With January officially in the bag, 2015 is off to a great start, especially for some of our customers who have recently published. I wanted to take a minute to share them with you.
In recent months we have been updating our public annotation library to include the most recent versions of existing sources as well as include new sources. Each of these annotation sources are compatible with our three major products (SVS, GenomeBrowse and VarSeq) and can be used for visualization, annotation and filtering.
One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes project for some examples.
The Plant & Animal Genome XXIII Conference (PAG) was again a success. It’s the venue for leading genetic scientists and researchers involved in plant and animal research to meet with their peers. If anything the event continues to grow. The largest population of registrations tend to be from an Academic background (64%), with Industry (25%) and Government (11%) sectors comprising the remainder. This year well over 3000 attendees from over 50 countries worldwide visited. Without exaggeration it is a truly global event with about 40% of attendees traveling from outside the USA.
One of the highlights were the plenary sessions. The Town & Country Ballroom was packed each and every time. Here is a brief overview:
Golden Helix and the NorthShore University HealthSystem recently announced our collaboration as the NorthShore puts the VarSeq software to work in it’s gene panel pipeline. VarSeq will be used in Northshore’s clinical lab to help them realize their aggressive expansion plan for 2015.
The NorthShore Next Generation Sequencing (NGS) lab focuses primarily in Oncology, both somatic mutations in a variety of tumor types as well as inherited cancer syndromes. The lab hopes to move forward with exome sequencing later in 2015.
We are very excited to work with NorthShore in the coming year and we look forward to support our many other collaborations as well. Read the full press release here.
In 1914 the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome”. At this time his ideas were equally revolutionary as they were highly contested. Fast forward. More than hundred years later, Next-Generation Sequencing effectively permits a highly sensitive analysis of cancer cells. It can help us to understand mutations associated with cancer development and progression. It also reveals other genomic rearrangements previously unknown to occur in the cancer genome. Translation of these findings for clinical purposes is increasingly part of standard care today. I fully believe that next-generation sequencing will rapidly become a powerful tool for the personalized diagnosis and management of cancer. This e-book will focus on the parts of this process that are best understood: Cancer Gene Panels.
The Integrative Therapies Institute is soon hosting the annual, ITI 2015 conference January 23rd through the 25th in sunny San Diego and our own Dr. Andreas Scherer has been invited to speak.
Some of the most prominent genomic and integrative medicine specialists will gather at ITI 2015 to share case studies and protocols with the community. Attendees can expect to get keen insights into best practices, aimed at improving patient outcomes.
Dr. Scherer will present Bioinformatics of Cancer Gene Panels at 5:30 pm on Friday, January 23rd. The talk will address the value of NGS in a clinical setting as well as the bioinformatics tools and best practices used to achieve the goal of a reproducible workflow for analyzing NGS gene panel data.
For more information or to register for ITI 2015, please visit the official website here.
If you haven’t been closely watching the twittersphere or other headline sources of the genetics community, you may have missed the recent chatter about the whole genome sequencing of 17 supercentenarians (people who live beyond 110 years).
While genetics only explains 20-30% of the longevity of those with average life-spans, it turns out there is a number of good reasons to think extreme longevity has a very large genetic component (and interestingly not a lot to do with lifestyle choices like smoking, alcohol use, exercise etc).
The collaboration between Stanford researchers (including the visionary Dr Leroy Hood) and the Supercentenarian Research Foundation resulted in an open access paper in PloS One about the sequencing and analysis of 17 of the 22 supercentenarians alive in the US.
This group clearly wants their data and results to have the best chance of making an impact and being of significance to the genetics community. Along with the paper being open, there are supplemental tables of various sets of interesting variants, as well as a reference to their project’s website with directions for requesting access to the full raw variant calls for each individual.
There is a lot we can be grateful for at Golden Helix. The past year was marked by two major breakthrough launches. Earlier in 2014, we shipped SVS 8 which unified SVS with our GenomeBrowse product. We were able to improve SVS’ data management and visualization capabilities. In addition we added a number of new methods in SVS, such as SKAT-O, MM-KBAC, and various genomic prediction algorithms.
Once again, we will be kicking off our year with our annual trip to San Diego for PAG XXIII. This year, it could not come at a better time. Over the last few weeks, it has been bitter cold in Montana with temps barely reaching above zero degrees and I for one am looking forward to the warm sun. And moreover, this being my first PAG, I am really looking forward to meeting some of you!
This year you will find us at booth 124 and with the addition of Genomic Prediction to SVS, we have some great product demonstrations as well as t-shirt give-aways lined up for you. If you haven’t seen our latest designs, you can check them out here.
Here is our demo and t-shirt give-away schedule (bold times are t-shirt give-aways!) :
Sunday, January 11
- 3:15 pm – GenomeBrowse: Curating Your Own Reference Sequence and Gene Track
- 5:00 pm – GWAS using Sus Scrofa as a model
- 7:00 pm – GenomeBrowse: Using Evernote to Share Publication Quality Plots and Notes
Monday, January 12
- 11:00 am – Genomic Prediction with gBLUP and Bayes C-Pi
- 1:30 pm – GenomeBrowse: Curating Your Own Reference Sequence and Gene Track
- 3:30 pm – GWAS using Sus Scrofa as a model
Tuesday, January 13
- 10:15 am – RNASeq Differential Expression using Public Data from Mus musculus
- 1:30 pm – Genomic Prediction with gBLUP and Bayes C-Pi
This year’s PAG is certain to be superb with a great line-up of speakers, workshops, and presentations. We can’t wait and we hope to see you there!