Treat the Pathway, not the Gene (from Precision Medicine and the Reinvention of Human Disease)
Treat the key pathway, not the genetic mutation (fromPrecision Medicine and the Reinvention of Human Disease)Some of the earliest and most successful Precision Medication drugs have targeted specific mutations occurring in specific subsets of diseases. One such example is ivacaftor, which targets the G551D mutation present in about 4% of individuals with cystic fibrosis [135]. It is seldom wise to argue with success, but it must be mentioned that the cost of developing a new drug is about $5 billion [136]. To provide some perspective, $5 billion exceeds the total gross national product of many countries, including Sierra L...
Source: Specified Life - February 5, 2018 Category: Information Technology Tags: clinical trials convergent pathways cost of precision medicine precision treatment Source Type: blogs
National Patient Identifiers (from Precision Medicine and the Reinvention of Human Disease)
Readers from outside the United States are probably wondering why the United States agonizes over the problem of patient identification. In many other countries, individuals are given a unique national identifier, and all medical data associated with the individual is kept in a central data repository under the aegis of the government ’s health service. A single, permanent identifier is used by a patient throughout life, in every encounter with a hospital, clinic, or private physician. As a resource for researchers, the national patient identifier ensures the completeness of data sets and eliminates many of the problems ...
Source: Specified Life - February 4, 2018 Category: Information Technology Tags: confidentiality identification medical identifier national patient identifier privacy Source Type: blogs
Paradoxes of Classification (and terrible Class definitions)
The formal systems that assign data objects to classes, and that relate classes to other classes, are known as ontologies. When the data within a Big Data resource is classified within an ontology, data analysts can determine whether observations on a single object will apply to other objects in the same class. Similarly, data analysts can begin to ask whether observations that hold true for a class of objects will relate to other classes of objects. Basically, ontologies help scientists fulfill one of their most important tasks; determining how things relate to other things.A classification is a very simple form of ontolo...
Source: Specified Life - February 3, 2018 Category: Information Technology Tags: big data classification ontologies paradoxes precision medicine taxonomy Source Type: blogs
Precision Medicine and the Reinvention of Human Disease (not just about genes)
If everything you know about Precision Medicine comes from the lay press, you may have an unrealistic notion of what ' s happening in this field. The news seems to stress the one gene-> one disease paradigm that is easy to understand, but largely irrelevant to all the common diseases that occur in humans.The one gene-> one disease paradigm is this: the clinical expression of each disease is caused by a genetic mutation in a particular gene responsible for that particular disease, or a particular subtype of a disease, in a particular individual. By finding and targeting the gene responsible for an individual ' s disease, Pr...
Source: Specified Life - February 1, 2018 Category: Information Technology Tags: common diseases complex diseases disease biology monogenic pathogenetic precision medicine rare diseases Source Type: blogs
Precision Medicine and the Reinvention of Human Disease (a better definition)
We can define Precision Medicine as an approach to the prevention, diagnosis, and treatment of disease that is based on a deep understanding of the sequence of biological events that lead to disease. With this approach we are learning:(1) that we can develop new drugs that target specific steps in the development of disease;(2) that drugs developed to interfere with a cellular event or pathway may serve as effective treatments for those individuals whose disease is driven by the pathway; and(3) that a treatment effective for a subtype of one disease may also be effective against other diseases that happen to be driven by t...
Source: Specified Life - January 28, 2018 Category: Information Technology Tags: definition pathogenesis precision medicine Source Type: blogs
Precision Medicine and the Reinvention of Human Disease (not just the genome)
If you believe the lay press, Precision Medicine involves sequencing a patient ' s genome and determining the proper treatment based on the individual ' s unique genetic attributes. The NIH (National Institutes of Health) seems to be encouraging this interpretation of the field. From the US National Institutes of Health comes the following description: " Precision Medicine is an emerging approach for disease prevention and treatment that takes into account people ' s individual variations in genes, environment, and lifestyle. The Precision Medicine Initiative will generate the scientific evidence needed to move the concept...
Source: Specified Life - January 27, 2018 Category: Information Technology Tags: definition genomics individualized treatments precision medicine Source Type: blogs
Precision Medicine and the Reinvention of Human Disease (from Preface)
Something has happened in the past two decades that has changed the way that modern biomedical scientist thinks about diseases. Because the changes in our perceptions have happened slowly, few of us have really taken notice of what it all means. The purpose of my latest book,Precision Medicine and the Reinvention of Human Disease, published January, 2018, is to show how advances in the field of Precision Medicine will forever change the way we understand and treat disease. Specifically, these advances are:Diseases develop in steps. Modern methodology has enabled us to dissect the biological events and metabolic pathways th...
Source: Specified Life - January 26, 2018 Category: Information Technology Tags: pathogenesis precision medicine rare diseases subtypes Source Type: blogs
Precision Medicine and the Reinvention of Human Disease (The Myth)
If you believe the hype, we are entering a new era of medicine in which each individual will receive unique treatment, determined by the sequence of his or her genome. This widely promulgated notion is simply ridiculous. There is no practical way to develop a unique treatment, test the treatment for safety and effectiveness, and titrate the correct dose, all for one person.The terms " Precision Medicine " and " Personalized Medicine " have given us the false impression that medical science is moving away from off-the-rack remedies and is seeking treatments tailored to the individual. In actuality, science has always been a...
Source: Specified Life - January 25, 2018 Category: Information Technology Tags: complex diseases jules berman Ph.D. jules j berman M.D. precision medicine precision treatment subsets of common diseases Source Type: blogs
Precision Medicine and the Reinvention of Human Disease (Book Index)
In January, 2018, Academic Press published my bookPrecision Medicine and the Reinvention of Human Disease. This book has an excellent " look inside " at itsGoogle book site, which includes the Table of Contents. In addition, I thought it might be helpful to see the topics listed in the Book ' s index. Note that page numbers followed by f indicate figures, t indicate tables, and ge indicate glossary terms.AAbandonware, 270, 310geAb initio, 34, 48ge, 108geABL (abelson leukemia) gene, 28, 58ge, 95 –97Absidia corymbifera, 218Acanthameoba, 213Acanthosis nigricans, 144geAchondroplasia, 74, 143ge, 354geAcne, 54ge, 198, 220geAcq...
Source: Specified Life - January 23, 2018 Category: Information Technology Tags: index jules berman jules j berman precision medicine Source Type: blogs
Announcement: Precision Medicine and the Reinvention of Human Disease
In January, 2018, Academic Press is publishing my latest book,Precision Medicine and the Reinvention of Human DiseaseHere is the book description, from the back cover:Despite what you may have read in the popular press and in social media, Precision Medicine is not devoted to finding unique treatments for individuals, based on analyzing their DNA. To the contrary, the goal of Precision Medicine is to find general treatments that are highly effective for large numbers of individuals who fall into precisely diagnosed groups.We now know that every disease develops over time, through a sequence of defined biological steps, and...
Source: Specified Life - January 22, 2018 Category: Information Technology Tags: book announcement carcinogenesis causality classification of disease genomics jules j berman pathogenesis precision medicine Source Type: blogs
CLASS BLENDING: Simpson's Paradox
For the past two days, we ' ve been posting on < a href= " http://julesberman.blogspot.com/2016/03/intro-to-class-blending.html " > < b > Class Blending < /b > < /a > . Simpson ' s paradox is a special case that demonstrates what may happen when classes of information are blended. < br > < hr > < br > Simpson ' s paradox is a well-known problem for statisticians. The paradox is based on the observation that findings that apply to each of two data sets may be reversed when the two data sets are combined. < br > < br > One of the most famous examples of Simpson ' s paradox was demonstrated in the 1973 Berkeley gender bias ...
Source: Specified Life - March 29, 2016 Category: Information Technology Tags: classification classifications complexity data science data simplification irreproducible results ontologies ontology Simpson ' s paradox Source Type: blogs
CLASS BLENDING: Simpson's Paradox
For the past two days, we've been posting on Class Blending. Simpson's paradox is a special case that demonstrates what may happen when classes of information are blended. Simpson's paradox is a well-known problem for statisticians. The paradox is based on the observation that findings that apply to each of two data sets may be reversed when the two data sets are combined. One of the most famous examples of Simpson's paradox was demonstrated in the 1973 Berkeley gender bias study RbicaR. A preliminary review of admissions data indicated that women had a lower admissions rate than men: Men Number of applicants.. 8,442...
Source: Specified Life - March 29, 2016 Category: Information Technology Tags: classification classifications complexity data science data simplification irreproducible results ontologies ontology Simpson ' s paradox Source Type: blogs
Open for Comment
For the past several years, I've kept this blog closed to comments. Prior to that, most of the comments were thinly disguised advertisements for pharmaceuticals, and I got tired of rejecting them. For the past month or so, I've re-opened the blog for readers' comments, without announcing the change; just to check whether I'd be inundated with computer-generated promotions. It seems that neither software agents or readers have noticed the change. So, please, if you are a human and would like to send a comment, feel free to use the comments link at the bottom of every post. Your comments will be moderated, but I intend...
Source: Specified Life - March 28, 2016 Category: Information Technology Tags: announcement blog comments postings Source Type: blogs
Expunging a Blended Class: The Fall of Kingdom Protozoa
In yesterday's blog, we introduced and defined the term "Class blending". Today's blog extends this discussion by describing the most significant and most enduring class blending error to impact the natural sciences: the artifactual blending of all single cell organisms into the blended class, Protozoa.For well over a century, biologists had a very simple way of organizing the eukaryotes (i.e., the organisms that were not bacteria, whose cells contained a nucleus) (1). Basically, the one-celled organisms were all lumped into one biological class, the protozoans (also called protists). With the exception of animals and pl...
Source: Specified Life - March 27, 2016 Category: Information Technology Tags: Apicomplexa classification complexity data science irreproducible results ontologies ontology protists protoctista protozoa Source Type: blogs
Intro to Class Blending
I thought I'd devote the next few blogs to a concept that has gotten much less attention than it deserves: blended classes. Class blending lurks behind much of the irreproducibility in "Big Science" research, including clinical trials. It also is responsible for impeding progress in various disciplines of science, particularly the natural sciences, where classification is of utmost importance. We'll see that the scientific literature is rife with research of dubious quality, based on poorly designed classifications and blended classes. For today, let's start with a definition and one example. We'll discuss many more spe...
Source: Specified Life - March 26, 2016 Category: Information Technology Tags: classification complexity data science irreproducible results ontologies ontology Source Type: blogs
