https:\/\/www.antibodysociety.org\/airrc\/meetings\/communityiv\/<\/a>).\nIt was the fourth AIRR conference, and I was nice to see lots of\nfield-leading people participating. Compared to the last AIRR meeting\nalmost 2 years ago, the agenda of the conference was dominated by\nmachine learning and big data topics. In my short blog post, I will\ndiscuss two talks that covered these two exciting topics.<\/p>\n\n\n\n\n\n\n\n\nRecent advances in leukapheresis enabled researchers to collect all\nB-cells that are found in peripheral blood in human body. However,\nthe majority of individual\u2019s B-cells resides in lymphoid organs,\nwhich are outside of leukapheresis reach. Briney et al., (1)\nemployed next-generation sequencing technology (NGS) to interrogate\nB-cell receptor (BCR) sequences across ten individuals of\napproximately same age, but from different gender and ethnicity\ngroups. By employing leukopaks as a source of peripheral B-cells,\nthey generated 3 billion sequences, of which 300 million sequences\nwere high quality. They showed that despite the vastness of allowed\nantibody space, non-trivial sequence convergences were observed. They\ndid not find any statistically significant differences in BCR\nrepertoire overlaps between different ethnicities and genders.\nAuthors mentioned that they were performing another round of leukopak\nblood analysis on the same cohort of donors after one year to\ninterrogate dynamics of the human immune system. It will be\ninteresting to see the longitudinal sequence overlap analysis within\nthe same B-cell donor. The authors also discussed ways to analyse\nAIRR data and to present annotated sequences upon publication.<\/p>\n\n\n\n
Another exciting talk was given by Lindsay G Cowell from UT Southwestern (2). In their work, they have developed a classifier to identify tumor samples based on collections of T-cell receptors (TCR). Instead of simply employing TCR sequences as features in their classifier, they mapped TCR sequences to amino acid biophysical properties. Every TCR sequence in TCR repertoires was split into 4-mer snippets. Five Atchley Factors were applied to every amino acid in the snippet and the overall score was devised. Atchley Factors include amino acid hydrophobicity, secondary structure associations, size, codon usage and electric charge. These scores were used in their machine learning model to identify tumor and healthy samples. Using this model, they successfully identified all colorectal tumor samples. With the ever-increasing amount of available BCR data from various disease states, it will exciting to see if their model works with BCR sequences to distinguish disease states. Since somatic hypermutation (SHM) changes BCR sequences, it will be exciting to see structural paratope convergence in disease states using Atchley Factors.<\/p>\n\n\n\n
Thanks!<\/p>\n\n\n\n
Best,<\/p>\n\n\n\n
Alex<\/p>\n\n\n\n
Having been a member\nof OPIG for an entire 5 weeks, I thought it was about time I attended\na conference abroad. Becoming the self-nominated chief Foccaccia\nTaster at the AIRR meeting was a tough role, but one I believe I\nfulfilled with tenacity and boundless enthusiasm. A special shout out\ngoes to Mario and Alessandro for the neverending cups of coffee, and\nfor beers being provided every lunchtime. Leaving aside the fantastic\nculinary experiences for a moment, the introductory workshops held on\nDay 1 were a really great overview for someone relatively new to the\nfield. I attended Victor Greiff\u2019s \u201cAIRR-seq data analysis and\nprocessing\u201d, a 3 hour crash course in AIRR-seq data acquisition,\nerror-correction, and useful types of analysis. Following this, the\ntalks and poster sessions held over subsequent days were of a very\nhigh quality. My favourite poster was presented by Michael Poeschla\nfrom the Max Planck Institute; the work focussed on characterising\nantibody repertoire aging in the killifish, a short-lived vertebrate\nmodel that interestingly, upon eating bacteria taken from the gut of\nyounger killifish, lives longer than it\u2019s usual lifespan. \n<\/p>\n\n\n\n
– Sarah<\/p>\n\n\n\n
We had a great time at the AIRR community meeting in Genoa in early May, where we joined some 150 researchers from across North America and Europe (which is appreciably larger than the 50-strong turn-out seen at previous meetings). We had a range of short talks in both basic and translational science, and concerning both sides of the great lymphocyte divide. The theme of the meeting was \u201cBridging the Gaps\u201d and there were a number of on-theme talks on the challenges related to storing and analysing data sets in excess of hundreds of millions of sequences.<\/p>\n\n\n\n
We enjoyed the keynote sessions, the first of which was given by Prof. Sai Reddy of ETH Zurich. As Alex mentioned, machine learning techniques are becoming increasingly commonplace in repertoire analysis. While the other ML talks tackled the problem of repertoire-wide classification of immune status, Sai Reddy presented work relating to the identification of antigen-specificity at the level of individual sequences, which made for a really exciting talk.<\/p>\n\n\n\n
The second keynote speaker was the distinguished immunologist Antonio Lanzavecchia MD from USI. His talk was a return to more classical immunology in the theme of the day which was Clinical and Translational Science. The audience was particularly wowed by a result which was published in Nature in 2016, the natural occurrence of an insertion of an entire 98 a.a. collagen-binding domain either right at the tip of the H3 or in the VH-CH1 elbow of antibodies. This sort of insertion is apparently more common than we might anticipate, if not largely invisible to those in Ig-seq because of sequencing read length limitations. The PDB code of the solved structure of a LAIR1 fusion antibody is 5NST if you want to have a look.<\/p>\n\n\n\n
All best wishes<\/p>\n\n\n\n
Eve<\/p>\n","protected":false},"excerpt":{"rendered":"
Hi everyone, Today is the day for another blog post from me. Last month I attended an AIRR conference in Genoa, Italy (https:\/\/www.antibodysociety.org\/airrc\/meetings\/communityiv\/). It was the fourth AIRR conference, and I was nice to see lots of field-leading people participating. Compared to the last AIRR meeting almost 2 years ago, the agenda of the conference […]<\/p>\n","protected":false},"author":58,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[1],"tags":[],"ppma_author":[540],"class_list":["post-4705","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":540,"user_id":58,"is_guest":0,"slug":"eve","display_name":"Eve Richardson","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/9891300fda41850fb2fc859ef2ee18aae341c49e520511adc5684413cc356ff7?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4705","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/58"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=4705"}],"version-history":[{"count":2,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4705\/revisions"}],"predecessor-version":[{"id":4708,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/4705\/revisions\/4708"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=4705"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=4705"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=4705"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=4705"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}