Interesting "New Yorker" Article

The January 6, 2014 "New Yorker" had an article. "The Gene Factory," by Michael Specter.  It profiles Beijing Genomics Institute (BGI) a Chinese powerhouse in the biotech field.  The website of BGI proudly announces:

"-- World’s largest genome center to purchase 50 Ion Proton™ Sequencers from Life Technologies--

CARLSBAD, Calif., and Shenzhen, China, October 21, 2013 -- Life Technologies Corporation (NASDAQ: LIFE) and BGI, the world’s largest genomics center and service provider, jointly announced that BGI has purchased 38 Ion Proton™ Sequencers and plans to add at least a dozen more by the end of the year, strengthening the organization’s leadership position in the genomics industry. BGI also signed a supply and licensing agreement with Life Technologies, further enhancing BGI’s ability to perform basic, agricultural and clinical research."  

Reading further in the press release:

"Life Technologies Corporation (NASDAQ: LIFE) is a global biotechnology company...[w]ith a presence in more than 180 countries, the company's portfolio of 50,000 end-to-end solutions is secured by more than 5,000 patents and licenses that span the entire biological spectrum—scientific exploration, molecular diagnostics, 21st century forensics, regenerative medicine and agricultural research. Life Technologies has approximately 10,000 employees and had sales of $3.8 billion in 2012."

That's right, 5,000 patents and licenses.

Patent on Human Embryonic Stem Cells

The Wisconsin Alumni Research Foundation (WARF) has obtained a patent on Human Embryonic Stem Cells, USPN 7,029,913.  The validity of the patent is opposed by the Consumer Watchdog (formerly known as the Foundation for Taxpayer and Consumer Rights), a non-profit located in California with an office in D.C.  

The alleged inventor claims:

"I claim:

1. A replicating in vitro cell culture of human embryonic stem cells comprising cells which (i) are capable of proliferation in in vitro culture for over one year without the application of exogenous leukemia inhibitory factor, (ii) maintain a karyotype in which the chromosomes are euploid through prolonged culture, (iii) maintain the potential to differentiate to derivatives of endoderm, mesoderm, and ectoderm tissues throughout the culture, and (iv) are inhibited from differentiation when cultured on a fibroblast feeder layer.

2. The preparation of claim 1, wherein the stem cells will spontaneously differentiate to trophoblast and produce chorionic gonadotropin when cultured to high density.

3. The preparation of claim 1 wherein the cells are negative for the SSEA-1 marker, positive for the SSEA-4 marker, and express alkaline phosphatase."


I will report more on this later.

Background Information on Seqenom

March 28, 2012

From Clinical Sequencing News

"Sequenom could also face heightened skepticism because of its past problems. The company was preparing to introduce another prenatal Down syndrome test in 2009 when it abruptly announced that the data it had promoted to investors could no longer be trusted.

It turned out that a top research official had known which samples were positive and negative and had told subordinates to adjust the parameters of the test to improve its accuracy.

Five executives, including the chief executive and the research official, were fired. The research official, Elizabeth A. Dragon, pleaded guilty to conspiracy to commit securities fraud. (She died this February, before sentencing.)

Sequenom’s stock, which had been over $25 early in 2009, collapsed after the scandal. On Monday it rose 24 cents to close at $5.56.

The Sequenom test correctly identified 209 of the 212 Down syndrome samples, a rate of 98.6 percent. It incorrectly characterized three of 1,471 negative samples as showing Down syndrome. The test could not determine any answer for 13 pregnancies, or about 0.8 percent of cases.

...

The test counts small fragments of DNA in the mother’s blood. While most of this DNA is from the mother, some is from the fetus. Sequenom uses high-speed gene sequencers to determine the sequence of millions of the fragments. Using knowledge of the human genome, it determines which chromosome each fragment comes from. If the fetus has three copies of chromosome 21, there will be more than the expected number of fragments coming from chromosome 21.

One of the first papers on this approach was published in 2008 by Stephen Quake, a professor of bioengineering and applied physics at Stanford. Verinata has the rights to his discoveries, setting up a potential patent battle with Sequenom.

Professor Quake said that by increasing the number of fragments counted, it would be possible to prenatally diagnose abnormalities that do not involve entire extra chromosomes, even single mutations that cause diseases likecystic fibrosis."

Sequenom Goes to CAFC

As expected the Sequenom case has been appealed to the CAFC, the high patent court. The docket entry appears below:

"USCA Case Number 14-1142 USCA for the Federal Circuit for 153 Notice of Appeal filed by Sequenom, Inc.. (ysS, COURT STAFF) (Filed on 12/5/2013) (Entered: 12/06/2013)."

I am 85% certain the lower court's decision will be overturned by the pro-patent CAFC despite the decision in the Myriad case.  The only question I have is whether the Supreme Court will grant cert once the Sequenom case is decided.  Stay tuned for more on this case.

Footnote on Ariosa

According to the complaint in one of the cases now styled Ariosa v Sequenom, the original plaintiff was a company called Aria.  According to the March 28, 2012 edition of a web based journal, Clinical Sequencing News:

"Aria Changes Name to Ariosa Diagnostics; Completes Clinical Validation of Prenatal Trisomy Test."

Sequenom agaonst Ariosa

Sequenom and Ariosa are the two parties named in the NYT article in the previous post.  As usual, it is not that simple.  There are several parties on both sides and a lot of cross suing going on.  But my research has revealed one of the patents (there may be more) involved in the case.  USPN 6,258,540 is directed to:

"Non-invasive prenatal diagnosis."

The Abstract of the Patent: "The invention relates to a detection method performed on a maternal serum or plasma sample from a pregnant female, which method comprises detecting the presence of a nucleic acid of foetal origin in the sample. The invention enables non-invasive prenatal diagnosis including for example sex determination, blood typing and other genotyping, and detection of pre-eclampsia in the mother."
Talk about ethics!  This one's a beaut.

Here's a link to the patent:

http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=6258540.PN.&OS=PN/6258540&RS=PN/6258540

Judge Invalidates Patent for a Down Syndrome Test

http://www.nytimes.com/2013/11/01/business/judge-invalidates-patent-for-a-down-syndrome-test.html?emc=edit_tnt_20131031&tntemail0=y&_r=0