variants, and identifying disease-linked genes. "We were very pleased and a little surprised at how much additional information can come from examining the full genomes of the same family," said Dr. David Galas, co-corresponding author on the article and senior vice president at ISB. "Comparing the sequences of unrelated individuals is useful, but for a family the results are more accurate. We can now see all the genetic variations, including rare ones, and can construct the inheritance of every piece of the chromosomes, which is critical to understanding the traits important to health and disease. The continuing decline in the difficulty and cost of sequencing now enables us to use these new strategies for deriving genetic information that was too difficult or expensive to access in the past.” A particular family of four with two children with extremely rare genetic diseases turned out to be ideal for the study. Although the parents had no genetic abnormalities, they each carried recessive genes that resulted in their son and daughter being born with two extremely rare conditions--Miller's syndrome and primary ciliary dyskinesia (PCD). Miller's syndrome, a disorder characterized by facial and limb malformations, is thought to occur in perhaps one in one million people and has been diagnosed in only two families in the world, along with a few sporadic other cases.

Personal Genome Sequencing Hits Home for Baylor Researcher

Dr. James Lupski (photo) of the Baylor College of Medicine (BCM) came to the end of a long personal quest earlier this year when the Baylor Human Genome Sequencing Center (BHGSC) sequenced his complete genome and identified the gene and mutations involved in his own form of Charcot-Marie-Tooth syndrome, which affects the function of nerves in the body's limbs, hands, and feet. The results were published in the March 11, 2010 issue of the New England Journal of Medicine, a journal chosen, in part, because the authors believe this type of information will be crucial to physicians; as well as to the research community. The authors hope that their results will help begin a new era of clinical sequencing. The sequencing was carried out using next-generation sequencing technology, which has dramatically increased throughput and reduced costs. "This is the first time we have tried to identify a disease gene this way," said Dr. Lupski, Vice Chair of Molecular and Human Genetics at BCM. "It demonstrates that the technology is robust enough that we can find disease genes by determining the whole genome sequence. We can start to use this technology to interpret the clinical information in the context of the sequence--of the hand of cards you have been dealt. Isn't that the goal or dream of personalized genomic medicine?" According to a summary in Science Now, the BHGSC sequencing effort cost $50,000. As it turns out, the same mutations could have been found by sequencing only the protein-coding regions of the genome—a process called “exome” sequencing—for about $4,000. But full sequencing will soon be just as cheap as exome sequencing and will catch disease mutations in noncoding regions as well, said Dr. Richard Gibbs, Director of the BHGSC.