# DNA Sudoku

Researchers get help from a venerable number theory and a popular puzzle game to solve genetic medical mysteries

The process allows researchers to pool dozens of samples and assign the pool—rather than individual samples—with a bar-code identifier. After the sequencing machine returns results from a whole pool, a decoder program can use the theorem to work backward and locate a particular specimen. To find a mutation in a cystic fibrosis study, for example, the decoding program would use each pool's results as the constraints to pinpoint the location of the mutated specimen.

"Think about Sudoku as a pooling theory," he says. "You have a constraint in a row and column [to] have all nine digits. We have the same thing—maybe not as neat—but we have all the sequences in the same pool." From there, he explains, a program can go back and use the same logic to find the mutant DNA.

In the future, sequencing and analysis that would have taken months and \$10 million could require just a few days of machine time and \$50,000 to \$80,000, the study authors note. All thanks to ancient Chinese number logic and a popular pen-and-paper puzzle game—which Erlich now plays regularly.

Rights & Permissions

View
1. 1. PaoloMagrassi 12:36 PM 7/2/09

Chinese Remainder Theorem [Britannica]: ancient theorem that gives the conditions necessary for multiple equations to have a simultaneous integer solution. [...] It addresses the following type of problem. One is asked to find a number that leaves a remainder of 0 when divided by 5, remainder 6 when divided by 7, and remainder 10 when divided by 12. The simplest solution is 370. Note that this solution is not unique, since any multiple of 5 ෠౲ (= 420) can be added to it and the result will still solve the problem.

2. 2. riverboots 05:11 PM 7/2/09

Does the Chinese Remainder Theorem become case-sensitive in neurological conformity?

3. 3. emueses 10:46 AM 7/6/09

Interesting article. BTW, thanks for using my picture.

4. 4. jwr257 12:50 PM 7/12/09

Here is an easier solution..use the idle time on your computer (Windows, Mac, or Linux) to cure diseases, study global warming, discover pulsars, and do many other types of scientific research. It's safe, secure, and easy by using BOINC at http://boinc.berkeley.edu/. BOINC ( The Berkeley Open Infrastructure for Network Computing) is a non-commercial middleware system for volunteer and grid computing.

5. 5. Benedict9 in reply to riverboots 12:56 AM 7/13/09

Why naturally!

6. 6. ervedge 12:59 AM 7/30/09

The reference/url for "the paper" by Erlich should be:
http://genome.cshlp.org/content/19/7/1243
http://hannonlab.cshl.edu/dna_sudoku/main.html

7. 7. bertwindon 02:35 PM 4/3/10

Baloni

You must sign in or register as a ScientificAmerican.com member to submit a comment.
Click one of the buttons below to register using an existing Social Account.

## More from Scientific American

• News | 10 hours ago | 1

### NASA Funding Shuffle Alarms Planetary Scientists

• News | 10 hours ago | 1

### 25 Train Tragedies Could Have Been Prevented in the Past Decade by This Technology

• News | 11 hours ago | 1

### Earliest Human DNA Shows Unforeseen Mixing with Mystery Population

• TechMediaNetwork | 15 hours ago | 2

### 'Noisy' Icebergs Could Mask Whale Calls

• News | 16 hours ago | 3

More »

## Latest from SA Blog Network

• ### The Cryptozoologicon (Volume I): here, at last

Tetrapod Zoology | 14 hours ago
• ### Not Your Typical Laboratory Equipment Promo Video!

PsiVid | 15 hours ago
• ### Dog Farts Part 1: What Are Dog Farts Made Of?

MIND
Dog Spies | 17 hours ago
• ### The Replication Myth: Shedding Light on One of Science s Dirty Little Secrets

Guest Blog | 17 hours ago
• ### Wordless Wednesday: #DNLeeLab Research Snapshots 2

The Urban Scientist | 20 hours ago

## Science Jobs of the Week

DNA Sudoku

X

Give a 1 year subscription as low as \$14.99

X

X

###### Welcome, . Do you have an existing ScientificAmerican.com account?

No, I would like to create a new account with my profile information.

X

Are you sure?

X