Arthur Gilly | Principal Bioinformatician

Gilly, Arthur

Arthur's work focuses on the analysis of high-throughput sequencing data, with the objective of finding actionable targets for the prevention and treatment of common diseases. He designs pipelines, develops new statistical methods and performs bioinformatic follow-up of association discoveries.

In the past five years, I have been analysing sequencing data from the HELIC study (ca. 3000 participants). First, I focused on very low depth (1x) data, whose interpreation posed numerous analytical challenges due to the high amount of missingness and low signal-to-noise ratio among variant calls. I have established a quality control and imputation pipeline for very low-depth sequence data, and have carried out association analysis with over 60 quantitative traits.

I am now working with high-depth (>15x) sequencing data on the same samples, which opens up new analytical perspectives and challenges. In particular, high depth allow reliable calling of rare variants, whose contribution to the aetiology of complex traits is not currently known. I have developed a rare variant association study (RVAS) analysis pipeline with a piece of software that corrects for overlapping samples in large-scale meta-analyses of genetic association studies, as well as a copy number variant caller that works on SNP genotypes (as opposed to sequencing read data). Feel free to check out our team github account or my own for interesting data visualisation and analysis tools.

Publications

  • Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits.

    Southam L, Gilly A, Süveges D, Farmaki AE, Schwartzentruber J et al.

    Nature communications 2017;8;15606

  • Very low-depth sequencing in a founder population identifies a cardioprotective APOC3 signal missed by genome-wide imputation.

    Gilly A, Ritchie GR, Southam L, Farmaki AE, Tsafantakis E et al.

    Human molecular genetics 2016;25;11;2360-2365

  • Using population isolates in genetic association studies.

    Hatzikotoulas K, Gilly A and Zeggini E

    Briefings in functional genomics 2014;13;5;371-7

  • Evaluation of shared genetic aetiology between osteoarthritis and bone mineral density identifies SMAD3 as a novel osteoarthritis risk locus.

    Hackinger S, Trajanoska K, Styrkarsdottir U, Zengini E, Steinberg J et al.

    Human molecular genetics 2017;26;19;3850-3858

  • Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

    Xue Y, Mezzavilla M, Haber M, McCarthy S, Chen Y et al.

    Nature communications 2017;8;15927

  • Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits.

    Southam L, Gilly A, Süveges D, Farmaki AE, Schwartzentruber J et al.

    Nature communications 2017;8;15606

  • The mountainous Cretan dietary patterns and their relationship with cardiovascular risk factors: the Hellenic Isolated Cohorts MANOLIS study.

    Farmaki AE, Rayner NW, Matchan A, Spiliopoulou P, Gilly A et al.

    Public health nutrition 2017;20;6;1063-1074

  • A reference panel of 64,976 haplotypes for genotype imputation.

    McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR et al.

    Nature genetics 2016;48;10;1279-83

  • Very low-depth sequencing in a founder population identifies a cardioprotective APOC3 signal missed by genome-wide imputation.

    Gilly A, Ritchie GR, Southam L, Farmaki AE, Tsafantakis E et al.

    Human molecular genetics 2016;25;11;2360-2365

  • TE-Tracker: systematic identification of transposition events through whole-genome resequencing.

    Gilly A, Etcheverry M, Madoui MA, Guy J, Quadrana L et al.

    BMC bioinformatics 2014;15;377

  • Genetic characterization of Greek population isolates reveals strong genetic drift at missense and trait-associated variants.

    Panoutsopoulou K, Hatzikotoulas K, Xifara DK, Colonna V, Farmaki AE et al.

    Nature communications 2014;5;5345

  • Using population isolates in genetic association studies.

    Hatzikotoulas K, Gilly A and Zeggini E

    Briefings in functional genomics 2014;13;5;371-7

  • Mapping the epigenetic basis of complex traits.

    Cortijo S, Wardenaar R, Colomé-Tatché M, Gilly A, Etcheverry M et al.

    Science (New York, N.Y.) 2014;343;6175;1145-8

Career/Research Highlights

Gilly, Arthur
Arthur's Timeline
2016

Principal Bioinformatician, Wellcome Trust Sanger Institute

2013

Senior Bioinformatician/Statistical Geneticist, Wellcome Trust Sanger Institute

2012

Research Engineer, at National Sequencing Center, Evry, France

2011

R&D Engineer, at Misys Sophis, Paris, France

Junior Consultant, at Sophis Asia, Hong Kong, PRC

2010

Graduated from Grenoble INP - ENSIMAG, France (diplôme d'ingénieur, Applied Mathematics)