Saturday, January 25, 2014

California's $40 Million Genomics Round: Charges of Unfairness, Factual Error and More

Scientists at two major California research institutions have leveled charges that the state stem cell agency's $40 million genomics round is tainted with unfair and non-scientific considerations along with factual errors, manipulation of scores and apparent preferential treatment.

The statements were contained in letters (see here and below) to the governing board of the state agency from researchers at UC San Francisco and the Scripps Research Institute in La Jolla, who were competing in the round. The allegations involve the agency's closed-door grant review process in which a seven-member consortium led by Stanford University appears the likely winner.

CIRM President Alan Trounson has recommended approval of Stanford's $33 million bid. It was the only application that he supported out of four recommended for funding by CIRM's prestigious grant reviewers. Trounson also specifically recommended not funding the three other applications, including those from UCSF and Scripps. The board's longstanding practice has been to fund all awards recommended by reviewers.

Pui-Yan Kwok
UCSF photo
Pui-Yan Kwok, leader of the UCSF bid, and Jeanne Loring, who heads Scripps effort, have taken their complaints about the process to the agency's 29-member board which meets Wednesday in Berkeley to act on the applications to create one or two stem cell genomics centers in California.

In an e-mail to the California Stem Cell Report today, Kwok said his team has examined the summaries of the grant reviews posted on the CIRM Web site. He said,
“We were surprised to see that the genomic center scores of the top two applications were based on the reviewers removing from consideration the poorest performing center-initiated projects.  The fact that the reviewers could propose removal of individual center-initiated projects was never mentioned in the RFA. 
“Even more appalling is that this was applied only to the two applications (that) ended up with the highest scores.  The end result is that two centers' scores were artificially inflated to 88 and 82, respectively.  Despite this uneven application of the review process, two other applications received Tier 1 (recommended for funding) scores.  This appearance of preferential treatment makes the process suspect."
In his letter late yesterday to the board, Kwok said such actions are “inconsistent” with practices of the National Institutes of Health, whose standards are the norm for virtually all scientific grant reviews. The stem cell agency's review practices are patterned after those of the NIH.

Jeanne Loring
Scripps photo
In her letters to the board and the CIRM staff, Loring addressed four major factual errors that she said were made by reviewers. They ranged from a belief by reviewers that the RFA sought a matching financial commitment from applicants to a belief that Loring's partner in the project, Illumina, Inc., of San Diego, would not make its scientific tools easily available to researchers.

Loring said, however, the only “serious concern” expressed by reviewers in the CIRM review summary was the “lack of material commitment” from the applicants.

Loring said,
“This comment...suggests that other applications did offer to provide extra money for their (genomic) centers. Since there was no written request for additional funds, and we were not informed that contributions would be expected or considered as a measure of scientific merit, we were put at a significant disadvantage.”
(Reviewers praised the Stanford application for its “very substantial matching funds from multiple participating institutions.”)

Loring also stressed the benefits of the partnership with Illumina, a world leader in genomics. The firm recently announced a device that can sequence a human genome for $1,000, which sent its stock jumping this month. She said that Illumina's sequencer is the only one approved by the FDA for clinical diagnostics. She said that partnering with Illumina will give researchers access to tools that can have an “immediate impact” on their clinical studies on cancer, heart disease and inherited diseases.

(On Jan. 27, the agency released a statement defending its procedures. An item dealing with that can be found here.)

The stem cell agency has long come under fire from the biotech community because of the tiny percentage of its funding that goes to industry. Loring noted that last week that the only body charged with overseeing the finances of the agency, the Citizens Financial and Oversight Committee, stressed that it was necessary to form partnerships with industry.

In addition to Illumina, Loring is working with researcher Nicholas Schork, who this month joined Craig Venter's institute in the San Diego area. Venter is internationally famed for his genomics work. She said that the linkage with the institute will provide her project with “even broader access to genomic expertise.” The Venter Institute is involved with the Stanford application as is UC Santa Cruz.

Illumina also sent a letter to the CIRM written by Mostafa Ronaghi, the company's senior vice president and co-project director on the Loring application. Ronaghi said that Illumina makes affordable research tools and will help with planning experiments and analysis. Also involved in the Scripps-Illumina bid is co-investigator Jian-Bing Fan of Illumina.

Kowk said Ophir Klein of UCSF and Steven Brenner of UC Berkeley are co-directors of their effort. Other researchers involved are Michael McManus, Joe Costello, Susan Fisher, Neil Risch and Arnold Kriegstein, all of UCSF; Lin He and Dan Rokhsar, both of UC Berkeley, and Amander Clark of UCLA.

The California Stem Cell Report has queried Stanford concerning a list of its participants.

The names of the other applicants in genomics round are not known. The stem cell agency will not release the names of winning applicants until after the board acts and never releases the names of rejected applicants. The agency also withholds the names of applicants from the board prior to its action on them unless the applicants “self-identify,” usually in the form of letters to the board, which are a public record. Board members also do not have access to the actual application nor does the public. Some board members have complained in the past about not having enough information to act when applicants appear directly before the board.

Directors have final legal say on all applications. They do not, however, have to act on any of them. They can increase funding beyond the $40 million originally budgeted for this round or lower it. They can also send the applications back to reviewers for reconsideration or approve them with conditions.

Here is a copy of Kwok's letter, which the stem cell agency has not yet posted.


  1. Anonymous1:43 PM

    The 2nd highest ranked application was UCLA not Scripps or UCSF.

  2. Anonymous3:39 PM

    Given that the two of the four recommended applications are from STATE institutions, why aren't they moved to the top? CIRM is funded with taxpayer money, so why is government money supporting a private institution (Stanford), with all of the accruing intellectual property rights and income going to Stanford and not to a California institution with intellectual property income returning to the public purse. Centers should be offered to STATE institutions so the money is used for public purposes and not to support private entities, all things being more or less equal.


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