Author Interviews, Cancer Research, Genetic Research / 08.08.2019 Interview with: Upekha Liyanage MBBS |  PhD Student School of Medicine | University of Queensland Statistical Genetics Laboratory QIMR Berghofer Medical Research Institute What is the background for this study? What types of skin cancers are linked to these genes? Response: Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) collectively referred to as “keratinocyte cancers” are the commonest forms of cancers of the skin. Although these cancers are less aggressive than melanoma, due to their large numbers, they pose a significant burden to the healthcare expenditure. Also, these cancers are relatively understudied when compared with melanoma. Notably, BCC and SCC are not routinely reported in cancer registries. In Australia, Medicare data are used to estimate the incidence and costs associated with these cancers. Expenditure in Australia for the diagnosis, treatment and pathology, almost exceeds $700 million for both BCC and squamous cell carcinoma. In Unites States, the average annual cost for skin cancer including melanoma is approximately $8.1 billion. Previous research has led to identification of 29 BCC and 11 squamous cell carcinoma genetic risk variants and 7 of them overlap with both BCC and SCC risk. So, to strengthen the preventive efforts and to reveal new therapeutics, it is very timely and critical to explore more on the genetic susceptibility of these deadly cancers. We analysed ~48,000 cancer cases with ~630,000 skin cancer free controls from European ancestry population in Australia, UK and USA.  (more…)
Author Interviews, Genetic Research, Microbiome / 13.04.2019 Interview with: Kyung Mo Kim Senior research scientist Korea Polar Research Institute. Professor Gustavo Caetano-Anollés Carl R. Woese Institute for Genomic Biology University of Illinois Arshan Nasir Distinguished Fellow Los Alamos National Laboratory in New Mexico What is the background for this study? What are the main findings? Response: Horizontal gene transfer is the process by which unrelated microorganisms can exchange genes. The famous examples would be transfer of antibiotic resistance genes among bacteria that renders many commercially expensive antibiotics useless. From an evolutionary point of view, it complicates our understanding of how bacteria are related since even distantly-related bacteria can share genes and then cluster together on evolutionary trees. Thus better understanding horizontal evolution is important for both public health and our basic understanding of microbial taxonomy and evolution. There are some excellent existing methods of HGT detection that compare DNA features (e.g. GC%, codon usage) or statistical similarity between genomes to identify foreign genes. However, these methods work better to identify recently transferred genes. Transfers that happened millions or billions of years ago cannot be reliably detected since DNA sequences evolve over time during which foreign DNA can become more host-like. That is why we focused our attention on utilizing approaches that are based on sound evolutionary principles. If a gene is horizontally acquired, then a phylogenetic tree of that gene will be different from the reference or known tree of the organisms. The true phylogenetic tree of organisms describes how organisms have descended from a common ancestor through inheritance of genes. If a gene is acquired from a source outside the parents or from an unrelated organism, then there will be a conflict between gene tree and the reference/known species tree. This conflict can be indication of HGT. (more…)
Author Interviews, Genetic Research, Nature / 08.10.2016 Interview with: Victor Guryev PhD Team Leader European Research Institute for the Biology of Ageing (ERIBA) What is the background for this study? Response: Decoding of human genomes progresses at an enormous speed. Thirteen years after completion of the first human genome reference, we now obtained full genome information for tens of thousands individuals. This number is expected to reach millions in the next few years. Processing this information is a challenge on its own: we learned how to detect small changes such as single nucleotide variants (SNVs), but identification of larger, structural DNA variants (SVs) is far from being perfect. (more…)
Author Interviews, Genetic Research, McGill, Nature / 12.03.2015

Prof. Moshe Szyf Ph.D. James McGill Professor of Pharmacology and Therapeutics McGill Interview with: Prof. Moshe Szyf Ph.D. James McGill Professor of Pharmacology and Therapeutics McGill University Medical Research: What is the background for this study? What are the main findings? Dr. Szyf: Humans exhibit a marked variation in traits both physical and behavioral and different susceptibilities  for developing disease. What causes this inter-individual variation? The prevailing dogma has been that changes in the sequences of genes or heritable genetic differences are responsible for these  differences. We tested here an alternative hypothesis that perhaps some of the reason for this natural variation in traits is not caused by differences in inherited genes but by “epigenetic” changes that alter the way genes work without changing the genes.  The main difference between genetic and epigenetic changes is that epigenetic changes could be introduced by experience and exposure to environment. The experiences that can cause epigenetic changes include physical as well as social environments. Although we had known that epigenetic differences occur in humans and animals we didn’t have evidence that these changes are behind the natural variation in traits that is observed in humans and animals. Ants are an exciting biological paradigm that exhibits quantitative variations in size and therefore provided a unique opportunity to test this hypothesis. (more…)