Where did first Manhattan plot appear

Question

[johnS]

Hello Friends-

Just out of curiosity where or in which paper did the first Manhattan plot appear?

The first GWAS project paper got published here "Initial sequencing and analysis of the human genome" in nature genetics in 2001. And later around 2004 Manhattan plot became popular. But can't spot in where it first appeared.

In 2002 paper "A Short History of the Genome-Wide Association Study: Where We Were and Where We Are Going" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543921/ ) describes many studies until then but those papers don't mention about Manhattan plot visualization. So assuming it happened later.

[igor]

Do you have any examples from 2004?

[dsull]

There are -log(P-value) vs. position plots in 2004; e.g. Figure 1 of Kammerer et al., Cancer Research, 2004 (for association fine mapping).

I can't find any instance of people calling them "Manhattan" plots per se in 2004 or earlier. My guess is that people made those plots as a convenient way to represent data from association studies of many genetic variants, and then later on, started calling them "Manhattan" plots.

[johnS]

Looks like you got it right dsull

[johnS]

Here is the manual that I was able to find which released in March 2005 where they call it Manhattan plot http://jjwanglab.org/gwasrap/static/images/gwasrank/user_manual.pdf

But I am assuming if it need to be there in a manual, it should be mentioned somewhere in 2004. I am pretty new to the field. So I thought like the experienced people out here who have seen the evolution of GWAS studies from early 20th century might be knowing that when they started seeing it.