Integrating Large-Scale Genomic Information into Clinical Practice Workshop Summary (2012) / Chapter Skim
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3 The Analysis of Genomic Data
3 The Analysis of Genomic Data
Pages 11-24
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From page 11... ...
Technologies such as whole-genome sequencing generate a tremendous amount of data, and reducing those data down to clinically applicable information will require a robust analysis process. As Debra Leonard from Weill Cornell Medical Center introduced the speakers, she stated some of the key questions and challenges for analysis of genomic data: What standards will be applied to the analysis of genomic data?
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From page 12... ...
Later, the science progressed to evaluating single biomarkers, such as analyzing estrogen receptors in tissue. Since that time, testing for breast cancer has advanced through biomarker panels, expression profiles, targeted sequencing of specific genes, exome sequencing, and, finally, to whole-genome sequencing.
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From page 13... ...
There is no single repository for laboratory directors to find up-todate standard-of-care guidelines. Current CLIA regulations specify that the responsibility for clinical validation rests with the medical director of the laboratory.
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From page 14... ...
LABORATORY-BASED SOLUTIONS The Emory Genetics Laboratory is a not-for-profit clinical testing laboratory that focuses on rare genetic disorders, Hegde said. It is a comprehensive laboratory that performs biochemical, cytogenetic, nutritional, and clinical testing.
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From page 15... ...
The current policy of the Emory Genetics Laboratory is to report only the data that have been requested, an approach that allows the laboratory to avoid many of the interpretation issues that Monzon described. From the data collected from the tests it runs, the laboratory constructs databases of mutations, unclassified variants, and benign changes.
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From page 16... ...
, and myopathic changes on an electromyogram and that are usually associated with a dystrophic muscle biopsy. The gene mutations considered on the CMD panel result in muscle weakness soon after birth (Peat et al., 2008)
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From page 17... ...
Structured data make it possible to use clinical support tools that can leverage genetic data even as algorithms and use cases change over time. Whole-genome sequence records can be accessed in EMRs as clinical symptoms arise or as adverse-event warnings are received, and proactive alerts can be generated as new clinically actionable knowledge is learned.
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From page 18... ...
As our understanding of associations is refined, it will become possible to use new models and algorithms to evaluate actions based not only on genetic variants but also on lifestyle, environmental influences, and other factors. This will require extensive information technology support to search databases for variants, and a centralized and standardized open-access variant database with standardized nomenclature and careful curation, Rehm said.
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From page 19... ...
Hegde added that the role of genetic counselors as intermediaries between the laboratory and the clinician is very important. PCPGM has been planning a genetic consulting service that would enlist cardiologists with genetics expertise who could combine information about a patient's phenotype and family history with the results from the genetic report in order to generate patient and family care packages.
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From page 20... ...
This is necessary since the laboratory often does not have reliable methods for determining who is currently caring for a patient or how to reach a patient or physician. The GeneInsight Interface can also be used to direct researchers to patients who have certain genetic variants so that they can be notified of relevant clinical trials.
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From page 21... ...
More than 5,000 people are currently enrolled in the collaborative study. In order to enter the study, participants are required to fill out extensive medical and family history and lifestyle questionnaires, which are used to report quantitative risks based on environmental or family history information.
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From page 22... ...
"This is a dynamic group," said Christman. "They know that they will find out new information, but they don't know exactly what." Potentially actionable conditions that are currently approved to be reported by the CPMC study include several drug metabolism variants and the following complex diseases: • Age-related macular degeneration • Bladder cancer • Breast cancer • Chronic obstructive pulmonary disease • Colon cancer • Coronary artery disease • Diabetes, types 1 and 2 • Hemochromatosis • Inflammatory bowel disease • Lupus • Melanoma • Obesity • Prostate cancer • Rheumatoid arthritis • Testicular cancer
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From page 23... ...
The strongest evidence code is reserved for situations in which the reference drug has shown actual clinical outcomes in a randomized clinical trial. Study Parameters In order to put together a representative sample, the project is trying to match the demographics of the Delaware Valley, which is about 15 percent African American and 15 percent Hispanic.
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