Mendelspod Podcast

In 2004, California voters approved Prop 71 to fund the field of stem cell research by setting up the California Institute of Regenerative Medicine, or CIRM, with $3 billion. George W. Bush was in the White House at the time, and since 2001, his administration had been limiting research that used embryonic stem cells.

We toss the term "precision medicine" around with ease today, and yet payers continue to refuse to pay for diagnostic tests. These are tests that might indicate which treatment will work for a specific patient, thereby saving perhaps hundreds of thousands of dollars, not to mention protecting the patient from unnecessary harm. These are tests which prevent invasive procedures such as unnecessary biopsies.

Josie Briggs is Director of the National Center for Complementary and Integrative Health (NCCIH) at the NIH. She is also currently serving as interim director of the president’s new Precision Medicine Initiative (PMI). What has happened since the president announced the initiative, what is the proposed timeline going forward, and how much money will there be for the project ongoing?

As the FDA works away on final guidance for regulating LDTs, various professional groups unhappy with the course of the FDA have put together and hurried their own proposals up to Captiol Hill. The Diagnostic Testing Working Group (DTWG) has had their proposal drafted into legislation which has already been revised once in the House Energy and Commerce Committeee, while proposals from the College of American Pathologists (CAP) and the Association of Molecular Pathology (AMP) have been presented to both the Senate and the House.

Here on the show, we’ve talked about the lack of reproducibility for much of biological research. We’ve bandied around various percentages--is it 50% or up to 90% that can't be replicated? And we’ve poked around various issues that may be causing such poor science. Nicole Perfito is the manager of the Reproducibility Project: Cancer Biology, an effort between Science Exchange and the Center for Open Science. The goal of this project is to take nearly forty “high impact” papers in the field of cancer and try to replicate them.

By listening to him, you wouldn’t know that Peter Maag, the CEO of CareDx, was fighting to keep his company from the brink. We booked Peter for the show after news came out that CMS was once again threatening to lower reimbursement rates of established diagnostic tests.

Today’s story is one of a personal quest, of groundbreaking science, and the creation of a new movement in human genomics. Jim Lupski is a professor at Baylor College of Medicine where he’s on the frontline of incorporating genomic research into everyday clinical practice. The story begins with Jim’s own genome, which is perhaps the most sequenced genome ever. Jim's life as a leading genomic researcher has been driven in part for a strong personal reason. He has a rare genetic disease named after three researchers who first defined it, Charcot Marie Tooth Neuropathy.

Cliff Reid, CEO of Complete Genomics, is back on the conference circuit, touting a new product. After years of building his company to do sequencing as a service, Cliff presented data at last week's ASHG meeting on Complete's first sequencer as a product, or what they are calling the Revolocity supersequencer. Cliff was a pioneer in developing the service model, offering only whole human genome sequencing. But after being bought out by BGI, who already had a service business in China, he was compelled to shift his business model to that of selling sequencers.

Earlier this year, the California Life Sciences Association (CLSA) launched, becoming the first statewide policy and advocacy group for biotech. The new nonprofit, a merger between BayBio and the California Healthcare Institute, is led by CEO Sara Radcliffe, former Executive VP of Health at the international Biotechnology Industry Organization (BIO) in Washington.

One of the popular questions on the program this past year is how those doing sequencing decide between the quality of Pacific Bioscience's long reads and the cheaper short read technology, such as that of Illumina or Thermo Fisher. Today’s guest provides the most clear and dramatic answer yet: use the PacBio system exclusively.

K Thomas Pickard is not at all into sports cars. So when he hit midlife crisis, it wasn’t a Porsche or a golf club membership that would reenergize his quiet moments. Nope. K T got his genome sequenced.

The last time we talked with Chris Mason of Weill Cornell Medical College the Supreme Court had just decided the controversial Myriad gene patent case. How forever ago two years can seem. Since then Chris has swabbed and sequenced the microbiome of New York City and began the project of sequencing in space. His favorite research this year has been to longitudinally profile the genome, epigenome, transcriptome, metabolome and microbiome of identical twins, one in space and one on earth.

Classes for the school year begin this week at Stanford University. New to the faculty is Carolyn Bertozzi, an American chemist who made her name across the bay at Berkeley and was wooed to Stanford by a chance to do research and teach chemistry in a new interdisciplinary institute known as ChEM-H. The institute will bring chemists, engineers, biologists and medical doctors together to understand life at a chemical level. We’ve often heard of biology and engineering institutes, or bringing bio and IT. This institute ups the ante and includes chemistry and medicine.

Though recent guests at Mendelspod say we're not quite to the $1,000 genome, we're close enough to use that benchmark in genomics discussions. But what are we getting for that almost $1,000? Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project.

What is a human genome? Well it’s the three billion letters of our DNA. But how is it measured? How do we know when we have it accurately represented? These are questions that will have to be answered as precision medicine takes hold; for we must have defined standards that will be the basis for regulatory policy, commerce, and better research. These are also the questions that are foremost on the mind of today’s guest.

It's no secret that America's molecular testing laboratories by and large are worried that the FDA's plan to regulate laboratory developed tests, or LDTs, will severely harm patients. Now they have a new proposal which they are taking directly to Capitol Hill. Roger Klein is the Medical Director of Molecular Oncology at the Cleveland Clinic. He’s also serving as the spokesperson for the Association for Molecular Pathology (AMP) on the controversial topic of regulating LDTs.

Diagnostics can be a tough business. The FDA is making a strong push to bring more oversight. Obtaining reimbursement can be outright Sisyphean. And clinicians are slow on the uptake. All of which makes today’s story so good.

The race to the $1,000 genome has been full of breathtaking advances, one after the other. But is next gen sequencing reaching maturity? Will there be that many more significant innovations?

A slow week in life science left us scratching our heads about the purpose of some new studies. The first, a major project to study the microbes in about 1,200 homes appeared under headlines such as this from Tech Times, "Household Bacteria Can Reveal Volumes about Home Residents." Volumes? Really? A second study claimed that we are less successful at biomedical research today because life expectancy is not going up at the same rate as the growth in funding or the increasing number of scientists. That's a high bar to set.

It’s taken some time, but the NCI is finally sponsoring a big time clinical trial for cancer where the patients are organized by the genomic pathway that defines their cancer rather than the organ type.