Featured Research

from universities, journals, and other organizations

DNA fingerprinting enters 21st century

Date:
April 27, 2012
Source:
Whitehead Institute for Biomedical Research
Summary:
Researchers have created a three-step algorithm, lobSTR, that in one day accurately and simultaneously profiles more than 100,000 short tandem repeats in one human genome sequence -- a feat that previous systems could never complete.

As any crime show buff can tell you, DNA evidence identifies a victim's remains, fingers the guilty, and sets the innocent free. But in reality, the processing of forensic DNA evidence takes much longer than a 60-minute primetime slot.

To create a victim or perpetrator's DNA profile, the U.S. Federal Bureau of Investigation (FBI) scans a DNA sample for at least 13 short tandem repeats (STRs). STRs are collections of repeated two to six nucleotide-long sequences, such as CTGCTGCTG, which are scattered around the genome. Because the number of repeats in STRs can mutate quickly, each person's set of these genetic markers is different from every other person's, making STRs ideal for creating a unique DNA fingerprint.

The FBI first introduced their STR identification system in 1998, when STRs were the darling of the genetics community. However, other identifying genomic markers were soon discovered and gained in popularity. Around the same time, high throughput sequencing allowed researchers to process vast amounts of DNA, but using methods that were ineffectual in repeated DNA, including STRs. STRs were mostly forgotten by geneticists, and innovations to study them stalled.

Now Whitehead Institute researchers have pulled STR identification into the 21st Century by creating lobSTR, a three-step system that accurately and simultaneously profiles more than100,000 STRs from a human genome sequence in one day -- a feat that previous systems could never complete. The lobSTR algorithm is described in the May issue of Genome Research.

"lobSTR found that in one human genome, 55% of the STRs are polymorphic, they showed some difference, which is very surprising," says Whitehead Fellow Yaniv Erlich. "Usually DNA's polymorphism rate is very low because most DNA is identical between two people. With this tool, we provide access to tens of thousands of quickly changing markers that you couldn't get before, and those can be used in medical genetics, population genetics, and forensics."

To create a DNA fingerprint, lobSTR first scans an entire genome to identify all STRs and what nucleotide pattern is repeated within those stretches of DNA. Then, lobSTR notes the non-repeating sequences flanking either end of the STRs. These sequences anchor each STR's location within the genome and determine the number of repeats at the STRs. Finally, lobSTR removes any "noise" to produce an accurate description of the STRs' configuration.

According to Melissa Gymrek, who is the first author of the Genome Research paper, lobSTR's ability to accurately and efficiently describe thousands of STRs in one genome has opened up many new research opportunities.

"The first and simple next step is to characterize the amount of STR variation in individuals and populations," says Gymrek, who was an undergraduate researcher in Erlich's lab when she worked on lobSTR. "This will provide knowledge of the normal range of STR alleles at each locus, which will be useful in medical genetics studies that would like to determine if a given allele is normal or likely to be pathogenic. Another direction we are looking at is to look at STRs in case/control studies to look for STRs associated with disease. The list goes on, but these are some of the first questions we're looking to tackle."


Story Source:

The above story is based on materials provided by Whitehead Institute for Biomedical Research. The original article was written by Nicole Giese Rura. Note: Materials may be edited for content and length.


Journal Reference:

  1. Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich. lobSTR: A short tandem repeat profiler for personal genomes. Genome Research, 2012

Cite This Page:

Whitehead Institute for Biomedical Research. "DNA fingerprinting enters 21st century." ScienceDaily. ScienceDaily, 27 April 2012. <www.sciencedaily.com/releases/2012/04/120427163418.htm>.
Whitehead Institute for Biomedical Research. (2012, April 27). DNA fingerprinting enters 21st century. ScienceDaily. Retrieved July 29, 2014 from www.sciencedaily.com/releases/2012/04/120427163418.htm
Whitehead Institute for Biomedical Research. "DNA fingerprinting enters 21st century." ScienceDaily. www.sciencedaily.com/releases/2012/04/120427163418.htm (accessed July 29, 2014).

Share This




More Health & Medicine News

Tuesday, July 29, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Generics Eat Into Pfizer's Sales

Generics Eat Into Pfizer's Sales

Reuters - Business Video Online (July 29, 2014) Pfizer, the world's largest drug maker, cut full-year revenue forecasts because generics could cut into sales of its anti-arthritis drug, Celebrex. Fred Katayama reports. Video provided by Reuters
Powered by NewsLook.com
Nigeria Ups Ebola Stakes on 1st Death

Nigeria Ups Ebola Stakes on 1st Death

Reuters - Business Video Online (July 29, 2014) Nigerian authorities have shut and quarantined a Lagos hospital where a Liberian man died of the Ebola virus, the first recorded case of the highly-infectious disease in Africa's most populous economy. David Pollard reports Video provided by Reuters
Powered by NewsLook.com
Running 5 Minutes A Day Might Add Years To Your Life

Running 5 Minutes A Day Might Add Years To Your Life

Newsy (July 29, 2014) According to a new study, just five minutes of running or jogging a day could add years to your life. Video provided by Newsy
Powered by NewsLook.com
Ebola Outbreak Poses Little Threat To U.S.: CDC

Ebola Outbreak Poses Little Threat To U.S.: CDC

Newsy (July 29, 2014) The Ebola outbreak in West Africa poses little threat to Americans, according to officials with the Centers for Disease Control and Prevention. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins