Genomic data is powerful only when reliable.
The 6Cs of quality—completeness, continuity, collinearity, correctness, contamination, concordance—show where things go wrong and how errors ripple downstream.
Check out our latest blog post to learn more:
Thanks, Marc! I really appreciate your support
Thanks, Arnoud! I’ve been doing similar work in lots of different contexts already, but Sequity is an exciting new challenge. And training has become my forte over the years - I’ve long lost count of the workshops I’ve led!
I’m deeply passionate about this, and I can’t wait to share more over the coming weeks.
👉 Follow @sequity.bsky.social for updates
👉 Message me if you’re curious
Whether you’re starting your first project or scaling to many thousands of samples per month, we work shoulder-to-shoulder with you to define genomics strategy, build resources, train staff, and make it happen.
That’s why I’m launching Sequity- your partner to turn genomics goals into real, impactful outcomes, in a way that’s both accessible and sustainable.
The words "INTRODUCING Sequity" and "Your Partner for Microbial Genomics" are shown with the Sequity logo. Above this text is an illustration of four people in a lab setting working with equipment and a laptop.
At the top there is a map of the world showing pins and illustrations of hospitals and laboratories. The text reads SEQUITY MAKES GENOMICS WORK FOR YOU Developing solutions that work with your unique lab, challenges and epidemiology CONTEXT-DRIVEN Delivering outcomes aligned with your objectives GOAL-ORIENTED
This image is text only. This reads, YOUR PARTNER FOR GENOMICS SUCCESS STRATEGY Figuring out what will work in your unique context RESOURCES Developing everything- from bioinformatics workflows to SOPs TRAINING Ensuring you have the knowledge and skills to deliver ON-DEMAND SUPPORT Ongoing support through the day-to-day
An abstract image at the bottom shows scientists working through a process, generating ideas. The text at the top reads, FROM IDEA TO IMPACT END-TO-END SUPPORT From study design to sample, wet lab, bioinformatic, and reporting VALUED-OUTCOMES Unlock information and real-world impact
I’ve got something exciting to share. After years of working with labs around the world, I’m starting something new!
I’ve seen how many labs want to do more with genomics, but the path forward isn’t always clear. The process is complex, and without the right guidance, it’s easy to get stuck.
Since it is that time of year:
One of the most rewarding parts of being faculty is paying forward mentorship with students, residents+ fellows for their research projects. So far, as 4th year faculty, I’ve mentored ~40 trainee projects (17 completed). Here are what I talk about at 1st meeting:
Answer: Countries that are high on the Welcoming Countries Rankings and where logistics would be great for hosting conferences. 🙏
My Canadian university, Queen's, is offering TWENTY 4-year funded PhDs (40k CAD/yr) for a student of ANY citizenship who has been accepted at a top 100 US university but have had offer rescinded OR are reconsidering offer due to US policy.
Details found here👇
www.queensu.ca/grad-postdoc...
Amazing work from our colleagues in Sierra Leone, Nigeria, and elsewhere, making the first sequences available from the ongoing Mpox epidemic in Sierra Leone.
More to come - for now, head over to @pathoplexus.org:
pathoplexus.org/seqsets/PP_S...
The spread of Mpox in Sierra Leone is unlike anything we have ever seen - and we have been keeping an eye on this bug in the region for >15 years.
Given geographical spread, 50/50 men vs women, this is no "sexual network".
This could be the next one.
clt.npha.gov.sl/outbreak.aspx
Really pleased to see this! Helps to address such a critical question for genomic interpretation
Well done, @katholt.bsky.social et al!
It's official: the #PandemicAccord is officially adopted by the World Health Assembly!
My warmest congratulations to @who.int Member States for their commitment to keeping their people and the world safer.
What a moment in global health history. Together!
All the best, Alan. Your leadership at MK had a huge impact, both on the scale of national testing and for all the other folks in the lab during pretty tough times. I was glad to be there with you. Thank you for making your voice heard in the inquiry
Have said before that conference organisers when deciding on a host country should consider how easy it is for people to get visas (particularly for those from the Global South). For example, applying for a Canadian visa from the UK takes 344 days (www.canada.ca/en/immigrati...).
Hello, I'm always trying to spread the word about the Academic Editing Circle, which organizes professional editors to volunteer time for Black and/or Indigenous scholars.
I can't promise that a volunteer can donate time for a whole book-length dissertation, but maybe we can help.
A must-read for anyone doing Global North-South work: Ways to level the highly unequal playing field
"the African academic is spending
their precious time contributing to your success. How are you contributing to theirs?"
As more Global North countries swing towards the far right & openly become anti-immigrant, global health is even more a field for those with visa privilege
www.forbes.com/sites/madhuk...
Trump's actions seem to be having a knock-on effect all over the place
www.theguardian.com/politics/202...
Another is to support getting journals into local, high quality networks like @scielo.org. Resources like Redalyc (Mexico), TCC Africa, etc. We shouldn't force non-English communities to index in "our" indices. #r2rconf
Thanks, Sara. This is great. Are there any resources you can point to for providing this expertise on indexing?
That's a lot of underheard important voices, and a lot of neglected areas of research/neglected populations. What do you think we can do to increase the visibility across these areas?
Figure 6: Overall annual potential savings and costs by use of the proactive genomic epidemiology approach The health economic assessment uncovered yearly net cost savings of approximately € 1·25 million if initiated IPC measures completely halt transmission of clinical isolates after the second patient. The reduction in costs is due to a lower rate of costs for non-MDRO (red) and MDRO (blue) infections, respectively as well as colonization with MDRO (green). The costs for non-MDRO infections (red) are made up of the additional days a patient has to spend in hospital due to the infection (7·8 days), multiplied by the costs per patient for an additional day in hospital (€325). The costs for the colonization with MDRO (green) is composed of the average number of days a patient spends in the hospital (4·6 days), multiplied by the extra-costs incurred per patient per day for the isolation of the patient (€325). The cost for MDRO infections (blue) results from the average number of days a patient with an MDRO infection has to spend in hospital (7·8 days) multiplied by the additional costs incurred per day by a patient with an MDRO infection (€650).
Landmark paper claxon!
'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting'
www.medrxiv.org/content/10.1...
Significant savings associated with proactive genomic epidemiology.
Jeez, Alan. Don't remind me!
I looked through that page. Where is the "gender ideology" that they're warning against? Or is "sex" the problem? 🤣
www.cdc.gov/hiv/preventi...
The image is a chart illustrating the relationship between different DNA extraction methods, the molecular weight of DNA they can recover, and the associated labor and time required. The x-axis represents the molecular weight of DNA, ranging from 60 Kb to over 1 Mb. The y-axis represents labor and time, increasing from bottom to top. Different DNA extraction methods are shown as yellow boxes positioned according to the molecular weight they can handle and their required labor/time. The methods are arranged in an ascending staircase-like pattern: Spin column (low labor/time, suitable for ~60 Kb DNA) Magnetic bead (~100 Kb) Gravity-flow column (~100 Kb) Phenol-chloroform (~150 Kb) Dialysis (~200 Kb) Plug extraction (high labor/time, suitable for >1 Mb DNA)
I'm always comparing to this reference for fragment lengths from different extraction methods. Oldish but still v good. Sharing for anyone who might find it helpful lab.loman.net/2018/05/25/d...
Ah interesting. I haven't seen read lengths from this kit before. I assume it's usually longer? Struggling to see on the website what approach this uses (maybe magnetic beads?)
Ah, amazing. How are you doing your DNA extractions?
I love it. How are you planning to resequence/reassemble to resolve these plasmids?
