Category: Papers

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!


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! 🙂

 


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


Our Comment “Melanoma: a global perspective” is now out!

Bottle of bubbly to celebrate Raul's 1st first author publication!

Our Comment piece on the importance of studying melanoma in all populations has now been published in Nature Reviews Cancer – Click here to read it!

Congratulations to Raúl (PhD student in the lab) for this piece, hard work pays off 🙂 (Don’t forget to check out his superb global map on melanoma subtype incidence in the Supplementary Material).