Hutch News Stories

SIFTing the truth about inborn variants

With a computer program, Henikoff graduate student Pauline Ng invents genetic 'chef' that senses what's wrong with human recipe
Pauline Ng discusses her new computer program with Dr. Steve Henikoff
Pauline Ng, graduate student, discusses her new computer program with Dr. Steve Henikoff of the Basic Sciences Division. Photo by Clay Eals

Marriages between first cousins have long been taboo in the United States for fear that such unions produce children with severe birth defects and genetic diseases. Yet studies show such offspring are only slightly more likely to be born with health problems.

That observation suggests that humans are unlikely to be carriers of many potentially harmful gene variants, a conclusion supported by new evidence from researchers in the Basic Sciences Division.

Using a computer program she developed last year, Pauline Ng, a graduate student in Dr. Steve Henikoff's group, found that previous reports predicting the number of deleterious variants in an individual's genome to be in the thousands are likely to be gross overestimates.

Their findings, published in the March issue of Genome Research, will aid cancer researchers, including those at Fred Hutchinson, who seek to identify the critical differences in DNA sequences that determine an individual's disease susceptibility.

Unique, useful tool

Henikoff said the program, called SIFT for "sorting intolerant from tolerant," is a unique and useful tool that enables researchers to hone in on the portions of genes most sensitive to small changes in DNA sequence.

"The idea that you can predict whether a difference is deleterious - say, in a cancer-susceptibility gene - could really help a researcher trying to identify variation that is significant," he said.

A major interest in human genetics is to understand which DNA sequence differences that cause changes in proteins impact a person's health.

Just as journalists choose words with similar meanings to spice up their writing, nature exploits genetic variation to make each individual in a species unique while preserving common characteristics.

Much of this variation is invisible to the casual observer. For example, despite DNA differences, most humans have 10 fingers and 10 toes, transport oxygen through their blood and burn sugar for metabolic fuel.

Yet sometimes, small changes cause dramatic differences, in biology as well as literature. Just as a single letter can be the difference between "live" and "love," an alteration of a single letter of the DNA code for one protein is enough to cause a life-threatening disease like cystic fibrosis.

Scientists hope to use information generated by the human-genome sequence to predict those DNA differences that might have harmful effects, such as predisposing individuals to cancer and other diseases.

Genetic 'meaning'

But they struggle to answer a crucial question: What types of genetic variation change the "meaning" of a gene?

The SIFT program, which has been made available to the scientific community on an Internet site and is used by about 200 research groups, serves as a kind of genetic thesaurus to guide such analysis.

SIFT takes advantage of the fact that many genes are members of large gene families that make proteins with related functions. While family members may have unique biological roles, each member generally uses the same mechanism to carry out its function.

Parts of proteins shared by all family members likely are critical for common functions, so changes in the parts often have damaging effects. SIFT detects what's common among proteins and predicts changes are deleterious.

Ng likens the consequences of genetic variability to constraints faced by a baker preparing a cake.

"Butter, eggs, and sugar are typical components of all cake recipes," she said. "Although a recipe can tolerate small differences in the amounts of these ingredients, significant changes could have serious consequences. SIFT is like a chef tasting a cake and sensing what, if anything, is wrong with the recipe."

In their assessments of human genetic variation, other research groups have predicted that thousands of potentially deleterious variants may lie in an individual's genome.

"But their estimates had biases," Ng said. "Using SIFT, we find that the number of such deleterious differences is too small to measure, suggesting that there are many fewer than predicted."

Henikoff said his laboratory's findings correlate with human experience.

"If you look at what happens to first-cousin marriages and also in ancient Egypt, where there were reportedly brother-sister marriages, it seems clear that there could not be such large numbers of deleterious variants for these marriages to produce healthy offspring," he said.

Ng and Henikoff based their conclusions on SIFT analysis of a large collection of human DNA variants known as nsSNPs, for non-synonymous single-base nucleotide polymorphisms.

A nucleotide is a "letter" in the DNA code. Changes in the DNA code result in variants known as polymorphisms. The polymorphisms result in changes in the protein building blocks made from the DNA code. Such "non-synonymous changes" could potentially alter the "recipe" of a protein and have deleterious consequences.



PHS, Human Biology scientists use SIFT for cancer research

Drs. Neli Ulrich and John Potter in the Public Health Sciences Division use SIFT, as well as another program known as PARSESNP developed by Dr. Elizabeth Greene, the center's Biocomputing consultant, to study genetic variation in enzymes for prostaglandin metabolism.

Prostaglandins are messenger molecules produced in many of the body's tissues and are thought to play a role in the development of colon cancer. This conclusion is based in part on the observation that drugs known as non-steroidal anti-inflammatories, including aspirin and other analgesics, inhibit prostaglandin synthesis and have a protective effect against colon cancer.

Ulrich and Potter hope to characterize sequence differences in proteins responsible for prostaglandin synthesis to see whether certain individuals possess variants that put them more or less at risk for colon cancer. SIFT allows them to focus their analysis on variation within the portions of these enzymes that are likely to be critical for their function.

SIFT also will augment research to identify and study key genetic variations in mice that are similar to those in humans, including mutations that may play a role in cancer and other chronic diseases, said Dr. Chris Kemp of the Human Biology Division.

Kemp is a co-investigator of the Fred Hutchinson/University of Washington Comparative Mouse Genomics Center, a project aimed at developing mouse models for characterizing human diseases with the goal of understanding how subtle genetic variation and environmental exposures interact to affect disease susceptibility.

Kemp said a link to the SIFT program is available on his consortium's Internet site. "The program will be part of the armament of tools we use to sift through gene variants to figure out those that are important for causing diseases including cancer," he said.

Help Us Eliminate Cancer

Every dollar counts. Please support lifesaving research today.


There are no tags on this page. A list of tags will appear here once there are.