Plenge Lab

As readers of my blog know, I am a strong supporter of a disciplined R&D model that focuses on: picking targets based on causal human biology (e.g., genetics); developing molecules that therapeutically recapitulate causal human biology; deploying pharmacodynamic biomarkers that also recapitulate causal human biology; and conducting small clinical proof-of-concept studies to quickly test therapeutic hypotheses (see Figure below).  As such, I am constantly on the look-out for literature or news reports to support / refute this model.  Each week, I cryptically tweet these reports, and occasionally – like this week – I have the time and energy to write-up the reports in a coherent framework.

Of course, this model is not so easy to follow in the real-world as has been pointed out nicely by Derek Lowe and others (see here).  A nice blog this week by Keith Robison (Warp Drive Bio) highlights why drug R&D is so hard.

Here are the studies or news reports from this week that support this model. 

(1) Picking targets based on causal human biology:  I am a proponent of an “allelic series” model for target identification.  Here are a couple of published reports that fit with this model.

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Date posted: March 24, 2017 | Author: | No Comments »

Categories: Drug Discovery Human Genetics Precision Medicine

Like many, I waited with bated breath for results of the anti-PCSK9 (evolocumab) FOURIER cardiovascular outcome study last week. There have been many interesting commentaries written on the findings.  A few of my favorites are listed here (Matthew Herper), here (David Grainger), here (Derek Lowe), and here (Larry Husten), amongst others, with summaries provided at the end of this blog.  Most of these articles focused on clinical risk reduction vs. what was predicted for cardiovascular outcome, as well as whether payers will cover the cost of the drugs.  These are incredibly important topics, and I won’t comment on them further here, other than to say that the debate is now about who should get the drug and how much it should cost.

In this blog, I want to emphasize key points that pertain to human genetics and drug discovery.  And make no mistake: the anti-PCSK9 story and FOURIER clinical trial outcome is a triumph for genetics and drug discovery. This message seems to be getting muddled, however, given the current cost of evolocumab and the observation that cardiovascular risk reduction was less than expected, based on predictions from a 2005 study published by Cholesterol Treatment Trialists (CTT) (see Lancet study here).

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Date posted: March 9, 2017 | Author: | No Comments »

Categories: Drug Discovery Human Genetics Precision Medicine

Yesterday I participated in the National Academy workshop, “Enabling Precision Medicine: The Role of Genetics in Clinical Drug Development” (link here).  There were a number of great talks from leaders across academics, industry and government (agenda here).

I was struck, however, by a consistent theme: most think that “precision medicine” will improve delivery of approved therapies or those that are currently being developed, whether or not the therapies were developed originally with precision medicine explicitly in mind.  Many assume that the observation that ~90% medicines are effective in only 30% to 50% is the result of biological differences in people across populations (see recent Forbes blog here).  This hypothesis is very appealing, as there are many unique features to each of us.

An alternative explanation is that most medicines developed without precision medicine from the beginning only work in ~30% patients because the medicines don’t target the biological pathways that make each of us unique.

I believe the most likely application is in the discovery and development of new therapies.  That is, I believe that the greatest impact will come when precision medicine strategies are incorporated into the very beginning of drug discovery, and will only rarely have an impact on therapies that were not developed with precision medicine in mind from the start.…

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Date posted: February 13, 2016 | Author: | No Comments »

Categories: Drug Discovery Embedded Genomics Human Genetics Precision Medicine

A study published last week in Science described a large-scale genetic association study of Neandertal-derived alleles with clinical phenotypes from electronic health records (EHRs). Here, I focus less on the Neandertal aspect of the study – which to me is really just a gimmick and not medically relevant – and more on the ability to use EHR data for unbiased association studies against a large number of clinical traits captured in real-world datasets. I also provide some thoughts on how this same approach could be used for drug discovery.

[Disclaimer: I am a Merck/MSD employee. The opinions I am expressing are my own and do not necessarily represent the position of my employer.]

The study used clinical data from the Electronic Medical Records and Genomics (eMERGE) Network, a consortium that unites EHR systems linked to patient genetic data from nine sites across the United States. The clinical data was primarily from ICD9 billing codes, an imperfect but decent way to capture clinical data from EHRs. In total, a set of 28,416 adults of European ancestry from across the eMERGE sites had both genotype data and sufficient EHR data to define clinical phenotypes (n=13,686 in the Discovery set; n=14,730 in the replication set).…

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Date posted: May 26, 2015 | Author: | No Comments »

Categories: Drug Discovery Human Genetics Precision Medicine

This week I want to focus on the role of biomarkers in drug discovery and development, which is one of the three pillars of a successful translational medicine program (see slide deck here). The focus is on Alzheimer’s disease, based on recent articles published in JAMA. At the end of the blog you will find postings for new biomarker positions in Merck’s Translational Medicine Department.

[Disclaimer: I am a Merck/MSD employee. The opinions I am expressing are my own and do not necessarily represent the position of my employer.]

Before I start, I want to point to a few blogs that provide counterarguments to some of the optimistic opinions expressed in this blog. The first is David Dobb’s negative view on big data (here); the second on Larry Husten’s concerns about conflicts of interest between academics and industry, as it relates to a recent NEJM series (here). I will not comment further, but it is worth pointing readers to these blogs and related blogs for a balanced view on complicated topics.

I have expressed the strong opinion that what ails drug discovery and development is that we pick the wrong targets, don’t develop robust biomarkers, and we don’t test therapeutic hypotheses quickly enough in clinical trials.

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The primary purpose of this blog is to recruit clinical scientists into our new Translational Medicine department at Merck (job postings at the end). However, I hope that the content goes beyond a marketing trick and provides substance as to why translational medicine is crucial in drug discovery and development. Moreover, I have embedded recent examples of translational medicine in action, so read on!

[Disclaimer: I am a Merck/MSD employee. The opinions I am expressing are my own and do not necessarily represent the position of my employer.]

There is a strong need to recruit clinical scientists into an ecosystem to develop innovative therapies that make a genuine difference in patients. This ecosystem requires those willing to toil away at fundamental biological problems; those committed to converting biological observations into testable therapeutic hypotheses in humans; and those who develop therapies and gain approval from regulatory agencies throughout the world.   The first step is largely done in academic settings, and the other two steps largely done in the biopharmaceutical industry…although I am sure there are many who would disagree with this gross generalization!

The term “Translational Medicine” has been broadly used to describe the second step, thereby bridging the Valley of Death between the first and third steps.…

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I admit upfront that this is a self-serving blog, as it promotes a manuscript for which I was directly involved. But I do think it represents a very nice example of the role of human genetics for drug discovery. The concept, which I have discussed before (including my last blog), is that there is a four-step process for progressing from a human genetic discovery to a new target for a drug screen. A slide deck describing these steps and applying them to the findings from the PLoS One manuscript can be found here, which I hope is valuable for those interested in the topic of genetics and drug discovery.

[Disclaimer: I am a Merck/MSD employee. The opinions I am expressing are my own and do not necessarily represent the position of my employer. However, the PLoS One study was performed while I was still in academics at BWH/Harvard/Broad.]

Before I provide a summary of the study, I would like to highlight a few recent news stories that highlight that the world thinks this type of information is valuable. First, the state of California is investing US $3-million in a precision medicine project that links genetics and medical records to develop new therapies and diagnostics (here, here).…

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There was an eruption in Iceland last week. No, this was not another volcanic eruption. Rather, there was a seismic release of human genetic data that provides a glimpse into the future of drug discovery. The studies were published in Nature Genetics (the issue’s Table of Contents can be found here), with insightful commentary from Carl Zimmer / New York Times (here), Matthew Herper / Forbes (here), and others (here, here).

[Disclaimer: I am a Merck/MSD employee. The opinions I am expressing are my own and do not necessarily represent the position of my employer.]

As I have commented before, human genetics represent a very powerful approach to identify new drug targets (see here, here). I have articulated a 4-step process (see slide #5 from this deck): (1) select a phenotype that is relevant for drug discovery; (2) identify a series of genetic variants (or “alleles”) that is associated with the phenotype; (3) assess the biological function of phenotype-associated alleles; and (4) determine if those same alleles are associated with other phenotypes that may be considered adverse drug events.

There is an important assumption about this model: genes with an “allelic series” will be identified from large-scale genetic studies, and these phenotype-associated alleles will serve as an estimate of function-phenotype dose-response curves.…

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Date posted: January 25, 2015 | Author: | No Comments »

Categories: Drug Discovery Human Genetics Precision Medicine

Dear Mr. President,

I was very pleased to listen to your State of the Union address and learn of your interest in Precision Medicine. As I am sure you know, this has led to a number of commentaries about what this term actually means (here, here, here). I would like to provide yet another perspective, this time from someone who has practiced clinical medicine, led academic research teams and currently works in the pharmaceutical industry.

Let me start by acknowledging that I know very little about your plan, but that is because no plan has been announced. However, that inconvenient fact should not prevent me from forming a very strong opinion about what you should do. Similar behavior is observed in politics (which you know well) and sports radio (see for example “Deflate-gate”). So here it goes…

I want to clarify my definition of “precision medicine” (see here for my previous blog on how this is different from “personalized medicine”). In the simplest of terms, precision medicine refers to the ability to classify individuals into subpopulations based on a deep understanding of disease biology. Note that this is different than what clinicians normally practice, which is to classify patients based on signs and symptoms (which can be measured by clinicians as part of routine clinical appointments).…

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Date posted: November 15, 2014 | Author: | No Comments »

Categories: Drug Discovery Human Genetics Precision Medicine

At the Harvard-Partners Personalized Medicine Conference last week I participated in a panel discussion on complex traits. When asked about where personalized medicine for complex traits will be in the future, I answered that I envision two major categories for personalized therapies.

(1)Development of drugs based on genetic targets will lead to personalized medicine; and

(2)Large effect size variants will be detected in clinical trials or in post-approval studies and will lead to personalized medicine.

This answer, I said, was based in part on current categories of FDA pharmacogenetic labels and in part on how I see new drug discovery occurring in the future.  But did the current FDA labels really support this view? 

The answer is “yes”.  In reviewing the 158 FDA labels (Excel spreadsheet here), my crude analysis found that 31% of labels fall into the “genetic target” category (most from oncology – 26% of total) and 65% fall into the “large effect” category (most from drug metabolism [42% of total], HLA or G6PD [15% of total]).

A subtle but important point is that I predict that category #2 (PGx markers for non-oncology “genetic targets”) will grow in the future.  In other words, development of non-oncology drugs will riff-off the success of drugs developed based on somatic cell genetics in oncology. …

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Date posted: March 16, 2013 | Author: | 1 Comment »

Categories: Precision Medicine

For our website, we have chosen the term “precision medicine” rather than “personalized medicine”.  A recent News article in Nature Medicine reinforces this concept (see here). 

I have had many of my non-genetic physician colleagues comment to me: “We practice personalized medicine every day.  It’s called basic patient care!”  Their point: physicians see patients and make decisions about the best course of treatment based on patient preferences.  For example, one RA patient may prefer to have a drug infusion once per month and another patient may prefer to take a pill each day. 

The Nature Medicine article emphasizes  “the idea that molecular information improves the precision with which patients are categorized and treated“.  While personalized medicine might say “patient X with disease Y should get drug Z”, precision medicine says “patient X has a subset of disease Y — actually, disease Y3, not disease Y1, Y2 or Y4 — and patients with disease Y tend to respond more favorably to drug Z”.  Said another way bt Charles Sawyers, an oncologist at the Memorial Sloan-Kettering Cancer Center in New York: “we are trying to convey a more precise classification of disease into subgroups that in the past have been lumped together because there wasn’t a clear way to discriminate between them“.…

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