Use our family health history tool to print and share your pedigree with your current healthcare provider or other family members.
Explore Progeny Clinical, our patient management system that tracks pedigrees, family health history and clinical data and integrates with your EMR.
Progeny is a subsidiary of Ambry Genetics, providing custom pedigree, family history and patient data management solutions. You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 I, 2013 II, 2014 I, 2014 II. This entry was posted in Tip of the Week and tagged genome editing, pedigree, visualization on December 23, 2015 by Mary. Unfortunately, the videos aren’t uploaded to YouTube, you have to go to the June 10 Meeting page and obtain them from there.
PhenomeCentral is a repository for secure data sharing targeted to clinicians and scientists working in the rare disorder community.
Certainly people in bioinformatics are familiar with the really crucial information from OMIM and Orphanet. What this new strategy will do is let doctors and researchers take the phenotype and genotype data (you can upload VCF files), and make predictions about the genes involved.
So although I used the GA4GH talk as a launching point to learn more about the features and conceptual parts of the PhenomeCentral software, I also came across this other webinar that was more specific about the software features (which is what I typically prefer for our tips, the specific software tools).
What I didn’t realize from the GA4GH overview was that there are additional tools, including a pedigree tool in the PhenoTips part.
This entry was posted in Tip of the Week and tagged GA4GH, pedigree, precision medicine on July 8, 2015 by Mary. Typically, our Tips-of-the-Week cover a specific software tool or feature that we think readers would maybe like to try out. Conceptually, the Human Phenotype Ontology (HPO) is much like other controlled vocabulary systems you may have used in genomics tools–like Gene Ontology, Sequence Ontology, or others that you might find at the National Center for Biomedical Ontology. The early part is about the concepts of specific terms, synonyms, and shared terms that can mean completely different things (think American football and European football). He also notes how tools like DECIPHER, NCBI Genetic Testing Registry, GWAS Central, and many more include the human phenotype vocabulary.
This entry was posted in Tip of the Week and tagged Gene Ontology, ontology, pedigree, phenotype on May 6, 2015 by Mary. But I can also see the need to collect some of this information on mobile devices, during conversations with patients and families.
The app enables the user to create complex family pedigrees by fully implementing, with minor exceptions, the nomenclature outlined by the Pedigree Standardization Work Group (PSWG) in Bennett et al. So if you need to draw pedigrees for clinical or research situations, or maybe for genealogies, you might want to have a look at this app. If you are new to pedigree drawing, or need a reminder of the basics, there’s a terrific intro video by this Genomics Education group. Edited to note that the app is now freely available, and changed the screen shot accordingly. This entry was posted in Tip of the Week and tagged EHR, electronic health records, pedigree on April 29, 2015 by Mary. I think from this I’ll be able to tell, quite clearly, that I will have a high propensity towards heart disease and heart attack. I looked at the list of disease risks, and from what I know of my family health history, I don’t expect many surprises. African, possibly from the regions of what is now Nigeria and Angola (from some research I did a while back). This entry was posted in General Science, Genomics Resource News and tagged ancestry, Madeline, pedigree, personal genomics on December 21, 2010 by Trey.
As I and my family await our 23andme kit to scan our genomes, family history has come back to the forefront of my thoughts. But there is a specific issue that is directly related to genomics, genomics tools and my family: same-gender headed household representation in pedigree and genealogy software. With the rising use of personal genomics data, there is a corresponding rise in the use of pedigree software for medical purposes and genealogy software for family history purposes.
A paper published last year entitled When Family Means More (or less) than Genetics by Burns and Edwards focuses on this inability of current tools to model family histories that aren’t within this norm. One challenge in using family history as a health technology is that the geneticist or clinician defines family based on biology, whereas individuals often include those linked socially. Genetic heritage and history is indeed important in determining disease susceptibilities, but ignoring or misunderstanding socially-defined kinship can lead to misdiagnosis, the lack of understanding of environmental influences and worse. Tools for modeling pedigrees must be able to flexibly model these family structures in order to be useful. The researchers look at two groups and conclude that current tools are inadequate to model their family structures.
When Samoan American participants were asked, “tell me about your family,” persons fulfilling social roles were described by that relationship.
For example, the Western postmodern family has looser kinship ties than in the past, with relationships that are diverse and fluid (Stacey, 1998). So, let me side step adoption or other non-genetic descent issues for a moment, and hone in on gay families and representation in current pedigree tools available. And in the future, descendants will look at their family genealogies and it will be very important to them that one of their ancestors was raised by two men, or two women whether adopted or biological from one parent. Yet, for software available it is impossible, a complicated workaround or awkward to allow for same-gender parents in the representation (not to mention paper family trees!). In a world where the number of same-sex couples is increasing annually (not to mention adoption, blended families and many other types of structures) and increased interest in family history through both genomics and culture and history, I look forward to seeing the software catch up to the ability to model my family for future researchers and historians.
This entry was posted in Genomics News and tagged 23andme, adoption, genealogy, Madeline, pedigree, personal genomics, tree drawing on December 6, 2010 by Trey. This entry was posted in General Science, Genomics Research, New Resource and tagged pedigree, plant on April 23, 2009 by Mary. Long ago, when our blog was young (less than 2 months old – where does the time go?), Mary wrote a post about the pedigree drawing programs that she knew of, or that were mentioned on the Mouse Genome Informatics (MGI) mailing list. The first thing I learned is how easy it was to find useless information (at least to me) by googling for ‘pedigree’ – as in almost 23 million hits with the top I-don’t-know-how-many linking to information or coupons for Pedigree dog food.


Once I got a few promising hits, found some promising sites I tried to extend my searches using the words that were on the sites that I had found.
This entry was posted in General Science, Genomics Resource News and tagged pedigree, software on October 31, 2008 by Jennifer.
Progeny Clinical is the gold standard clinical platform that allows you to quickly manage family history data without the time-consuming and expensive costs of setting up and maintaining your own secure database and infrastructure. Patients can fill out questionnaires and provide family history data before their clinic visit. We have completed or collected around 400 little tidbit introductions to various resources through this past year, 2015. PhenomeCentral encourages global scientific collaboration while respecting the privacy of patients profiled in this centralized database.
The Genetic Alliance is a patient-centric group interested in answers for genetic and genome-variant medical situations, actively working with advocacy groups and researchers to bridge the needs of both. We find a lot of people find our blog searching for pedigree tools, so I wanted to be sure to mention that specifically. And from the GA4GH video I learned that there is a special journal issue coming up in the fall that will have papers related to these projects. We’ve covered the idea of broad parent terms, increasingly precise child terms, and standard definitions in tutorial suites. It’s a seminar-length video, but it covers both the key conceptual features of the HPO, provides some examples of how it can be useful in translational research settings, and also describes the range of tools and databases that are using the HPO now.
This is a great sign for a project like this, that’s it is being adopted by so many groups and tools world-wide. This one is already loaded with things you should check out, so be sure to come back for further exploration of the HPO-related tools and projects that are worth exploring. So they have boots on the ground, and are dealing with real patient situations and have this need. I come from, on my maternal side, a long line of very proud Virginians, FFV in fact (with the expected boasts of 2 presidents, 2 signers, and several governors). He had two grandparents born in Germany with German surnames, German ancestors, two grandparents of English ancestry, surnames and ancestors.
Perhaps some questions answered (is the Lathe surname and ancestry from the Danelaw and Viking settlements of old as stories would have us believe), but for the most part I don’t expect anything new or surprising. I used to be very fascinated by my own genealogy, and with adopted children, the concepts of descent, biology and culture have taken adjusted meanings for me.
For example, an individual raised as a brother was identified as a brother whether or not there was a biological basis to the relationship. Blended, adoptive, and gay families, as well as those resulting from a variety of assisted reproductive technologies, place an emphasis on choice rather than genetics. As these genealogies are built, those relationships which are very important to their family culture and histories should be represented. There has been so much interest in that post, as judged by clicks, that we began looking into pedigree analysis tools with the idea of creating one of our trainings on the ‘best’ tool we found.
So much of the software I have found is fairly old, many of which are no longer supported by their creators. As I searched, I also learned how many different things people mean by pedigrees – there are pedigrees for keeping track of livestock breeding programs, laboratory mouse strains, dog breeds, and fancy bird crosses. thoroughbred, others are for historians or hobbyists tracing their roots.
Using search terms such as ‘kinfolk’ and ‘ancestry’ lead me to Anabaptist family databases and presidential genealogies, but not so many drawing programs.
At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. There may be lists of features of a condition, but how they appear in a given patient’s situation might vary.
You can try it out by entering fake data in the playground over there, and accessing the Pedigree Tool from that record.
It’s got a conceptual piece that is important, as well as referencing several software tools that work with this crucial concept to enable interoperability of many tools, helping us link different data types in a common framework. It’s important to standardize and share the same language to describe the same things among different projects, software providers, and as we move more genomics to the clinic, sharing descriptors for human phenotypes and conditions will be crucial. There are examples of research that leads to phenotypes that are then used as discovery and diagnostic tools. They’ve also worked with key large-scale projects in this arena to ensure that the vocabulary is suited and workable, and update them when needed.
Families have been encouraged to collect their own family histories by the Surgeon General’s office in the US.
Standardized Human Pedigree Nomenclature: Update and Assessment of the Recommendations of the National Society of Genetic Counselors, Journal of Genetic Counseling, 17 (5) 424-433. I expect that sometime over the next few weeks to get some results for myself, my husband and our two daughters.
Similarly, individuals adopted in to or out of a family were described as the children of the family in which they were raised, not as offspring of the biological family. In my and my colleague’s research so far we have yet to find a software or online medical pedigree tool that easily accepts same-gender parental groups, or represents them well.
Though there is the ability to model adoptive relationships, there is yet no way to model same-gender couples. I know I personally will hope that this will be the case for our family history in the years to follow. I have been working on finding a great tool to train on – public (free), broad applicability and web-based. But the idea is that with patient details one could search for matches with other similar patients (depending on the privacy level of the records, of course). This was also handy for me because I didn’t create a login for the main PhenomeCentral site due to the privacy issues. I expect there will be metrics about algorithms in use and other technical details that are important for fully evaluating the tool. He talks about tools that utilize the HPO right now, including Phenomizer for obtaining or exploring appropriate terms, PhenIX, Phenotypic Interpretation of eXomes for prioritization of candidate genes in exome sequencing data sets.


The team is actively seeking out feedback, though, and some of these things may have changed. And they are piloting a server piece that will integrate the pedigree data with other parts of electronic health records systems. The difference between our cultural genealogy and our genetic genealogy has been become quite clear to me. Nonbiological social factors, such as role behavior, determine family membership, so that a mother’s sister’s son who has been raised with you is your brother (Finkler, 2001).
The culture you received from your parents and they from theirs is pretty close to the genetic descent.
I did find a nice little tool named PediDraw, and did a tip of the week on that, but it is so easy to use it doesn’t really warrant a full tutorial. Last week I noticed that Mary’s blog was linked to in a blog post by Gregor Gorjanc, and I must confess that it felt great to know that he was having a similar slog for the ‘right’ pedigree program. The area that is closest to my personal interests are those that are medically relevant, but even those are amazingly diverse – pedigree can mean everything from a family history given by a patient (riskApps) to e-pedigrees soon to be required by some states for pharmaceutical manufacturers to reduce the chances of dangerous counterfeit chemicals.
However, I think THE BEST hit (by far) that I found was the linkage software list at Rockefeller University, and I found it with the search phrase ‘linkage analysis software’. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. It sounded to me like a kind of BLAST for medical conditions (they didn’t call it that). There is also PhenoTips, that can help you to collect and analyze patient data (and also edit pedigrees).
They have been presenting posters at conferences like ACMG and ASHG, and also reaching out in other ways too.
That I have had hypertension since 18 doesn’t bode well for good news from my maternal side (where heart disease and heart attacks are unknown).
Obtaining our family ancestry through these tests will bring a lot of these issues back to focus. But even when the biological relationship was known, the Samoan Americans reported family relationships based on social rather than biological ties.
No, there was ability to do this, but considering adopt-in and adopt-out relationships are model, it would make sense to include same-gender couples.
Gregor’s post has some nice background information and information on for plotting large, complex animal breeding animal pedigrees.
If you have missed any of them it’s a great way to have a quick look at what might be useful to your work. But there are other strategies needed to connect physicians and patients with other folks who might help them get to answers. But it also has ways to semantically link phenotype concepts, because they might be entered differently by different evaluating physicians, yet be the same type of issue underneath. I expect to be exploring HPO in some other upcoming tips as well–this is going to be increasing important as we collect more sequencing data from individuals and try to figure out what it all means. The first is a pedigree following heart disease on my paternal side (there has not been any reported on my maternal side). It was not well documented, but after I became a Mormon* at the age of 18, I documented a lot of it, some lineages back 200-300 years.
Though her maternal side is well-documented Mattaponi, there are questions about further back (her grandfather was said to be of African descent, and it appears to be some early Anglo-Scottish mixing).
What is important to who you are from a cultural or historical perspective might not at all be related to who are you from a genetic one, and who you are is as much cultural as it is genetic. I won’t repeat his information here but his post, as well as others he links to, convinced me I should share some of the gems of knowledge that I have acquired. Though my searches I have come to believe that pedigree drawing software is somewhat like religion – it is a very personalized thing & only you can know which is best for you. That Human Phenotype Ontology (HPO) that I’ve covered a couple of times lately enables this.
They also provided a data sheet with updates listed from March, so I’m certain they are continuing to actively develop this tool.
I was diagnosed with hypertension at the age of 18 (at which time I was 140lbs, 6′ tall, non-drinker, non-smoker, physically active). Of course, as with all software and online tools, funding, timing and priorities I know will be an issue.
I am as interested in where I got my cultural ancestry as where I got my genetic one, this has become quite clear to me as we’ve adopted children. The native American tribes of Virginia were well-known to have inter-married and mixed with both the African-American and Anglo-American populations.
Though my paternal side can tend to burly, they are for the most part within healthy ranges.
Nonetheless, you just have to look at photos (and birth certificates of my great grandmother to know she was a Mattaponi.
So as to not single Madeline out, no other tools that we know of (see here, here and here) allow for same-gender couples or headed families. It lists over 450 programs in an alphabetized list and provides information such as system availability, recent publications, brief description for each.
If I were hunting for the perfect pedigree drawing program for my research, I would search here rather than Google! My hat is off to those who maintain this wonderful list at the Laboratory of Statistical Genetics at Rockefeller University!!



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