Vivek Iyer | Human Genetics Informatics Team Lead

Iyer, Vivek

I lead the Human Genetics Informatics Team, which connects the Human Genetics faculty groups to the best methods and biological pipelines to support their experiments.

At Sanger we have the privilege of running experiments at very large scales: my job is to deal with the myriad requirements of Human Genetics analysis at these scales, to help my group create, evaluate and run cutting edge biological pipelines and methods, so that we can best help the Human Genetics faculty groups. We have the freedom to both find and use best practice, and also to explore experimental strategies (for instance, when querying and filtering very large genetic datasets). I believe we have to aggessively pursue both approaches!

I have been involved in analysing germline and somatic human variant data, RNASeq data, designing and doing statistical analyses around targeted, genome-wide and paired-guide CRISPR screens. I was also involved in writing and leading the development of LIMS systems producing mutant ES Cells and mice in high throughput, for the EUCOMM, KOMP and IMPC programs - two LIMS systems (here and here) and a coordinating system (iMITS) for IMPC mouse production. That field has been revolutionised by the advent of CRISPR-based genome editing, and our software interests followed that change with WGE, a CRISPR-design tool.

Publications

  • No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice.

    Iyer V, Boroviak K, Thomas M, Doe B, Riva L et al.

    PLoS genetics 2018;14;7;e1007503

  • UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs.

    Gozdecka M, Meduri E, Mazan M, Tzelepis K, Dudek M et al.

    Nature genetics 2018;50;6;883-894

  • Enhancing the genome editing toolbox: genome wide CRISPR arrayed libraries.

    Metzakopian E, Strong A, Iyer V, Hodgkins A, Tzelepis K et al.

    Scientific reports 2017;7;1;2244

  • Genomic analysis and clinical management of adolescent cutaneous melanoma.

    Rabbie R, Rashid M, Arance AM, Sánchez M, Tell-Marti G et al.

    Pigment cell & melanoma research 2017;30;3;307-316

  • Revisiting olfactory receptors as putative drivers of cancer.

    Ranzani M, Iyer V, Ibarra-Soria X, Del Castillo Velasco-Herrera M, Garnett M et al.

    Wellcome open research 2017;2;9

  • WGE: a CRISPR database for genome engineering.

    Hodgkins A, Farne A, Perera S, Grego T, Parry-Smith DJ et al.

    Bioinformatics (Oxford, England) 2015;31;18;3078-80

  • Off-target mutations are rare in Cas9-modified mice.

    Iyer V, Shen B, Zhang W, Hodgkins A, Keane T et al.

    Nature methods 2015;12;6;479

  • The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

    Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H et al.

    Nucleic acids research 2014;42;Database issue;D802-9

  • A conditional knockout resource for the genome-wide study of mouse gene function.

    Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W et al.

    Nature 2011;474;7351;337-42

  • BioMart as an integration solution for the International Knockout Mouse Consortium.

    Oakley DJ, Iyer V, Skarnes WC and Smedley D

    Database : the journal of biological databases and curation 2011;2011;bar028

  • The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.

    Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD et al.

    Nucleic acids research 2011;39;Database issue;D849-55

  • Ensembl 2006.

    Birney E, Andrews D, Caccamo M, Chen Y, Clarke L et al.

    Nucleic acids research 2006;34;Database issue;D556-61

  • The otter annotation system.

    Searle SM, Gilbert J, Iyer V and Clamp M

    Genome research 2004;14;5;963-70

  • Apollo: a sequence annotation editor.

    Lewis SE, Searle SM, Harris N, Gibson M, Lyer V et al.

    Genome biology 2002;3;12;RESEARCH0082

  • No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice.

    Iyer V, Boroviak K, Thomas M, Doe B, Riva L et al.

    PLoS genetics 2018;14;7;e1007503

  • UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs.

    Gozdecka M, Meduri E, Mazan M, Tzelepis K, Dudek M et al.

    Nature genetics 2018;50;6;883-894

  • Enhancing the genome editing toolbox: genome wide CRISPR arrayed libraries.

    Metzakopian E, Strong A, Iyer V, Hodgkins A, Tzelepis K et al.

    Scientific reports 2017;7;1;2244

  • Genomic analysis and clinical management of adolescent cutaneous melanoma.

    Rabbie R, Rashid M, Arance AM, Sánchez M, Tell-Marti G et al.

    Pigment cell & melanoma research 2017;30;3;307-316

  • Revisiting olfactory receptors as putative drivers of cancer.

    Ranzani M, Iyer V, Ibarra-Soria X, Del Castillo Velasco-Herrera M, Garnett M et al.

    Wellcome open research 2017;2;9

  • WGE: a CRISPR database for genome engineering.

    Hodgkins A, Farne A, Perera S, Grego T, Parry-Smith DJ et al.

    Bioinformatics (Oxford, England) 2015;31;18;3078-80

  • The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

    Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H et al.

    Nucleic acids research 2014;42;Database issue;D802-9

  • A conditional knockout resource for the genome-wide study of mouse gene function.

    Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W et al.

    Nature 2011;474;7351;337-42

  • The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.

    Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD et al.

    Nucleic acids research 2011;39;Database issue;D849-55

  • Ensembl 2006.

    Birney E, Andrews D, Caccamo M, Chen Y, Clarke L et al.

    Nucleic acids research 2006;34;Database issue;D556-61

  • The otter annotation system.

    Searle SM, Gilbert J, Iyer V and Clamp M

    Genome research 2004;14;5;963-70

Iyer, Vivek
Vivek's Timeline
2019

Team Lead, Human Genetics Informatics, WSI

2015

Principal Bioinformatician, Experimental Cancer Genetics, WTSI

2007

Software Team Leader, High Throughput Gene Targeting, WTSI

2006

Software Developer, High Throughput Gene Targeting, WTSI

2002

Ensembl developer, WTSI

1997

Software Developer, Chicago

1996

PhD, Gravitation, University of Chicago

1990

BSc(Hons), Mathematical Physics, University of Adelaide