Alternative medicine

There’s a breathtakingly ignorant comment that has done the rounds of late, and it goes like this:  there are only two types of medicine, that which works and alternative medicine.  This suggests that modern medicine is an open house, a “come all ye” of every therapy and treatment that has been proven to work, while alternatives are the festering dump of scoundrels, fraudsters and quacks who prey on the weak and desperate.  As quantum physicist Richard Feynman said of very daft theories, the statement is so far off the grid that it isn’t even wrong.

Modern medicine is an interesting amalgam of church and industry: as a church it has set beliefs about the body and disease, and any other opinions are dismissed as heresy, and, as an industry, its primary purpose is to deliver drugs to the sick

To maintain its beliefs and purpose, it will—if absolutely necessary—commit fraud, massage data, and sneer at any alternative.  This modus operandi is brought into sharp focus by our Special Report this month on cancer.  Inspired by the recent High Court struggle by Sally Roberts to block radiotherapy on her son, Neon, it reviews the evidence for the efficacy of conventional cancer treatments, and the unseemly way it has traduced promising alternative therapies.

It’s a story of spin and half-truths that has sometimes even beguiled the oncologist, not to mention the poor patient and the ever-obliging media.  A favourite trick of the researcher, for example, has been to use relative risk instead of the more meaningful absolute risk when presenting its conclusions; in relative terms, the chemotherapy patient has a 50 per cent chance of living a further five years, but in absolute terms, his chances are just 2 per cent.

Medicine is as fast and loose with the truth when it comes to assessing alternatives, as Dr Nicholas Gonzalez found out to his cost when his enzyme therapy was selected by the National Cancer Institute for a controlled study.  It ended in tears.  Bias from the outset resulted in a poorly-conducted trial that yielded the results the head researcher wanted; he, by the by, had been a pioneer of a new chemotherapy regime that was being tested against Gonzalez’s therapy, and so independence was impossible.

Ultimately, we have to conclude that health and disease is far too important an issue to be left in the hands of the church of medicine

Personal Genome Project Canada launches

The Personal Genome Project Canada (PGP-C) launches this week giving Canadians an unprecedented opportunity to participate in a groundbreaking research study about human genetics and health.

A collaborative academic research effort with Harvard Medical School’s Personal (PGP-HMS), PGP-C aims to sequence the genomes of 100 Canadians over the next year. Combined, the projects will sequence 100,000 individuals over 10 years and the collected will be deposited into a public repository that researchers from around the world can use as control data. Founded in 2005, PGP-HMS currently has more than 2,100 enrolled volunteers with publicly available genetic and health information, including more than 100 whole genomes.

The sequenced genomes will serve as a valuable resource to researchers searching for the  for diseases, including cancer and autism, as well as scientists working on computer software to better analyze  information.

“It is estimated that we will need to decode 100,000 genomes worldwide to begin to make sense of those genetic variants that are involved in disease and those which protect us from it,” says Dr. Stephen Scherer, Director of the University of Toronto’s McLaughlin Centre and The Centre for Applied Genomics at The Hospital for Sick Children.

Dr. Scherer’s group is actively involved in research studying the genomes of individuals with disorders like autism. His team also hosts the Database of Genomic Variants, a resource that supports diagnostic laboratories worldwide in their interpretation of clinical .

 sequencing is entering  and we need to know from the Canadian perspective how to deal with the data from all aspects of the technology, information sciences, privacy and health economic impact,” says Scherer.

Through a partnership with Life Technologies, PGP-C recently used the Ion Proton™ System to complete the whole genome sequence of the first research participant, Jill Davies or “PGPC-1,” and aims to incrementally grow the number of individuals with genome sequences over time. Davies is a genetic counselor at Toronto’s Medcan Clinic, Canada’s largest private clinic. The Clinic is supporting Scherer’s research team to enable the collection of participants and to help determine the clinical significance of the data. Each genome encodes six billion genetic letters, which now takes about a week to sequence and twice that time to generate a rudimentary description of its contents. PGP-C will accelerate the process of understanding how to fully decode this information.

The dramatic decline in the cost of whole genome sequencing now makes it possible for large numbers of Canadians to have their genomes analyzed.

“Run out of the University of Toronto’s McLaughlin Centre, the project will educate medical students, physicians, and health care workers and help them understand and apply the new genomic data to benefit patients and families,” says Dr. Catharine Whiteside, Dean of the Faculty of Medicine at the University of Toronto.

More information: Volunteers who are interested in sharing their genetic and self-reported health information should visit: www.personalgenomes.ca

100K genome project unveils 20 more foodborne pathogen genomes

The 100K Genome Project, led by the University of California, Davis, the U.S. Food and Drug Administration’s Center for Food Safety and Applied Nutrition, and Agilent Technologies, today announced that it has added 20 newly completed genome sequences of foodborne disease-causing microorganisms to its public database at the National Center for Biotechnology Information.

The genomes were determined using Single Molecule, Real-Time (SMRT®) Sequencing technology from Pacific Biosciences of California, Inc.

This brings to 30 the number of genomic sequences completed by the 100K Genome Project, which aims to sequence the genomes of 100,000 bacterial and viral genomes. This genome sequencing effort is focused on speeding the diagnosis and treatment of foodborne diseases, as well as shortening the duration and limiting the spread of . In the United States alone, foodborne diseases annually sicken around 48 million people and kill approximately 3,000, according to the Centers for Disease Control and Prevention.

The newly deposited sequences include several isolates of Salmonella, Listeria, Campylobacter, and Vibrio, as well as a full characterization of their epigenomes – a diagnostic feature that defines how the DNA is chemically modified and changes how the organism behaves.

“These finished genome sequences represent the highest quality standard, with each strain closed in a single  and the associated mobile DNA,” said Bart Weimer, director of the 100K Genome Project and professor at the school of veterinary medicine at UC Davis. “They also contain complete associated phage or plasmid elements, which are critical for understanding pathogenicity,  and other biologically important traits that are linked to survival.

“The genomes we have analyzed to date are from pathogens responsible for common and debilitating foodborne infections,” Weimer said, noting that the ready availability of this information will aid in reducing the time needed to diagnose and define outbreak strains.

“Making these genomic sequences publicly available through the National Center for Biotechnology Information database provides researchers and public health officials with information that will allow tracking of foodborne pathogens to their source,” said Marc Allard, an FDA genomics expert and advisor to the 100K Genome Project. “This will ultimately speed outbreak investigations, reduce illness, and facilitate the development of new rapid test methods to detect pathogens.”

The new genomes were sequenced and assembled using technology capable of detecting and identifying -wide methylation patterns as it performs DNA sequencing.

“Increasingly, microbiologists are recognizing that epigenetic information provides essential clues to the virulence of an outbreak strain,” said Jonas Korlach, chief scientific officer at Pacific Biosciences. “The automated pipelines that made the completion of these 20 genomes and epigenomes possible serve as a solid foundation for the production of many more high-quality, finished genomes of foodborne pathogens through this project in the near future.”