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!


This month’s news at the CG&Bio lab

This month has been pretty active in the CG&Bio lab! We have presented two talks at the XXIII International Congress of Dermoscopy in Mexico City, The National Council of Science and Technology profiled us and our work in their News [in Spanish], and one of our projects was selected for an oral presentation at the 15th International Congress for the Society for Melanoma Research to take place in Manchester, England next month!

Also, we will be teaching bioinformatics methods at the Next Generation Sequencing Bioinformatics course, from Wellcome Genome Campus, in Chile January 2019! So if you are based in Latin America and the Caribbean and would like to learn more, please apply here! Bursaries available.


We’ve been awarded a UC MEXUS – CONACYT Collaborative Grant Award!

This award, given by the University of California Institute for Mexico and the United States (UC MEXUS) and the National Council for Research and Technology of Mexico (CONACYT) is intended to help establish long-lasting collaborations between scientists based in University of California campuses and in Mexican institutions.

In this spirit, we are thrilled to be starting a formal collaboration with Prof. Ludmil Alexandrov, of the University of California, San Diego – widely recognised as the founder of the field of mutational signatures in cancer. This Award will allow PhD students from both groups to undertake reciprocal research internships to train in different specialised bioinformatic techniques (UCSD lab: Mutational signature analysis, UNAM lab: causal germline variant prioritisation), project planning meetings, as well as providing funds for expanding our institutional computer cluster and for performing bench experiments for hypothesis testing.

Kudos to Caro Castañeda, the PhD student in our lab who will be leading this collaboration from our side! Loads of exciting science to come 🙂

We are deeply thankful to UC MEXUS and CONACYT for this opportunity, and can’t wait to see what the results will be!


Daniela has been selected as a Forbeck Scholar Awardee!

The Forbeck Research Foundation was established in honour of 11-year-old Billy Forbeck, who sadly passed away from neuroblastoma in 1984. Every year, the Foundation organises a Forum to exchange ideas to further progress in the fight against cancer. The Annual Forum is held in an intimate venue where ~20 scientists and clinicians from around the world discuss unpublished work and seek opportunities for interaction – which has resulted in highly productive interdisciplinary collaborations. This year, the topic is Cancer Predisposition.

Each year the Foundation selects four young investigators from around the world as Forbeck Scholars to attend the Annual Forum in their year of election and four subsequent Scholar Retreats which offers the opportunity to set up collaborations, meet with experts from different areas of cancer research and discuss novel ideas. This year, Daniela has been selected as a Forbeck Scholar and will attend the Annual Forum in Lake Geneva, WI in November.

This news is very exciting as it will offer an opportunity to discuss the lab’s work in depth with other clinicians and scientists from around the world.

About the William Guy Forbeck Research Foundation:
About the Scholar Award: https://www.wgfrf.org/scholar-award/
Past winners: https://www.wgfrf.org/scholars


Congratulations to Isaac Garcia, our first student to graduate!

Last Friday, Isaac successfully defended his B.Sc. thesis (with honours!), entitled “Functional in silico analysis of SNPs influencing melanoma development and telomere length”. In it, he deploys a series of computational analyses (including genotype imputation, linkage disequilibrium calculations, epigenome state imputation and other functional predictions) in order to prioritise candidate variants underlying increased melanoma risk and telomere length. Based on his work, we are now planning some exciting experiments to test these functional hypotheses.

Congratulations on great work, Isaac, and looking forward to seeing all your future scientific contributions!


It’s been quiet lately but… we’ve had a good few weeks!

It’s been quiet lately at the CG&Bio Lab as students work on their projects and write their theses and postdocs and PI write grants… but these past weeks we’ve been busy so here’s an update: We have presented a poster at the 9th World Melanoma Congress / Society for Melanoma Research Meeting in Brisbane, Australia, and we won a Travel Award! We’ve also had good news in terms of funding: We’ve been awarded a Research Stimulus Grant from the Miguel Alemán Trust, based in Mexico, and we’ve had our application for project funding to the National University approved for the next year. We’re very grateful to these organisations as their support will allow us to continue studying the genetic causes of melanoma.