Arthur Gilly | Principal Bioinformatician

Gilly, Arthur

Arthur worked in the Human Genetics department from August 2013 to November 2018 in Ele Zeggini's lab. He is now Head of Analytics at the Institute of Translational Genomics, which is based at the Helmholtz Centre in Munich. This page is being maintained as a historical record of his work at the Sanger Institute is no longer being updated.

Arthur worked in the Human Genetics department from August 2013 to November 2018 in Ele Zeggini's lab. He focused on the development of new methods to empower the discovery of actionable targets for the treatment of common human diseases. He managed analytical projects, designed pipelines, developed new statistical methods and performed bioinformatic follow-up of association discoveries.

His main focus was on the analysis of sequencing data from the HELIC study (ca. 3000 participants). First, he worked 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. He established a quality control and imputation pipeline for very low-depth sequence data, and carried out association analysis with over 60 quantitative traits. He performed a thorough evaluation of the quality of such sequences by comparing it to other genotyping methods, in order to guide future study design choices.

Then, he transitioned to high-depth (>15x) sequencing data on the same samples, which opened up new analytical perspectives and challenges. In particular, high depth allows reliable calling of rare variants, whose contribution to the aetiology of complex traits is not currently known. With Daniel Suveges, he developed a rare variant association study (RVAS) analysis pipeline and applied it to genome-wide gene-based tests on the HELIC high-depth WGS data. This allowed to evidence a combined role of rare and low-frequency exonic and regulatory variants.

Software development was an important part of Arthur's responsibilities and interests. He wrote 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 browse the team's github account or his own for interesting data visualisation and analysis tools.

Publications

  • Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits.

    Gilly A, Suveges D, Kuchenbaecker K, Pollard M, Southam L et al.

    Nature communications 2018;9;1;4674

  • 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

  • Population-wide copy number variation calling using variant call format files from 6,898 individuals.

    Png G, Suveges D, Park YC, Walter K, Kundu K et al.

    Genetic epidemiology 2019

  • Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits.

    Gilly A, Suveges D, Kuchenbaecker K, Pollard M, Southam L et al.

    Nature communications 2018;9;1;4674

  • Genome-wide analyses using UK Biobank data provide insights into the genetic architecture of osteoarthritis.

    Zengini E, Hatzikotoulas K, Tachmazidou I, Steinberg J, Hartwig FP et al.

    Nature genetics 2018;50;4;549-558

  • Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes.

    Grarup N, Moltke I, Andersen MK, Dalby M, Vitting-Seerup K et al.

    Nature genetics 2018

  • 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)