Medicine as a data science (2)

The Evolution of Patient Diagnosis: From Art to Digital Data-Driven Science

Currently medical diagnosis is driven by a standard way to proceed. We could say that the pattern of the decision flow has not changed for years.

A physician takes a history, performs an examination, and matches each patient to the traditional taxonomy of medical conditions. Symptoms, signs, family history, and laboratory reports are interpreted in light of clinical experience and scholarly interpretation of the medical literature.

Data availability, and specifically genetic data could change completely diagnostic process.

Initiatives to develop genetic reference data at the population level could be grouped into 3 categories.First are well-known databases of genotype-phenotype relationships
as observed and submitted by researchers (eg, Online Mendelian Inheritance in Man, ClinVar, and the National Human Genome Research Institute’s Genome-Wide Association Study [GWAS] Catalog). Second are databases, such as the Genome Aggregation Database (gnomAD), the next iteration of the ExomeAggregation Consortium (ExAC) database, and the 1000 Genomes Project, that aggregate sequences
collected from other studies for secondary use. Third, patients and other study participants are invited to donate data to registries like GenomeConnect or enroll
in cohorts like the National Institutes of Health All of Us initiative, which is recruiting 1 million patients to contribute biological samples and EHR data for research.

The reference to these databases is crucial to understand what's going on in US medicine, and how european medicine stands behind.
JAMA article develops the concept of Clinical Information Commons:

There should be a new compact between patients and the health system, such that captured data and biospecimen by- products of the care deliverysystem should be aggregated and linked to build a clinical information commons (CIC) to aid diagnosis

I agree. Saluscoop started as an alternative focused in this approach. As usual, the big question is: who is going to invest in a digital commons?. Unless governments take this initiative as a whole, the future of a data driven medicine is uncertain.

Adrian Piper: A Synthesis of Intuitions, 1965–2016

MoMA, New York, New York

Sat 31 Mar 2018 to Sun 22 Jul 2018

Equity and QALYs, terra ignota

Incorporating equity in economic evaluations: a multi-attribute equity state approach

Ptolemy used the term terra ignota for regions that have not been mapped or documented. QALYs were born for maximizing health, without any distributive considerations. All the efforts to introduce equity in QALYs have failed up to now. The cartography of QALYs has a pending dimension.
Maybe this dimension is not possible to be defined under a technical perspective, its a societal and policy issue. And at this level decisions are difficult to take.
Anyway, after reading this article you may reach a similar conclusion than mine, or otherwise you can be optimistic about it. It's up to you.

PS. Today I'll give the kenote speech at Col.legi d'Economistes de Catalunya: "La producció eficient i equitativa de salut".

Ai Weiwei

DROPPING A HAN DYNASTY URN

Man and machine, sharing the decision making effort

Big Data and Machine Learning in Health Care

From JAMA article

It is perhaps more useful to imagine an algorithm as existing along a continuum between fully human-guided vs fully machine-guided data analysis. To understand the degree to which a predictive or diagnostic algorithm can said to be an instance of machine learning requires understanding how much of its structure or parameters were predetermined by humans. The trade-off between human specification of a predictive algorithm’s properties vs learning those properties from data is what is known as the machine learning spectrum

 Higher placement on the machine learning spectrum does not imply superiority, because different tasks require different levels of human involvement. While algorithms high on the spectrum are often very flexible and can learn many tasks, they are often uninterpretable and function mostly as “black boxes.” In contrast, algorithms lower on the spectrum often produce outputs that are easier for humans to understand and interpret.

The meta-informational challenge of molecular data

The future of DNA sequencing

Where does DNA sequencing goes from here?. Nowadays, this is an appropriate question to pose.  The answer appears in an article in an interesting article in Nature.

Now, geneticists would like to have DNA sequences for everyone on Earth, and from every cell in every tissue at every developmental stage (including epigenetic modifications), in health and in disease. They would also like to get comprehensive gene-expression patterns by sequencing the complementary DNA copies of messenger RNA molecules.

In a mere 40 years, the central goal of putting molecular data about cells to practical use has changed from an informational challenge to a meta-informational one. Take clinical applications of genome-sequence data. It may soon be possible to use DNA sequencing routinely to analyse body fluids obtained for any clinical purpose. But only a vast amount of well-organized data about the multi-year medical histories of millions of people will provide the meta-information needed to establish when to ignore such data and when to act on them.

The uncertain cost of clinical trials

How much do clinical trials cost?

A research on seven top pharmaceutical companies has provided fresh data about costs of clinical trials:

For the trials in the data set, the median cost of conducting a study from protocol approval to final clinical trial report was US$3.4 million for phase I trials involving patients, $8.6 million for phase II trials and $21.4 million for phase III trials.

If you compare these data with the total drug costs (2.6 billion), you may ask yourself how all these costs are estimated. Maybe all this information is wrong and useless.

PS. Waiting for the new book on Theranos scandal

Pharma sales 2017

Kupka au Grand Palais

Why is it so difficult to implement policies?

Governance and the Law

If you want to know an updated approach to policy reforms, then you have to read the World Development Report 2017
The main messages:

• Successful reforms are not just about “best practice.” To be effective, policies must guarantee credible commitment, support coordination, and promote cooperation.
• Power asymmetries can undermine policy effectiveness. The unequal distribution of power in the policy arena can lead to exclusion, capture, and clientelism.
• Change is possible. Elites, citizens, and international actors can promote change by shifting incentives, reshaping preferences and beliefs, and enhancing the contestability of the decision making process.
• Three guiding principles for rethinking governance for development are:
• Think not only about the form of institutions, but also about their functions.
• Think not only about capacity building, but also about power asymmetries.
• Think not only about the rule of law, but also about the role of law

You'll understand that the key element of any reform goes beyond evidence on what works and consensus. It should be clearly designed following specific steps. I suggest you have a look at it.

El gran Guillem Roma amb Alessio Arena

Integrating genome and epigenome studies

The Key Role of Epigenetics in Human Disease Prevention and Mitigation

I've said it many times: beware of snake-oil sellers. Nowadays you may find it everywhere, specially on internet. You may get a genetic test for a disease that creates a false illusion of safety, or another that provides an unnecessary and avoidable concern. Only evidence based prescribed tests can be considered appropriate.
Therefore, if you want to confirm that genome is not enough, you have to check the review at NEJM on epigenetics. At the end of the article you'll find the explanation on why we do need integrated genome and epigenome association studies. You'll understand that cancer is fundamentally an epigenetic disease.
The current knowledge is changing quickly some conventional truths and "known unknowns" that we've had for years. This is good news for citizens, and bad news for snake-oil sellers if detected. Governments should help citizens on this screening effort, and protect citizens from fake medical information.