Giulia KennedyPhD
AffymetrixChapter 04 · Strand A · Company

Affymetrix

Eight years as Senior Director at Affymetrix (January 2000 – March 2008), leading the Genomics Collaborations and Genotyping Technology R&D groups behind the GeneChip Mapping arrays.

JAN 2000 – MAR 2008SENIOR DIRECTOR; LED THE GENOMICS COLLABORATIONS AND GENOTYPING TECHNOLOGY R&D GROUPSAFFYMETRIX, INC.

Overview

Giulia Kennedy joined Affymetrix, Inc. in January 2000 and stayed until March 2008. Veracyte’s 2013 registration statement and prospectus both record the title and the dates: Senior Director at “a microarray technology company”.12 At Affymetrix she led the Genomics Collaborations and Genotyping Technology R&D groups,3 and trade press of the period quoted her as senior director of genomics collaborations.4 A later biography adds that she “accelerated commercialization of the company’s platform into multiple emerging markets”.5

Contributions

The eight years at Affymetrix coincide with the arrival of array-based whole-genome genotyping. Her groups’ work appeared as a sequence of methods papers: “Large-scale genotyping of complex DNA” in Nature Biotechnology in 2003, with Kennedy as first author,6 followed in 2004 by the Genome Research description of a one-primer assay genotyping more than 10,000 SNPs on a single array7 and the Nature Methods report of genotyping over 100,000 SNPs on a pair of arrays. BioWorld summarised the run as “Kennedy et al. publishing in Nature Biotech in 2003 and Matsuzaki et al. publishing in Genome Research and Nature Methods in 2004”.4 The research itself is the subject of the next chapter.

The same work entered the patent record. She is a named inventor on US 7,300,788, “Method for genotyping polymorphisms in humans”, granted November 27, 2007 to Affymetrix with Hajime Matsuzaki, Rui Mei and Mei-Mei Shen, with priority back to October 2002;8 on US 8,679,758, “Complexity management of genomic DNA”;910 and, with Manqiu Cao, on the 2003 application “Methods and kits for genotyping ultra-high-complexity DNA”.11

Impact

Affymetrix is where gene discovery turned into platform building: the step from finding individual genes to reading hundreds of thousands of variants at once. It also set up the move that followed. In April 2008, one month after leaving Affymetrix, she joined Veracyte as its first scientific executive.1

Roles

  1. JAN 2000 – MAR 2008Senior Director12
From the record

Facts

  • Was a Senior Director at Affymetrix, Inc., a microarray technology company, from January 2000 to March 2008.12
  • Led the Genomics Collaborations and Genotyping Technology R&D groups at Affymetrix.34
  • At Affymetrix she accelerated commercialization of the company's platform into multiple emerging markets.5
  • Named inventor on US 7,300,788, "Method for genotyping polymorphisms in humans" (granted November 27, 2007, assigned to Affymetrix Inc., with Hajime Matsuzaki, Rui Mei and Mei-Mei Shen) and on US 8,679,758, "Complexity management of genomic DNA" (with Hajime Matsuzaki, Xing Su, Sean Walsh and Rui Mei).8910
  • Named inventor, with Manqiu Cao, on US patent application 2004/0185475, "Methods and kits for genotyping ultra-high-complexity DNA", filed December 17, 2003 and published September 23, 2004.11

Contributions

  • Led the R&D groups whose whole-genome sampling assay and GeneChip Mapping 10K and 100K arrays were described in Nature Biotechnology (2003), Genome Research (2004) and Nature Methods (2004).467
  • Co-inventor on Affymetrix genotyping patents, including US 7,300,788 and US 8,679,758.89

Research

  • Whole-genome genotyping platforms

    JAN 2000 – MAR 2008

    At Affymetrix, where she was a Senior Director from January 2000 to March 2008 leading the Genomics Collaborations and Genotyping Technology R&D groups, Kennedy's teams published the methods that made array-based SNP genotyping practical: "Large-scale genotyping of complex DNA" (Nature Biotechnology, 2003, first author), the one-primer 10K assay (Genome Research, 2004), the 100K array set (Nature Methods, 2004) and the genotype-calling algorithms in Bioinformatics (2003, 2005). She is a co-inventor on the Affymetrix patent "Method for genotyping polymorphisms in humans".

Technologies
  • Affymetrix GeneChip Mapping arrays
  • Whole-genome sampling analysis (one-primer genotyping assay)

Publications

Achievements

  1. 27 NOV 2007patent

    US 7,300,788 granted: Method for genotyping polymorphisms in humans

    US 7,300,788 B2, "Method for genotyping polymorphisms in humans", granted November 27, 2007 and assigned to Affymetrix Inc., names Hajime Matsuzaki, Rui Mei, Mei-Mei Shen and Giulia C. Kennedy as inventors. It claims priority to provisional applications filed October 8, 2002 and May 14, 2003.8

Impact

  • US 7,300,788 GRANTED: METHOD FOR GENOTYPING POLYMORPHISMS IN HUMANS

    One of the Affymetrix genotyping patents from the period in which her group developed array-based whole-genome SNP genotyping.

Impact across the career