Tag Archives: deletion

Tip of the Week: Human Genome Structural Variation Viewer

Looking at the NHGRI News feed recently, I noticed this story (below) about a new genomic data collection that intrigued me. I found out about a new resource that I wanted to share as this week’s Tip of the Week. So this ~4 minute movie discusses my path to the Human Genome Structural Variation resource and a quick look at some of the data. But the paper was so influential on my thinking about the genome that I wanted to cover that in more detail in text form as well. So for a quick hit, watch the movie. For more detail, check out the text and links below.  Quick trip to the database: http://hgsv.washington.edu

Researchers Produce First Sequence Map of Large-Scale Structural Variation in Human Genome


….Other recently created maps, such as the HapMap, have catalogued the patterns of small-scale variations in the genome that involve single DNA letters, or bases. However, the scientific community has been eagerly awaiting the creation of additional types of maps in light of findings that larger scale differences account for a great deal of the common genetic variation among individuals and between populations, and may account for a significant fraction of disease. While previous work has identified structural variation in the human genome, a sequence-based map provides much finer resolution and location information….

I spend a lot of time thinking about the official or “reference” human genome sequence. This sequence–the one that was released to all that fanfare a few years back–is a composite of several people. Rather like a “generic” genome.

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Autism: regional duplications and deletions?

I was reading my local newspaper just now and spotted this intriguing information:

Boston researchers find genetic trigger for 1 percent of autism

….The discovery, reported on-line in the New England Journal of Medicine this afternoon, stems from the most extensive genome scanning for autism done so far. The scans found that in just over 1 percent of people with autism, a chunk of about 25 genes had been either duplicated or deleted, mainly in spontaneous mutations not carried by their parents….

The team was led by Mark Daly. I saw him recently at MGH giving a talk to students on genome-wide association studies. He is also responsible for developing great software, including HaploView and other tools. We have used HaploView to examine the HapMap data–you can pull data from the HapMap browser and load it right in to HaploView for a more detailed look at it.

I want to check out that paper: Association between Microdeletion and Microduplication at 16p11.2 and Autism

Fascinating information.