Pedigree-drawing software and "The Archers" Family Tree

Children's Hospital of Pennsylvania Department of Biomedical and Health Informatics (CHOP/BHI) has done a great job of trying to design a simple-to-use pedigree drawing software.  Their app, called Proband (available at http://probandapp.com/) is available to use on an iPad but not other platforms as far as I’m aware.  It seems to incorporate quite a few of the features on the wishlist in my previous post of February 2014.  

To illustrate the end product, I wanted to find a family tree that was already in the public domain and BBC Radio 4's The Archers fitted that category. The family is getting quite large now, and provides a reasonable test for Proband (and my drawing skills). The result is shown below- please scroll along to see all of it. 

The pedigree likely contains controversial entries and errors, and I'd be happy to have them pointed out to me at charles.shawsmith@gmail.com, with Archers in the subject line - please feel free.  

Irrespective of whether they are drawn by hand or by computer software, let us acknowledge that pedigrees provide a uniquely simple, clear and accessible way of appreciating family relationships.  I’m a bit surprised that the Archers official website doesn’t have one, and in fact having thoroughly scoured the internet for an Archers family tree, I could find only one, which was some years out of date, though still a good help to me in drawing mine.  It's available here. I did contact the author but no response.

A couple of points to make about the software, perhaps for the attention of CHOP/BHI if they are interested in feedback:

The really good part of it is the intuitive, simple to use way in which additional family members are created and linked in to the family tree, using the iPad touch screen.  

It is quite difficult to move people around the pedigree once it is in an advanced state.  It would be great to be able to 'group' individuals in a particular branch of the tree, as in Powerpoint, and move them.  This would enable the user to put siblings in the correct birth order, something I didn't do on this pedigree having overlooked the issue at the beginning. 

It would be useful if the 'align' button also had the effect of putting in even spacing of all the individuals on the pedigree- doing this manually is time-consuming.

There isn't an obvious way in the software to put in names and dates of birth, strangely, so these have gone in under 'diagnosis' - there must be a better way of doing that.  Ideally in my opinion, this software would enable the user to enter names by handwriting using a stylus on the touch-sensitive screen, which would then be converted to typeface once checked.

Overall, though, and with a few simple modifications, this software would be suitable for use in the genetics clinic for the purpose of updating pedigrees with new information.  It could mean an end to the hybrid system currently operating in our and I dare say other departments, where electronically drawn pedigrees are printed and manually annotated in the clinic, resulting in duplication of information and effort.

For the sake of balance I should point out that there are quite a few other pedigree-drawing software packages available. Progeny is one, a new pedigree-drawing software incorporated into Trakgene is another.  Here is another, doubtless there are more.  The point is that, in my view, we should be embracing these solutions which will help us to move towards an electronic patient record for Clinical Genetics.  

Clinical data entry for the 100,000 Genomes Project

Next Wednesday I will sit down with a colleague from Genomics England (GEL) and undertake a data entry blitz on upwards of 50 families recruited to the 100,000 Genomes Project.  The data will be transcribed from the patients' paper records into an electronic database administered by GEL.  The pile of paper records is quite substantial (see illustration below).  

The size of the pile has focussed the mind somewhat, and I would like to argue in this article that data should be collected from patients in the clinic electronically and in a way which is compatible with other formats, including the database held by GEL for patients and families enrolled in the 100,000 Genomes Project. 

The offending pile

Background on the 100,000 Genomes project is available here and here.  The project is, in my view, an entirely worthwhile attempt to improve the availability of state of the art genetic testing for patients and families affected by rare disorders.  The idea is to decrease the length of time it takes for these families to get a diagnosis, families such as that of the individual I met last month who has been trying to understand the reason for her three mentally handicapped sons since the first of them was born, in 1967.

The project has been funded by the UK government, but costs will be recouped, effectively by selling anonymized patient data, both clinical and genetic, to academic and industry partners.  The collection of good quality clinical data, which are stored centrally by Genomics England, is therefore an integral part of the project.

When the people at GEL came up with the idea for the project, they obviously thought that the data entry issue was going to be more straightforward than it has actually turned out to be.  From their draft protocol written last year:

A secure, web-based, information system will be provided for the collection of this data, removing the need for any additional, bespoke development within participating NHS organisations. An electronic facility will be provided for transmission of the same data from existing information systems. Where organisations have developed their own capacity for capturing and managing the same data, to the same standards, there will be no requirement for additional data entry 

[From: Genomic England Protocol for 100,000 Genomes Project, v2 date 16/01/2015,  p. 14]

To try to be fair to Genomics England, when they wrote '...transmission of the same data from existing information systems' in their protocol, I don't think that 'existing systems' referred to the stack of paper illustrated above, and that 'transmission' referred to manual transcription.  They thought that we were collecting data in electronic format and that this could be sucked into their system with minimal pain for all concerned. Speaking for my specialty, Clinical Genetics, I am not aware that any centre is collecting clinical data in a form which can be straightforwardly captured for the purposes of the 100,000 Genomes Project. All data is being re-entered into web forms such as OpenClinica, either from other electronic but so far not compatible IT systems, or from paper records. 

Clinicians are used to collecting data for NHS research projects. The problem in the 100,000 Genomes Project is that the data are being collected as if the project were research, whereas in fact the concept of the project as NHS transformation implies work which is carried out wholly within the arena of routine clinical practice.  The current data entry model is time-consuming and, in my view, a barrier to the success of the project, because clinicians are being asked to do data entry over and above the data collection which they routinely do as part of normal clinical care.

A couple of weeks ago I attended a meeting at Genomics England HQ at Queen Mary University of London. The meeting was attended by representatives from Genomics England, the UK Clinical Genetics community, and interested parties from industry.  The purpose of the meeting was, first, to draw the attention of Genomics England to the problem of duplicate data collection/entry, as outlined above; and, second, to try to identify a way forward.

The goal of drawing the attention of GEL was fairly straightforward to accomplish.  The second goal will be more challenging.  As I have previously discussed (here and here) it will involve a transformation of the way in which Clinical Geneticists work.   IT leads for (most of) the 23 UK Clinical Genetics centres have been meeting for the last few years, with myself as chair, to compare practice in this area and to try to help each other with progress towards an electronic patient record for Clinical Genetics. We have highlighted wide differences in IT systems in use and in the rate of progress in development towards that goal.  The 100,000 Genomes Project has brought these issues into sharp relief and this is one of several reasons why I think that it is a welcome initiative.

The potential value of having electronic rather than paper data collection for Clinical Genetics and the 100,000 Genomes Project cannot in my view be overstated.  The green files shown above are data 'silos'. They represent countless hours of careful collection of data which is then not available for potential other good uses: service development, clinical audit, research and, yes, the 100,000 Genomes Project.  And because the data is in these silos, it doesn't really matter if it is collected in a non-standardized way using non-standard descriptive and diagnostic terminology, because no-one else is looking at it. 

The best way of convincing sceptical colleagues, of which there are some, is to come up with a prototype electronic patient record that looks convincing, and works.  This is a major task, but in my view a worthwhile one.  It might even get me out of dealing with the pile.

Charles Shaw-Smith is a Consultant Clinical Geneticst based at the Peninsula Regional Genetics Service in Exeter, Devon UK, and Rare Disease Lead for the SouthWest Genomic Medicine Centre, 100,000 Genomes Project.