Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
In your hiding, you're alone. Kept your treasures with my bones.Coeur de Piratecrawl somewhere bettermore quotes

research: what we do


Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca
The Outbreak Poems — artistic emissions in a pandemic


data visualization + art

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The BC Cancer Agency’s Personalized Oncogenomics Program (POG) is a clinical research initiative applying genomic sequencing to the diagnosis and treatment of patients with incurable cancers.

Art of the Personalized Oncogenomics Program

Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry.
— Richard Feynman

Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Center / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The design on the posters is being used for the Vancouver Ride to Conquer Cancer cycling jersey. (buy a jersey, tour info)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The POG art shows 545 cases studied over the course of 5 years and is freely available as posters for printing and images for your desktop and presentation slides in both bitmap and PDF formats.

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases grouped by diagnosis (tissue type) and then by similarity within group. (zoom)

cancer is the difference of differences

As individuals, we all have slightly different genomes. If you compare the genomes of two people, you will find about 3 million base pair differences, which is about 0.1% of the genome.

This variation exists not only within the population but potentially also, to a lesser extent, among our cells, which number around 40 trillion. That's roughly 10,000 cells for each base in your 3 billion base genome. And each has a role to play.

POG cases, by tissue type
n %
Gastrointestinal 141 25
 
Breast 138 25
 
Thoracic 57 10
 
Gynecologic 45 8.3
 
Soft tissue 44 8.1
 
Skin 11 2.0
 
Urologic 8 1.5
 
Hematologic 7 1.3
 
Head and neck 6 1.1
 
Endocrine 5 0.9
 
Central nervous system 5 0.9
 
Other 78 14
 
ALL 545

One consequence of this complexity and variation is that changes in the genome (through mutation or other processes) can have very different effects, depending on both the change and the genome. Cancer is a phenomena in which cells' ability to organize themselves as they divide is altered due to changes in the genome. It is an incredibly complex biological phenomenon—considering all the genomes in the population and all the possible changes that may arise, there is truly an inexhaustible number of ways in which the genome can break.

classifying cancer

Cancers are classified according to their site of origin, such as lung, breast, liver, or colon. This is a coarse grouping—within each group there are many subtypes with differences in response to treatment and overall behaviour.

diversities among clinical cases

The design of the POG art highlights the diversity and similarity among cases. The diversity is what makes the study of cancer difficult and the similarities are what makes inference possible.

Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Center / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

Each case is represented by three concentric rings. The width of each ring represents the extent to which the case is similar (as measured by correlation) to cancers of the type encoded by the color of the ring (see Methods).

remixes

In additional to the posters, I've created remixes for your desktop at 4k resolution.


 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
png
5 Years of Personalized Oncogenomics Project at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. Cases ordered chronologically by case number. (zoom)

Ride to Conquer Cancer — Data-powered, Human-driven

This year, the cyclists in the Ride to Conquer Cancer will not only have the chance to raise money for research (as they've always done) but also do so while wearing data (as they've never done before).

You can purchase your own data-powered and human-driven cycling jersey.

VIEW ALL

news + thoughts

Virus Mutations Reveal How COVID-19 Really Spread

Mon 04-05-2020

Genetic sequences of the coronavirus tell story of when the virus arrived in each country and where it came from.

Our graphic in Scientific American's Graphic Science section in the June 2020 issue shows a phylogenetic tree based on a snapshot of the data model from Nextstrain as of 31 March 2020.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Virus Mutations Reveal How COVID-19 Really Spread. Text by Mark Fischetti (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: Nextstrain (enabled by data from GISAID).

Cover of Nature Cancer April 2020

Mon 27-04-2020

Our design on the cover of Nature Cancer's April 2020 issue shows mutation spectra of patients from the POG570 cohort of 570 individuals with advanced metastatic cancer.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Each ellipse system represents the mutation spectrum of an individual patient. Individual ellipses in the system correspond to the number of base changes in a given class and are layered by mutation count. Ellipse angle is controlled by the proportion of mutations in a class within the sample and its size is determined by a sigmoid mapping of mutation count scaled within the layer. The opacity of each system represents the duration since the diagnosis of advanced disease. (read more)

The cover design accompanies our report in the issue Pleasance, E., Titmuss, E., Williamson, L. et al. (2020) Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer 1:452–468.

Modeling infectious epidemics

Wed 06-05-2020

Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....
—Samuel Pepys, 1665

This month, we begin a series of columns on epidemiological models. We start with the basic SIR model, which models the spread of an infection between three groups in a population: susceptible, infected and recovered.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

We discuss conditions under which an outbreak occurs, estimates of spread characteristics and the effects that mitigation can play on disease trajectories. We show the trends that arise when "flattenting the curve" by decreasing `R_0`.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (read)

This column has an interactive supplemental component that allows you to explore how the model curves change with parameters such as infectious period, basic reproduction number and vaccination level.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Modeling infectious epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

The Outbreak Poems

Sat 04-04-2020

I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.

That moment
when
you know a moment.
Branch to branch,
flit,
look everywhere,
chirp.
Memory,
scent
of thought fleeting.
Distant pasts
all
ways in plural
form.

Read the poems and learn what a piku is.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

Tue 17-03-2020

A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.

The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

Using Circos in Galaxy Australia Workshop

Wed 04-03-2020

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Using Circos in Galaxy Australia workshop. (zoom)

Download workshop slides.

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).