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August 28, 2006
New map developed of genetic variation in human genome

BY holly korschun

Emory University scientists have identified and created a map of more than 400,000 insertions and deletions (INDELs) in the human genome that signal a little-explored type of genetic difference among individuals.
INDELS are an alternative form of natural genetic variation that differs from the much-studied single nucleotide polymorphisms (SNPs). Both types of variation are likely to have a major impact on humans, including health and susceptibility to disease.

The INDEL research, led by Scott Devine, PhD, assistant professor of biochemistry at Emory School of Medicine, has been posted online and will be published in the September issue of the journal Genome Research.

“We’re entering an exciting new era of predictive health where an individual’s personal genetic code will provide guidance on healthcare decisions,” Devine said. “Our maps of insertions and deletions will be used together with SNP maps to create one big unified map of variation that can identify specific patterns of genetic
variation to help us predict the future health of an individual.”

SNPs are differences in single chemical bases in the genome sequence, and INDELs result from the insertion and deletion of small pieces of DNA of varying sizes and types. If the human genome is viewed as a genetic instruction book, then SNPs are analogous to single letter changes in the book, whereas INDELs are equivalent to inserting and deleting words or paragraphs.

INDELs already are known to cause human diseases. For example, cystic fibrosis is frequently caused by a three-base-pair deletion in the CFTR gene, and transposon insertions have been identified in hemophilia, muscular dystrophy and cancer.

Devine and postdoctoral researcher Ryan Mills, PhD, used a computational approach to examine DNA re-sequences that originally were generated for SNP discovery projects, including the International HapMap Project. Thus far they have identified and mapped 415,436 unique INDELs, but they expect to expand the map to between 1 and 2 million by continuing their efforts with additional human sequences.

Devine said the next phase of the research is to “figure out which changes correspond to changes in human health and develop personalized health treatments.”

Ultimately, each person’s genome could be re-sequenced in a doctor’s office and his or her genetic code analyzed to make predictions about their future health. Devine believes the technology holds the promise of predicting whether a person will develop diabetes, mental disorders, cancer, heart disease and a range of other conditions.

All the INDELs identified in the study have been deposited into dbSNP—a publicly available SNP database hosted by the National Center for Biotechnology Information. The National Human Genome Research Institute of the National Institutes of Health funded the research.

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