We are still continuing our activities from home!

Screenshot from our last lab meeting, yesterday!

We are still working from home! It seems likely that we won’t be able to return to in-campus activities until next year, so we have adapted to work through Zoom and Slack! We have attended the 2020 AACR virtual Annual Meeting, participated in the 2020 virtual Genetics of Melanoma Consortium (GenoMEL) meeting, with Caro giving a talk on her PhD project, Daniela participating as guest in the new Your Digital Mentor podcast, and Christian and Daniela giving talks on their work for the BioScience App conference program. We are also meeting weekly and advancing our projects as much as possible.

Our PhD student Irving Simonin is also teaching a Bayesian statistics summer course to the wider LIIGH community, and we have been learning about conjugate models, Markov chain Monte Carlo and statistical software. We have also welcomed a new student, Rodolfo Arriaga, to do a virtual internship in our lab this semester.

We hope everyone is keeping safe to the extent of what’s possible during these difficult months, and hope that soon it becomes possible to meet our collaborators and friends in person again.

  Caro Castañeda finishing her talk at the 2020 international GenoMEL meeting

Christian starting his talk at the 2020 BioScience App seminar series


CGBio lab is still running (from home) under lockdown

CGBio lab members looking very focused during virtual lab meeting….

Hello everyone, an update from our lab during these difficult times…. We have had to interrupt all of our wet lab work (as the vast majority of labs in affected places have had to do!), but we are still trying to work remotely (when time permits, as of course new challenges have emerged with the lockdown situation). However, some good news: we are happy that a review we worked on for a very long time is now out on Pigment Cell and Melanoma Research! Click here to read “Acral lentiginous melanoma: Basic facts, biological characteristics and research perspectives of an understudied disease“, by Basurto-Lozada et al., it’s open access!

We have also found that a social session twice a week where we can play online games (those by Jackbox.tv are amazing!) and chat about non-work stuff goes a long way. Hopefully the situation will improve soon but for now, please take care and enforce social distancing rules whenever possible, and take care of your mental health!


CGBio lab’s activities during February

Christian Molina (far right) with members of Patricia Possik’s group (third from right to left) in Rio de Janeiro, Brazil

We have been active during this month! Postdoc Christian Molina is undergoing an internship at Patricia Possik’s research group, based at the Brazilian National Cancer Institute in Rio de Janeiro, where he is learning the details and protocols for the establishment of PDX models. These are animal models of human tumours that allow us to follow their evolution in vivo, and to test potential therapeutics – in our opinion, very important work for Latin American patients suffering from acral lentiginous melanoma. This is in the context of a collaboration enabled by our Medical Research Council grant, to whom we are very thankful for providing these learning opportunities.

Also, Daniela has been in Lima, Peru, participating as an invited speaker in the International Symposium on Immunology and Biotchnology, organised by the Peruvian Institute of Health. She discussed methodologies for identifying genes associated to disease, especially our work in melanoma, and you can watch her talk here. Next week, she will attend the Scientific Retreat of the Melanoma Research Alliance, in Washington, DC where she will chair a roundtable discussion and participate in the Melanoma Models Workshop.

Back at home, the other members of the CGBio group have been busy preparing a couple of book chapters and a review. We hope to be able to share them with you soon!


Congratulations to alumnus Isaac Garcia on his offer of a fully-funded PhD position at the Sanger Institute!

We are super pleased for our first alumnus, Isaac Garcia, who did his BSc thesis in our lab! He got an offer for a very comptetitive, fully-funded PhD position at the Sanger Institute, which he has accepted and will start in October! He is an excellent student and we wish him the very best in his future, and hope to keep in touch 🙂


Happy holidays from the CG&Bio Lab!

Another year has passed and it’s the time of the year when we think about what we’ve achieved, where we need to improve and our objectives for the year to come. During 2019:

Our Christmas tree made from wooden boxes and Poinsettias at the entrance of LIIGH!

  • We officially welcomed 2 new PhD students and one MSc student to our lab – Congratulations Paty, Irving and Fer! We are very excited about the projects they will be working on: Deciphering the mutational landscape and genetic risk factors of acral lentiginous melanoma, and our first effort into investigating the genomics of liver cancer. Welcome!
  • Talking about liver cancer, we obtained our first grant to work on the genomics and transcriptomics of this tumour type from CONACyT, which was mainly written by postdoc Christian Molina. Congratulations Christian! We also obtained funding to do more work on melanoma from CONACyT, the Wellcome Sanger Institute and UNAM.
  • PhD student Caro Castañeda attended a Cancer Epidemiology course at IARC and is now completing an internship at Prof. Ludmil Alexandrov’s lab at UCSD, supported by UC Mexus/CONACyT and the Academy of Medical Sciences, UK. We’re looking forward to seeing what she’s learnt and to our novel collaborations with Prof. Alexandrov’s group!
  • We hosted our collaborators Prof. Tim Bishop, Prof. Julia Newton-Bishop and Dr. Mark Iles from the University of Leeds, UK, at LIIGH-UNAM in March. They taught a week-long course on ‘Statistics for GWAS’ and will be coming back again in 2020 for the follow-up. Stay tuned for topics and dates!
  • We taught a NGS course for Latin American scientists in Chile, gave several talks at national and international venues and hosted an emeritus NIH professor, Heinz Arnheiter, at LIIGH during the summer months. An academically rich environment overall where we learnt loads.
  • Published 6 papers either from our own lab or in collaboration with others
  • Received appointments as a Wellcome Sanger Institute International Fellow and CONACyT SNI level II investigator, which will take effect from next year. Daniela also started working for eLife as a Reviewing Editor for the Cancer Biology and Genetics and Genomics sections, and will take a post as a Social Media editor for the journal PCMR from next year.

For 2020, we are hoping to see our first PhD students graduate, and finally see the first projects from our lab develop, after a few years in the making! We are also hoping to expand our new liver cancer research line and form new collaborators in this area.

Here’s to a great 2020. Happy holidays and see you next year! 🙂

 


2019 midyear update!

It’s been a while since we’ve posted an update, but that’s because the lab has been very busy this first part of the year! Here are some events that have happened:

Profs Julia and Tim and Drs Mark and Daniela with the attendants of the “Statistics for GWAS” course

– In January, Daniela participated as an instructor of the Next Generation Sequencing Bioinformatics course that took place during one week in Santiago de Chile, Chile. Caro Castañeda, a PhD student in the lab, attended as a course participant.

– In March, we hosted Prof. Julia Newton-Bishop, Prof. Tim Bishop and Dr. Mark Iles, from the University of Leeds in the UK, who came for a week to teach a course on Statistics for GWAS as part of our Newton Advanced Fellowship. We had participants from several schools at UNAM, as well as students and postdocs from other entities and states in Mexico.

– In April, our first alumnus, Isaac García, started his MPhil in Genome Sciences at the University of Cambridge (Sanger Institute)! Also, Daniela spoke at the 16th GenoMEL Annual Meeting in Athens, Greece, on the lab’s wet lab project investigating the effect of particular germline variants on melanoma risk.

– In May, Daniela spoke at the 11th European Melanoma Workshop in Otranto, Italy, on the lab’s project investigating acral lentiginous melanoma development in Mexico and Latin America, and in the Liquid Biopsy Symposium organised by INMEGEN, Mexico, on the analytical and bioinformatics challenges for the analysis of liquid biopsy specimens. Also, our guest Dr Heinz Arnheiter, scientist emeritus at NIH, arrived to our lab as a visiting professor. Heinz will stay for 2.5 months giving lectures to our academic community on various biological phenomena and interacting with students and postdocs.

– And finally, during June, our PhD student Caro started her academic internships attending the IARC Summer School on Cancer Epidemiology in Lyon, France. She will then visit our collaborators’ labs at the University of Leeds, UK, and then she will undertake a 2-month internship at Prof Ludmil Alexandrov’s lab at UCSD, part of our UC Mexus award investigating the somatic effects of genetic variants in melanoma patients. Also, Daniela spoke at the Noreen O’Neill Melanoma Research Symposium, which took place at The Wistar Institute in Philadelphia, PA, USA.

Also, the first official publication from our lab was published in Bioinformatics! VCF/Plotein is a web application that allows biologists, clinicians and bioinformaticians to prioritise and filter genetic data in the VCF format by displaying information graphically and interactively! Take a look at the paper and the website! You can also see other work that we have participated in in the Publications section.

We also got notification that CONACyT, Mexico’s Council for Science and Technology, will fund us through two awards: One to investigate the transcriptomic profiles of acral lentiginous melanoma tumours from Mexican patients (from the Health Sectoral Fund), and another one led by postdoc Christian Molina to start a new exciting collaboration with Dr Mauricio Díaz at the Neurobiology Institute at UNAM (from the Basic Scientific Research Sectoral Fund). This exciting grant will allow us to expand the repertoire of cancer types we study to investigate by transcriptomic analysis the effects of caloric restriction on liver cancer, which is the fourth most common cause of death from neoplasia in Mexico. This project is a follow-up of work that Christian did during his PhD (you can read the main paper here).

This may be all for the time being – we will try to update our website more frequently from now on! 🙂

 


Our year in review

A bit of a blurry picture of the CG&Bio lab + friends at the Christmas dinner

2018 was a great year for the CG&Bio lab! Overall, we:

-Celebrated the graduation of our first BSc student (Congratulations, Isaac!)
-Were joined by Diego, Paty, Estef and Kevin, who have been working on both computational and wet lab projects. Welcome!
-Published 7 papers/reviews/preprints either directed by our lab or in collaboration.
-Obtained one Fellowship (Newton Advanced Fellowship from the Academy of Medical Sciences, UK), two novel grant awards (Medical Research Council [UK] and UC Mexus [US/Mexico]), one Scholar Award (William Guy Forbeck Research Foundation, USA) and the renovation of our University grant (PAPIIT UNAM)
-Established novel national and international collaborations
-Gave several talks at both national and international events and attended international courses

Here’s to a successful and happy 2019. Bring it on!


Latest papers (VCF/Plotein!) and activities at the CG&Bio lab

It was snowing in Lake Geneva, WI, where the Forbeck Foundation meeting took place!

It was snowing in Lake Geneva, WI, where the Forbeck Foundation meeting took place!

The last two weeks have been intense for the CG&Bio lab… First, we have published our first preprint in bioRxiv! Click here to check it out! Also, the full code can be found here.

In this manuscript, we describe a new software tool we have developed, called VCF/Plotein, that allows any researcher with or without any bioinformatics expertise to visualise exome sequencing data in the VCF format and interact with this information, namely, identify mutated genes, filter them in various ways, see genetic variants and various information about them, and generate vector or pixel graphics for presentations or publications. Any comments or suggestions welcome! This is the result of lots of work by an amazing team: Raul and Diego with support from Isaac, Jair, Luis and advice from David Adams.

We have also recently published a commentary on a remarkable study of non-mutational mechanisms of drug resistance acquisition in melanoma cells. Check it out here!

Finally, we have been quite active, with Christian attending the Wellcome Genome Campus Course in Genomics for Dermatology in Hinxton, UK and Daniela giving talks at the International Congress of the Society for Melanoma Research in Manchester, UK and the Forbeck Foundation Annual Forum in Cancer Predisposition in Lake Geneva, WI, USA.

Christian at the Genomics for Dermatology course in Hinxton, UK!

Christian at the Genomics for Dermatology course in Hinxton, UK!

Daniela speaking at the International Congress of Society for Melanoma Research in Manchester, UK

Daniela speaking at the International Congress of Society for Melanoma Research in Manchester, UK


We have been awarded a Newton Advanced Fellowship!

Today we were notified that Daniela has been named a Newton Advanced Fellow by the Academy of Medical Sciences and the Royal Society of the UK! This Fellowship has been awarded to investigate the genetic susceptibility to acral lentiginous melanoma through population studies and the use of statistical genomics methodologies. Our partner in this project is Prof. Tim Bishop, Professor of Genetic Epidemiology and Director of the Leeds Institute of Cancer and Pathology. We are very excited as this project will allow students in the lab to undertake training in statistics and genetic epidemiology while exploring the genetics of acral lentiginous melanoma.

We are very thankful to the Academy of Medical Sciences, the Newton Fund, and the Royal Society for supporting us, our research and our international collaborations!


The MRC has funded our team research proposal!

We are thrilled to announce we’ve been awarded a grant, part of the Cancer Research and Global Health Initiative of the Medical Research Council (UK), to study potential drug targets of acral lentiginous melanoma (ALM) in Latin American patients. This proposal is also co-led by Dr David Adams (Sanger Institute, UK) and Dr Patricia Possik (Brazilian National Cancer Institute [INCA], Brazil), with the support of Prof Meenhard Herlyn (Wistar Institute, USA) and Dr. Hector Martinez-Said (Mexican National Cancer Institute, Mexico). This award will fund our research into animal models and potential drug targets of ALM for the next two years, and will officially start our collaborations with INCA. We’re very thankful to the MRC for this funding, and can’t wait to get to work!