Dr Natasha Karp | Senior Staff Scientist - Biostatistician

This person is a member of Sanger Institute Alumni.

Karp, Natasha

I am a biostatistician supporting the International Mouse Phenotyping Consortium by researching methods to optimise the experimental design and data analysis. My focus has been on developing robust statistical analysis pipelines that consider the complex data and variation in workflow within phenotying experiments.

My role requires cross discipline collaborations to address the complex data which has challenges that arise in identifying reproducible phenotypes and those that arise from the high throughput nature of the project. The research looks to understand the issues and identify solutions that will improve the ability of the experiments to answer the research question.

There have been published concerns over replicability of phenotyping studies. To address issues with replicability I have focused on two angles.

  • Firstly to optimise the data analysis methods applied. The high throughput pipelines provide a unique opportunity to explore large datasets and then develop and test various statistical methods using resampling and simulation studies. The methods I have developed have been made freely available to all through the development of an R package called PhenStat.
  • The second approach is looking at how we can improve the design and reporting of the experiment conducted. To improve reporting, I led the development of the Mouse Experimental Design Ontology to provide a standard language to capture how we conduct the experiments. Across the consortium, we have lead the field, and applied the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines to a database. Following my involvement in the development of the NC3Rs Experimental Design Assistant, we are testing programs to introduce the software at the institute.

Publications

  • Applying the ARRIVE Guidelines to an In Vivo Database.

    Karp NA, Meehan TF, Morgan H, Mason JC, Blake A et al.

    PLoS biology 2015;13;5;e1002151

  • Recommendations for minimum information for publication of experimental pathology data: MINPEPA guidelines.

    Scudamore CL, Soilleux EJ, Karp NA, Smith K, Poulsom R et al.

    The Journal of pathology 2016;238;2;359-67

  • Reporting phenotypes in mouse models when considering body size as a potential confounder.

    Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK and Karp NA

    Journal of biomedical semantics 2016;7;2

  • PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.

    Kurbatova N, Mason JC, Morgan H, Meehan TF and Karp NA

    PloS one 2015;10;7;e0131274

  • Impact of temporal variation on design and analysis of mouse knockout phenotyping studies.

    Karp NA, Speak AO, White JK, Adams DJ, Hrabé de Angelis M et al.

    PloS one 2014;9;10;e111239

  • A gene expression resource generated by genome-wide lacZ profiling in the mouse.

    Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA et al.

    Disease models & mechanisms 2015;8;11;1467-78

  • Robust and sensitive analysis of mouse knockout phenotypes.

    Karp NA, Melvin D, Sanger Mouse Genetics Project and Mott RF

    PloS one 2012;7;12;e52410

  • Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

    White JK, Gerdin AK, Karp NA, Ryder E, Buljan M et al.

    Cell 2013;154;2;452-64

  • Evaluating and Optimizing Fish Health and Welfare During Experimental Procedures.

    Goodwin N, Westall L, Karp NA, Hazlehurst D, Kovacs C et al.

    Zebrafish 2016

  • Recommendations for minimum information for publication of experimental pathology data: MINPEPA guidelines.

    Scudamore CL, Soilleux EJ, Karp NA, Smith K, Poulsom R et al.

    The Journal of pathology 2016;238;2;359-67

  • Reporting phenotypes in mouse models when considering body size as a potential confounder.

    Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK and Karp NA

    Journal of biomedical semantics 2016;7;2

  • A gene expression resource generated by genome-wide lacZ profiling in the mouse.

    Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA et al.

    Disease models & mechanisms 2015;8;11;1467-78

  • A mouse informatics platform for phenotypic and translational discovery.

    Ring N, Meehan TF, Blake A, Brown J, Chen CK et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2015;26;9-10;413-21

  • Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

    de Angelis MH, Nicholson G, Selloum M, White J, Morgan H et al.

    Nature genetics 2015;47;9;969-978

  • Applying the ARRIVE Guidelines to an In Vivo Database.

    Karp NA, Meehan TF, Morgan H, Mason JC, Blake A et al.

    PLoS biology 2015;13;5;e1002151

  • A high-throughput in vivo micronucleus assay for genome instability screening in mice.

    Balmus G, Karp NA, Ng BL, Jackson SP, Adams DJ and McIntyre RE

    Nature protocols 2015;10;1;205-15

  • PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data.

    Kurbatova N, Mason JC, Morgan H, Meehan TF and Karp NA

    PloS one 2015;10;7;e0131274

  • Disruption of the potassium channel regulatory subunit KCNE2 causes iron-deficient anemia.

    Salsbury G, Cambridge EL, McIntyre Z, Arends MJ, Karp NA et al.

    Experimental hematology 2014;42;12;1053-8.e1

  • Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen.

    Adissu HA, Estabel J, Sunter D, Tuck E, Hooks Y et al.

    Disease models & mechanisms 2014;7;5;515-24

  • 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

  • Impact of temporal variation on design and analysis of mouse knockout phenotyping studies.

    Karp NA, Speak AO, White JK, Adams DJ, Hrabé de Angelis M et al.

    PloS one 2014;9;10;e111239

  • Targeting of Slc25a21 is associated with orofacial defects and otitis media due to disrupted expression of a neighbouring gene.

    Maguire S, Estabel J, Ingham N, Pearson S, Ryder E et al.

    PloS one 2014;9;3;e91807

  • Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes.

    White JK, Gerdin AK, Karp NA, Ryder E, Buljan M et al.

    Cell 2013;154;2;452-64

  • High-fat feeding rapidly induces obesity and lipid derangements in C57BL/6N mice.

    Podrini C, Cambridge EL, Lelliott CJ, Carragher DM, Estabel J et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2013;24;5-6;240-51

  • Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome.

    Basel-Vanagaite L, Dallapiccola B, Ramirez-Solis R, Segref A, Thiele H et al.

    American journal of human genetics 2012;91;6;998-1010

  • Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project.

    Ayadi A, Birling MC, Bottomley J, Bussell J, Fuchs H et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2012;23;9-10;600-10

  • Experimental and husbandry procedures as potential modifiers of the results of phenotyping tests.

    Gerdin AK, Igosheva N, Roberson LA, Ismail O, Karp N et al.

    Physiology & behavior 2012;106;5;602-11

  • The role of sphingosine-1-phosphate transporter Spns2 in immune system function.

    Nijnik A, Clare S, Hale C, Chen J, Raisen C et al.

    Journal of immunology (Baltimore, Md. : 1950) 2012;189;1;102-11

  • The fallacy of ratio correction to address confounding factors.

    Karp NA, Segonds-Pichon A, Gerdin AK, Ramírez-Solis R and White JK

    Laboratory animals 2012;46;3;245-52

  • Robust and sensitive analysis of mouse knockout phenotypes.

    Karp NA, Melvin D, Sanger Mouse Genetics Project and Mott RF

    PloS one 2012;7;12;e52410

  • Optimising experimental design for high-throughput phenotyping in mice: a case study.

    Karp NA, Baker LA, Gerdin AK, Adams NC, Ramírez-Solis R and White JK

    Mammalian genome : official journal of the International Mammalian Genome Society 2010;21;9-10;467-76

  • Addressing accuracy and precision issues in iTRAQ quantitation.

    Karp NA, Huber W, Sadowski PG, Charles PD, Hester SV and Lilley KS

    Molecular & cellular proteomics : MCP 2010;9;9;1885-97

  • Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock.

    Deery MJ, Maywood ES, Chesham JE, Sládek M, Karp NA et al.

    Current biology : CB 2009;19;23;2031-6

  • Gel-based proteomics approach to the study of metabolic changes in pear tissue during storage.

    Pedreschi R, Hertog M, Robben J, Lilley KS, Karp NA et al.

    Journal of agricultural and food chemistry 2009;57;15;6997-7004

  • Comparison of DIGE and post-stained gel electrophoresis with both traditional and SameSpots analysis for quantitative proteomics.

    Karp NA, Feret R, Rubtsov DV and Lilley KS

    Proteomics 2008;8;5;948-60

  • Design and analysis issues in quantitative proteomics studies.

    Karp NA and Lilley KS

    Proteomics 2007;7 Suppl 1;42-50

  • Experimental and statistical considerations to avoid false conclusions in proteomics studies using differential in-gel electrophoresis.

    Karp NA, McCormick PS, Russell MR and Lilley KS

    Molecular & cellular proteomics : MCP 2007;6;8;1354-64

  • Glucocorticoid signaling synchronizes the liver circadian transcriptome.

    Reddy AB, Maywood ES, Karp NA, King VM, Inoue Y et al.

    Hepatology (Baltimore, Md.) 2007;45;6;1478-88

  • Impact of replicate types on proteomic expression analysis.

    Karp NA, Spencer M, Lindsay H, O'Dell K and Lilley KS

    Journal of proteome research 2005;4;5;1867-71

  • Maximising sensitivity for detecting changes in protein expression: experimental design using minimal CyDyes.

    Karp NA and Lilley KS

    Proteomics 2005;5;12;3105-15

  • Analysis of calibration methodologies for solvent effects in drug discovery studies using evanescent wave biosensors.

    Karp NA, Edwards PR and Leatherbarrow RJ

    Biosensors & bioelectronics 2005;21;1;128-34

  • DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results.

    Kreil DP, Karp NA and Lilley KS

    Bioinformatics (Oxford, England) 2004;20;13;2026-34

  • Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress.

    Prabakaran S, Swatton JE, Ryan MM, Huffaker SJ, Huang JT et al.

    Molecular psychiatry 2004;9;7;684-97, 643

  • Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis.

    Karp NA, Kreil DP and Lilley KS

    Proteomics 2004;4;5;1421-32

  • Protein profiling of human postmortem brain using 2-dimensional fluorescence difference gel electrophoresis (2-D DIGE).

    Swatton JE, Prabakaran S, Karp NA, Lilley KS and Bahn S

    Molecular psychiatry 2004;9;2;128-43

Karp, Natasha
Natasha's Timeline
2008

Joined the Sanger Institute as a biostatistician

2003

Started work as a Research Associate at Cambridge University

PhD in Chemistry with University College London

1993

R&D Scientist, Affinity Sensors, Cambridge