Innovation

Whole Exome Sequencing Closer to Becoming ‘New Family History’


Baylor College of Medicine (2)
By Glenna Picton | November 5, 2014

Approximately one-fourth of the 3,386 patients whose DNA was submitted for clinical whole exome testing received a diagnosis related to a known genetic disease, often ending a long search for answers for them and their parents, said researchers from the Baylor College of Medicine departments of molecular and human genetics and pediatrics and the Baylor Human Genome Sequencing Center and the University of Texas Health Science Center at Houston.

In an online report in the Journal of the American Medical Association, the scientists led by Yaping Yang, Ph.D., laboratory director of the Whole Genome Laboratory at Baylor, and Christine Eng, M.D., professor of molecular and human genetics at Baylor and senior director of Baylor’s Medical Genetics Laboratories, found a molecular diagnosis (meaning a genetic mutation or variation linked to a disease) in 25 percent of the large group of cases—confirming in this much larger group of patients the diagnostic yield from their initial report on the first 250 cases that appeared in the New England Journal of Medicine a little more than a year ago.

“The findings in this report, I believe, will forever change the future practice of pediatrics and medicine as a whole,” said James R. Lupski, M.D., Ph.D., professor of molecular and human genetics and pediatrics at Baylor and a coauthor of the report. “It is just a matter of time before genomics moves up on the physician’s list of things to do and is ordered before formulating a differential diagnosis. It will be the new ‘family history’ that, better yet, gets you both the important variants inherited from each parent and the new mutations that contribute to disease susceptibility.”

In fact, a large percentage of the diagnoses made were patients who inherited a new mutation (in the egg or sperm) that was not previously seen in their parents.

“The routine application of new genome methods in the clinic is not only benefiting patients but changing the way we think about research,” said Richard Gibbs, Ph.D., director of the Baylor College of Medicine Human Genome Sequencing Center and an author of the report.

“It has been wonderful to watch this very large team of colleagues bridging from the patient in clinic to the very most cutting-edge genomic technology to give families answers where previously there were none,” said Arthur Beaudet, M.D., professor of molecular and human genetics who was chair of the department when the Whole Gene Laboratory was begun and who began the Baylor College of Medicine Medical Genetics Laboratories.

“The diagnostic rate holds for the entire set of undiagnosed 3,386 patients who underwent whole exome sequencing between June 2012 and August 2014,” said Eng, who reported on a detailed analysis of 2,000 consecutive patients.

The procedure involved sequencing the DNA of the patients using new sequencing technologies referred to as next generation sequencing and comparing those results to the normal reference. Any disease-associated mutations were then also compared with the parent’s DNA to determine if the child inherited it from one or both parents to better understand the cause of the disease. In this study, the whole exome sequencing also identified ways in which physicians could intervene clinically to ameliorate or eliminate negative symptoms and to give families more information about the possible disease course.




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