Category: Biotechnology

Engineer Seeks Out Single Nucleotide Polymorphisms, Rare Needles in Huge Haystacks

What Anthony Berno does at Affymetrix, Inc., a Santa Clara biotechnology company, is a lot like devising a pitchfork that can dig through an enormous haystack and go straight to the needle. Affymetrix is the producer of GeneChip® nucleic acid probe arrays, incorporating a technology that borrows from semiconductor manufacturing techniques to create "DNA chips" that can analyze huge volumes of genetic information in parallel. One of its applications is in finding single nucleotide polymorphisms (SNPs), a type of genetic marker that will eventually be used to tailor drug therapies to an individual's genetic makeup. For Berno the haystack is the prodigious amount of data generated in the process of DNA analysis, and the needle is the specific location of an SNP.

"We're looking for rare phenomena in real sea of data," Berno said about the challenges of his job, which is to create specialized in-house software for SNP detection. The process begins with Data Desk and visual exploration. The patterns and relationships this reveals are turned into the algorithms that drive the company's analytical tools. Berno began using Data Desk a decade ago when "computers weren't very zippy and there weren't a lot of packages that could deal with large datasets." Even then, he was impressed its visualization capabilities. Now when more powerful computers and Data Desk make datasets of hundreds of thousands of points actually manageable, Berno says his use of Data Desk is still "mostly about visualization, understanding how known DNA sequences relate to unknown genetic material."

Click on the rotating plot to see a complete screenshot.

"GeneChip" is a registered trademark of Affymetrix, Inc.

Name: Anthony Berno

Company: Affymetrix, Inc.

Location: Santa Clara, California

Version: Data Desk 6.0, Windows 95

Typical Dataset: 10,000-100,000 points, drawn from a database of over 1 billion points.

Analysis: "Nothing very fancy in terms of statistics. For me the thing about Data Desk is visualization."

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