cancer


Knowing More about What We Don’t Know: John McPherson on Cancer Genomics

More than with any other major disease, the understanding and treatment of cancer is being transformed by genomics. And these are early days.

John McPherson has been involved in sequencing since the original Human Genome Project. He now directs the Genome Technologies Program at the Ontario Institute for Cancer Research. John chaired a panel on cancer genomics at the recent AGBT, or Advances in Genome Biology and Technology conference, and shares his thoughts on this year's meeting.

Like many others, John is excited about the new possibilities gained by long read sequencing, particularly in showing structural variations of various cancers.

We ask John which platforms he likes, and most importantly--in this day with increasing sequencing instrument options--how he decides how much to spend on sequencing to answer a specific question.

"Our goal is to be as accurate as we can," he says. "For single nucleotide variants (SNPs), we see about a 93-95% verification rate. And we’re pretty happy with that. The question becomes how many samples you do, and not what you do to a sample. Depending what question you’re asking, the number of samples affects your power overall.”

John works in Ontario. We ask him about the state of clinical genomics in Canada, a country with a single payer system.

Cancer Researcher at Mayo Says Illumina Platform Maxing Out, Looks to BGI/Complete

Today we bring you a story which you probably wouldn’t have heard at last week’s AGBT conference at Marcos Island. While PacBio and 10X Genomics were getting most of the buzz at the annual show on all things sequencing, it could be the new BGI/Complete Genomics platform that steals the show later this year, says David Smith, a cancer researcher at the Mayo Clinic.

In his research, David uses sequencing to analyze the connection between the human papillomavirus (HPV) with oropharyngeall cancer.

“A couple decades ago, the incidence of HPV in oropharyngeal cancer was less than 20%. And now at the Mayo Clinic, 80-90% of these cancers are HPV positive,” he says.

Why? A change in sexual practices, David says.

To find out just how HPV causes cancer and integrates into the genome, David is using ‘long read, mate pair’ sequencing. This is a new technology that essentially converts short reads got from such platforms as Illumina’s into long reads. David acknowledges the nice long reads coming from the PacBio machines, but says the cost is still prohibitive. He’s looking for a price that scales into the clinic, and for this, he's most excited about a product that BGI is rolling out later this year, i.e., an already assembled human genome sequencing for $1,000.

We finish the interview with a discussion about how well clinical genomics is being adopted into practice at Mayo.

Cancer 2014: The Year in Review with Anna Barker

Guest:

Anna Barker, Co-Director, Complex Adaptive Systems Center, ASU Bio and Contact Info

Listen (3:21) Andy's challenge

Listen (4:39) The year of immunotherapy

Listen (4:53) iSpy 2 and a new approach to clinical trials

Listen (6:42) The swan

Listen (6:35) A coalition of the willing

Listen (5:14) Six reasons biomarkers fail

In 2003, the then Director of the National Cancer Insitute, Andrew von Eschenbach, issued a challenge: “to eliminate the suffering and death from cancer, and to do so by 2015.”

Anna Barker is the former Deputy Director of the National Cancer Insitute, and she was at the meeting when Dr. von Eschenbach issued his challenge. Now at the end of 2014, we talk with Anna about the challenge and how far we have come. She offers her vote for the three most important developments in cancer this past year.

Who Do You Want to Hear From During the Holidays?

It's a tradition at Mendelspod to bring you unique shows that go off the beaten track at the end of each year. In the past, we've brought you interviews with a science historian, a science comedian, sci-fi writers, and futurists.

We're just planning our lineup for holiday season 2014, and we want your suggestions. On the list so far are a philosopher, a popular sci-fi writer, and the former Deputy Director of the NCI.

Make your suggestions here.

Thank you, Theral & Ayanna

What a Physicist Can Tell Us about Cancer

Guest:

Paul Davies, Principal Investigator, Center for the Convergence of Physical Science and Cancer Biology, ASU Bio and Contact Info

Listen (4:05) The phone call

Listen (3:39) Too focused on a cure

Listen (8:21) What is your theory about cancer?

Listen (4:55) Evolutionary roots of cancer can suggest new therapies

Listen (3:31) Is your message taking root?

Listen (5:21) We must have new ideas

Paul Davies has had a full career as a theoretical physicist. He’s the author of some popular books, most notably, God and the New Physics. In 2007 Paul received a call from someone he’d never heard of before, Anna Barker, then the Deputy Director of the NCI. She wanted to recruit him to the War on Cancer.

“Anna said that she felt that physicists had been very successful in their own sphere. They figured out how the atom works and how the universe works. What about figuring out how cancer works. My reply was that I didn’t know anything about cancer. And she said, 'that’s fine.’”

In today’s interview Paul explains the theory he has developed by following cancer back to its evolutionary roots.

“Cancer is a reversion, or throwback, or rewinding of the evolutionary clock at high speed,” he says.

And therefore, looking at the conditions of life and of the earth at the time cancer developed, Paul argues, can offer new ways of developing treatment. Paul says that we’ve been too focused on “the C word” or a cure. He thinks that rather, we should look at ways to be able to delay cancer.

Is his message taking root? Join us as we probe an entire new way of looking at cancer.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

'Moving Target Science:' Jonathan Brody on Pancreatic Cancer

Guest:

Jonathan Brody, Assoc Professor of Surgery, Thomas Jefferson University

Bio and Contact Info

Listen (8:17) BRCA testing being used for pancreatic cancer as well

Listen (3:31) The Tennis Ball Bucket Challenge

Listen (6:25) Moving target science

Listen (7:23) A seamless infrastructure

Listen (5:03) Patient consent

Look for Jonathan Brody, a scientist at Thomas Jefferson University, on Google, and you’ll likely find a picture of doctors having buckets of tennis balls dropped on their heads.

Based obviously on viral “Ice Bucket Challenge,” the “Tennis Ball Bucket Challenge” was a way for Jonathan and his colleagues to bring awareness to the lack of funding for pancreatic cancer. Though the outlook for pancreatic cancer patients is much bleaker than for those with breast or prostate cancer, funding into pancreatic cancer research is much lower. Jonathan makes sense of the connection.

“Patients [with pancreatic cancer] just have time to get angry and put up a fight. They don’t have time like breast cancer patients,” Jonathan points out in today’s show. "You go to a breast cancer run, and there’s hundreds and hundreds of survivors. You go to a pancreatic [cancer] fundraiser, and it’s really sad when they say, everyone who’s a survivor raise your hand. You might be lucky if it’s a big event, if there’s a dozen or so.”

Based in the Department of Surgery at Thomas Jefferson University, Jonathan is in a unique situation working with physician scientists to translate findings in cancer research directly into patient care. It’s what he calls moving target science. He shares his dream that one day we’ll look at cancer as we used to look at bacterial infections: diagnosis and tailored treatment.

The Progress of Clinical Genomics in Sweden with Ulf Gyllensten

Guest:

Ulf Gyllensten, Professor, Department of Immunology, Genetics, and Pathology, Uppsala University, Sweden Bio and Contact Info

Listen (4:24) What are your goals at the National Genomics Infrastructure?

Listen (4:42) PacBio revolutionizing HLA typing

Listen (4:01) Getting the word about long reads out to clinicians

Listen (3:17) What would you like to see from sequencing companies in the future?

Listen (8:03) An update on clinical genomics in Sweden

Listen (5:02) The Road Show

For our final show in the series on long read sequencing, we move to Sweden and talk to Ulf Gyllensten, Co-Director of the National Genomics Infrastructure.

Ulf and his team use all the major sequencing platforms, and one of their jobs at the NGI is to compare the platforms. In today’s interview, he tells of the goals at the NGI and how new long read technology from PacBio is opening up new applications.

Some of these applications are clinical, and Ulf gives an update on clinical genomics in Sweden where regulation and privacy concerns are much more straight forward than they are here in the U.S.

Podcast brought to you by: Pacific Biosciences - providers of long read sequencing solutions based on their Single Molecule Real Time technology.

Proteins Are Where It's At: Chip Petricoin, George Mason University

Guest:

Emanuel "Chip" Petricoin, Co-Director, CAPMM, George Mason University 

Bio and Contact Info

Listen (4:00) Beyond the genome

Listen (5:30) Challenges to mapping the proteome

Listen (10:35) A new level of resolution for studying protein activity

Listen (6:05) 95% of cancer patients treated at the community level

Listen (8:12) Taking the latest in tumor profiling to patients everywhere

Today we continue our series on the democratization of tumor profiling with Chip Petricoin, Co-Director for Applied Proteomics and Molecular Medicine at George Mason University.

Chip says we must now go beyond the genome to the proteome and metabolome to really understand the biology of disease. Chip is particularly interested in hard to treat cancers such as pancreatic cancer.

The proteins are where the action is, insists Chip. Proteins are the drug targets for approved therapies. They comprise most of the biomarkers looked at in routine therapy. And proteins form the pathways and networks that everyone has been talking about.

“There’s no such thing as a gene pathway,” Chip says in today's interview. "Genes don’t form pathways. Genes don’t move. Genes aren’t the software of the cell. Genes are the blueprint. Proteins form the pathways. They do the work."

What are the challenges in characterizing the human proteome, and what new strategies are researchers like Chip using to get at a new level of awareness of protein activity?

Chip's work is being commercialized at two companies. The first, Theranostics Health, is developing a diagnostic that will measure protein activation. Perthera, the second company, uses not only genomics, but also proteomics to profile tumors. Chip explains how Perthera is taking the latest research that, until now, has been accessible only at major research hospitals and makes it available to community oncologists everywhere.



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