Introduction to the statistical analysis of genome-wide association studies

Key information

Start date: To be confirmed

Attendance dates:

To be confirmed

Time commitment: 5 days

Venue:

Distance learning

Contact details:

Overview

This course will enable human geneticists to analyse their large-scale genetic data using standard analytical approaches and freely available software tools. It will cover statistical backgrounds for association studies; a primer on scripting in the most frequently used computational environments, design and analysis of such studies, interpretation of the results.

Who is this course for?

This course is for geneticists facing the need to analyse from small to large-scale human genotyping data in relation to their effect on common human traits and diseases.

Scientists and students in training aiming to undertake SNP-based association analyses, genome-wide association studies and their meta-analyses.

Researchers willing to understand better the statistical approaches and analytical procedures for the genetic association studies.

Learning outcomes

On successful completion of this course, you will be able to:

  • Undertake quality control, imputation and analysis of genome-wide data using standard statistical approaches and software tools
  • Complete meta-analysis of genome-wide association studies and analysis of rare variants
  • Evaluate critically the results of association analysis and visualise them
  • Understand the study design and findings for publications in peer-reviewed journals.

Course content

Three guest lectures will be given by renowned scientists in the field of human genetics.

Indicative content includes, some or all of the following topics:

  • Introduction to statistics for geneticists
  • Introduction to Linux and R
  • Genome-wide association studies (GWAS)
  • Quality Control (QC) for GWAS
  • Association analysis
  • Population structure
  • Imputation of GWAS
  • Meta-analysis of GWAS
  • Analysis of rare variants
  • Genetic risk scores
  • Mendelian randomisation.

Example programme

The final programme and timings will be given to applicants prior to the course starting.

Take a look at our example timetable (PDF) to get an idea of timings and the structure of the week.

Introduction to statistics for geneticists - Prof Inga Prokopenko and Dr Marika Kaakinen

Basics of probability theory, binomial and normal distribution, polygenic inheritance and complex traits, allele frequencies in population, Hardy-Weinberg equilibrium.

Introduction to Linux and R – Dr. Ayse Demirkan

Interface, command line and basic commands, functions, text editors, saving commands in scripts and running scripts, installing software tools for statistical analysis of genetic data, versions, data storage. Linux as environment for PLINK software tool. Basics of R usage to run graphical tools for genome-wide data and analysis results.

Introduction to genome-wise association studies (GWAS) – Dr. Marika Kaakinen

Principles of linkage disequilibrium (LD) and SNP tagging for genome-wide genotyping array design, analysis and imputation; haplotypes, study design, sample size and statistical power, use UCSC browser and NHGRI GWAS catalog.

Quality Control (QC) for GWAS – Prof Reedik Mägi

Sample and variant QC :on individuals (samples) for missingness, gender checks, duplicates and cryptic relatedness, population outliers, heterozygosity and inbreeding; and on SNPs for missingness, minor allele frequency and Hardy-Weinberg equilibrium.

Invited speaker session

This slot will be filled by one of our renowned scientist guest lecturers in the field of human genetics.

Statistical models for genetic association studies – Prof Krista Fischer

linear and logistic regression, additive genetic model, test significance, type I error and multiple testing.

Association analysis - Prof Inga Prokopenko

Analyses of data using PLINK software, including genetic models used for statistical analysis, covariates and adjustments, basic types of single-variant analyses, graphical representation of the output results

Population structure – Prof Andrew P. Morris

Identification of population outliers in GWAS and methods for detecting and accounting for structure within populations.  Use of PLINK for principal components analysis and association analysis adjusting for structure.

Imputation of GWAS - Prof Inga Prokopenko

GWAS reference panels, including HapMap and 1000 Genomes Projects, reference haplotypes, imputation with IMPUTE software, phasing and imputation steps, chromosome chunks, combining chinks for imputed data analysis, quality of imputation, imputed genotypes probability.

Invited speaker session

This slot will be filled by one of our renowned scientist guest lecturers in the field of human genetics.

Meta-analysis of GWAS - Prof Andrew P. Morris

Combining association summary statistics across GWAS using fixed-and random-effects meta-analysis.  GWAMA software to perform meta-analysis.

Genetic risk scores, Mendelian Randomisation - Prof Krista Fischer

Weighted and unweighted genetic risk scores. Dissecting causal relationships between exposures and complex traits using Mendelian Randomization. Instrumental variable approach.

Invited speaker and Q&A session

This slot will be filled by one of our renowned scientist guest lecturers in the field of human genetics and the Q&A will be held by all the course leaders.

Analysis of rare variants – Prof Andrew P. Morris

Rationale for rare variant analysis.  Methods for assaying rare variation.  Methods for the analysis of rare variants.  GRANVIL software for testing association with rare variants.

Assessment

There will be no assessment on this course, however, you will receive a course certificate provided you attend over 80 per cent of the taught course.

Course leader

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Professor Inga Prokopenko

Professor e-One Health and Head of Statistical Multi-Omics

Course contributors

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Dr Ayse Demirkan

Research Fellow

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Dr Marika Kaakinen

Organising Committee

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Kostiantyn Rudomotkin

Course secretariat and IT

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Dr Anna Ulrich

Research Fellow

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Liudmila Zudina

Postgraduate Research Student

Reading list

Pearson, T. A., & Manolio, T. A. (2008). How to interpret a genome-wide association studyJAMA299(11), 1335–1344.
DOI: 10.1001/jama.299.11.1335.

The Wellcome Trust Case Control Consortium., Management Committee., Burton, P. et al. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controlsNature 447, 661–678 (2007).
DOI: 10.1038/nature05911.

McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P., & Hirschhorn, J. N. (2008). Genome-wide association studies for complex traits: consensus, uncertainty and challengesNature reviews. Genetics9(5), 356–369.
DOI: 10.1038/nrg2344.

Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017). 10 Years of GWAS Discovery: Biology, Function, and TranslationAmerican journal of human genetics101(1), 5–22.
DOI: 10.1016/j.ajhg.2017.06.005.

Balding D. J. (2006). A tutorial on statistical methods for population association studies. Nature reviews. Genetics7(10), 781–791.
DOI: 10.1038/nrg1916.

Hirschhorn, J. N., & Daly, M. J. (2005). Genome-wide association studies for common diseases and complex traits. Nature reviews. Genetics, 6(2), 95–108.
DOI: 10.1038/nrg1521.

Winkler, T. W., Day, F. R., Croteau-Chonka, D. C., Wood, A. R., Locke, A. E., Mägi, R., Ferreira, T., Fall, T., Graff, M., Justice, A. E., Luan, J., Gustafsson, S., Randall, J. C., Vedantam, S., Workalemahu, T., Kilpeläinen, T. O., Scherag, A., Esko, T., Kutalik, Z., Heid, I. M., … Genetic Investigation of Anthropometric Traits (GIANT) Consortium (2014). Quality control and conduct of genome-wide association meta-analysesNature protocols9(5), 1192–1212.
DOI: 10.1038/nprot.2014.071.

Holland, D., Fan, C., Frei, O., Shadrin, A., Smeland, O., Sundar, V., Andreassen, O. and Dale, A., (2020). Estimating Inflation In GWAS Summary Statistics Due To Variance Distortion From Cryptic Relatedness. BioRxiv 164939.
DOI: 10.1101/164939.

Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., Cho, J. H., Guttmacher, A. E., Kong, A., Kruglyak, L., Mardis, E., Rotimi, C. N., Slatkin, M., Valle, D., Whittemore, A. S., Boehnke, M., … Visscher, P. M. (2009). Finding the missing heritability of complex diseasesNature461(7265), 747–753.
DOI: 10.1038/nature08494.

Khera, A. V., Chaffin, M., Aragam, K. G., Haas, M. E., Roselli, C., Choi, S. H., Natarajan, P., Lander, E. S., Lubitz, S. A., Ellinor, P. T., & Kathiresan, S. (2018). Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutationsNature genetics50(9), 1219–1224.
DOI: 10.1038/s41588-018-0183-z.

McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, A. R., Teumer, A., Kang, H. M., Fuchsberger, C., Danecek, P., Sharp, K., Luo, Y., Sidore, C., Kwong, A., Timpson, N., Koskinen, S., Vrieze, S., Scott, L. J., Zhang, H., Mahajan, A., Veldink, J., … Haplotype Reference Consortium (2016). A reference panel of 64,976 haplotypes for genotype imputationNature genetics48(10), 1279–1283.
DOI: 10.1038/ng.3643.

Boyle, E. A., Li, Y. I., & Pritchard, J. K. (2017). An Expanded View of Complex Traits: From Polygenic to OmnigenicCell169(7), 1177–1186.
DOI: 10.1016/j.cell.2017.05.038.

ESHG scholarships

A limited number of European Society of Human Genetics (ESHG) scholarships are available for young scientists in training from European countries.

Preference will be given to ESHG members and researchers from ESHG-specified countries which are disadvantaged economically (see a full list of qualifying countries) although scholarships are not limited these groups. Scholarships will cover the full attendance fee only, beneficiaries would still need to pay for their own travel and subsistence needs.

There is no extra application for these scholarships, we will let successful applicants on the course know if they are receiving the funding.

Entry requirements

There are no prerequisites required to do this course.

Recognition of prior learning

Applicants should understand basic genetic principles such as modes of inheritance, DNA and gene structure, SNPs and other genetic variants, principles of crossing over and recombination, concepts of heritability and penetrance.

Additionally, knowledge of basic statistical tests and some command line scripting skills would be an advantage.

Fees and funding

Price per person:

£500

Fee for academics

£700

Fee for non-academics

Payment information will be provided to applicants after their registration has been verified.

How to apply

Applications are not currently open, but please register your interest and we will be in touch with further information when it is  confirmed.

Register your interest

Terms and conditions

Definitions

1.1         When the following words with capital letters are used in these terms, this is what they will mean:

Application

Your application for a place on the course as submitted online via k.rudomotkin@surrey.ac.uk.

Course

University of Surrey’s “Introduction to the statistical analysis of genome-wide association studies” short course in respect of which you have submitted an application.

Event outside our Control

Defined in Clause 8.

Confirmed Place

Your place on the course in respect of which you have received a confirmation of booking from us.

University of Surrey (or We, Us)

University of Surrey, Stag Hill, Guildford GU2 7XH, UK.

Place Offer

Our offer to you of a place on the course which will be confirmed only when you have accepted the place offer and paid the tuition fee within the deadlines we have given.

Terms

The terms and conditions set out in this document.

Tuition Fee

The tuition fee for the course only, payment of which will be one of the conditions for receiving a confirmed place.

1.2         When We use the words “writing” or “written” in these Terms, this will include email unless We say otherwise.

2. Our contract with you

2.1         These are the terms and conditions on which University of Surrey shall deliver the Course to you.

2.2         Please ensure that you read carefully these Terms, and check that the details on the Application are complete and accurate, before you submit the Application.

2.3         You acknowledge that you are also subject to University of Surrey’s Short Course Regulations. In the event of any conflict between University of Surrey’s Short Course Regulations and these Terms, University of Surrey’s Short Course Regulations shall prevail.

2.4         After submitting an Application, you will receive an email from Us acknowledging receipt of your Application and (either at the same time or separately) confirming whether you have a Place Offer or we have rejected your Application.

2.5         If We make you a Place Offer, it will include an invoice which you will have to pay within fourteen days of receiving the invoice (invoices are deemed to have been received by you on the next business day after sending); details of how to pay will be included in the invoice. If you receive the invoice within 14 days of the start of the course you should pay at the latest at the start of the course.

2.6         Receipt of a Place Offer does not in itself indicate the existence of a contract between you and University of Surrey.

2.7         The contract between you and University of Surrey shall only come into being when you have accepted the Place Offer and paid the relevant Fees within the deadlines set out in clause 2.5 above. If you do not, your Place Offer will lapse.

2.8         The contract will shall be deemed terminated at the end of the Course, unless your Confirmed Place is cancelled under Clauses 4 or 5 in which case the contract shall be deemed terminated at that point.

3. Fees and payment

3.1         All payments must be made in GB Pounds Sterling. Any currency conversion costs or other charges incurred in making the payment or in processing a refund shall be borne by you, and shall not be deductible from the Tuition Fee due to University of Surrey.

4. Your rights to cancel and applicable refund

4.1         Your right to cancel within fourteen days: You have the right to cancel your Confirmed Place for no reason within fourteen days of the day you received notification of a Confirmed Place, provided that We receive your cancellation before the start of the Course.

4.2         Your general right to cancel: You have the right to cancel your Confirmed Place at any time if We are affected by an Event Outside Our Control or if We change these Terms under Clause 9 to your material disadvantage.

4.3         Applicable Refund: Other than in cases where clauses 4.1 or 4.2 apply, you will not qualify for a refund of all or any part of the Tuition Fee or Accommodation Fee unless there is evidence of exceptional mitigating circumstances. Any refund will be at the sole discretion of University of Surrey.

4.4         To cancel your Confirmed Place please inform us in writing, by emailing the course administrator at k.rudomotkin@surrey.ac.uk.

5. Our rights to cancel and applicable refund

5.1         We reserve the right to cancel the Course (and therefore your Confirmed Place):

(a)          Due to an Event Outside Our Control; or

(b)          If the Course fails to meet the minimum recruitment level by four weeks preceding commencement of the Course. We will contact you promptly if this happens.

5.2         If We have to cancel a Course under Clause 5.1 and you have a Confirmed Course Place, We will refund the Tuition Fee to you. We will not accept liability for any costs or losses incurred by you which are claimed to have arisen through cancellation of the Course and you are strongly advised to take out insurance against cancellation of the Course if your travel costs are likely to be substantial.

5.3         Where We have already started a Course by the time We have to cancel under Clause 5.1(a), We will refund you a pro-rata amount of the Tuition Fee.

5.4         We may cancel this contract at any time with immediate effect by giving you written notice if you breach the contract in any material way and you do not correct or fix the situation within the deadline we give you for doing so.

6. Academic credit, attendance and conduct

 6.1        This course carries no academic credit and it is up to you to attend the course in order to receive its benefits.

6.2         On successful completion of the course, You will receive an attendance certificate provided you attend over 80% of the taught course.

6.3         You shall conduct yourself appropriately at all times during delivery of the Course, and in particular in accordance with University of Surrey’s Regulations. We reserve the right to exclude you from the Course or take such other action as We deem appropriate if you behave in what We deem to be an unacceptable manner. In such case you will not be entitled to a refund of all or any part of the Tuition Fee.

7. Liability and insurance

7.1         The liability of University of Surrey in connection with the Course, whether arising in contract, tort, negligence, breach of statutory duty or otherwise, will, in all circumstances, be limited to the amount of the Tuition Fee paid by you (except in cases of liability for death or personal injury caused by University of Surrey’s negligence, fraud or fraudulent misrepresentation and any other liability which, by law, cannot be limited).

7.2         University of Surrey shall not be in breach of this agreement nor liable in the event that it has to postpone or cancel the Course as a result of Events outside its Control.

7.3         University of Surrey does not provide insurance for its students. Consequently, University of Surrey recommends that you investigate personal insurance coverage, particularly in respect of your personal possessions and medical expenses. Find out how to access NHS services in England if you are visiting from abroad.

7.4         You will be responsible for any damage you cause (including but not limited to furniture, fixtures, fittings and equipment).

7.5         You will indemnify University of Surrey against all claims, losses, damages, actions, proceedings and costs in respect of accident, loss and damage, including personal injuries, however caused, in any part of the building in which the Course is taking place or on campus, and for any items you might bring into such building.

8. Events outside our control

8.1         We will not be liable or responsible for any failure to perform, or delay in performance of, any or any part, of Our obligations under these Terms that is caused by an Event Outside Our Control.

8.2         An Event Outside Our Control means any act or event beyond Our Reasonable control, including without limitation, strikes, riot, invasion, terrorist attack or threat or terrorist attack, war, fire, explosion, storm, flood, earthquake, subsidence, epidemic or other natural disaster, or failure of public or private telecommunication networks.

9. Changes to the terms

 9.1        We may revise these Terms, from time to time, where such variation is necessary in order to comply with relevant laws and regulatory requirements.

9.2         If we have to revise these Terms under Clause 9.1, We will give you at least one month’s written notice of any changes to these Terms before they take effect. You can choose to cancel your Place accordance with clause 4.2.

9.3         All reasonable efforts will be made to deliver the Course as outlined in the Course Specification and on the website, however University of Surrey reserves the right to make reasonable changes to content listed in respect of the Course, including but not limited to the course structure, content, academic or other staff delivering, organising or assessing the Course, and the keynote speakers.

10. Visual and/or audio recordings               

10.1       Unauthorised visual and/or audio recordings of lectures and other learning and teaching activities by students participating in the Course are prohibited and may be destroyed.

11. How we may use your personal information

11.1       We will use the personal information you provide to Us

(a)          For standard administrative processes. More information about these administrative purposes can be found on the student privacy notice.

(b)          To process your Tuition Fee payment; and

(c)           To inform you about similar products or services that We provide, but you may stop receiving these at any time by contacting Us.

11.2       Any processing of personal data by Us will be made in accordance with the principles laid down in the Data Protection Act 1998 and related legislation, and with Our Data Protection Policy. Sensitive personal data as defined under the Data Protection Act 1998 will only be processed by Us with your consent or if the processing is necessary under the Act. Read the University's Data Protection Policy (PDF).

11.3       Under the Data Protection Act 1998 you have a right to access a copy of the data held about you by Us by making a written application to The Data Protection Officer dataprotection@surrey.ac.uk. Find out more information about how to go about submitting such an application, via the University's Data Protection Policy (PDF) and related Codes of Practice and Guidance.

11.4       Our registration with the Information Commissioner's Office (our notification number is Z6346945) and we are committed to ensuring that the personal data we process is handled in accordance with data protection legislation.

12. Intellectual property

 12.1      All intellectual property rights in works or materials provided by University of Surrey to you as part of the Course (“the Materials”) shall remain the property of University of Surrey or its licensors as appropriate. You are only permitted to use such Materials for your own personal use and are not permitted to copy, circulate or make them available to anyone without our consent.

13. Governing law and dispute resolution

13.1       This agreement and any dispute or claim arising out of or in connection with it or its subject matter or formation (including non-contractual disputes or claims) shall be governed by and construed in accordance with the laws of England and Wales.

13.2       You and University of Surrey irrevocably agree, for the sole benefit of University of Surrey, that, subject as provided below, the courts of England and Wales shall have exclusive jurisdiction over any dispute or claim arising out of or in connection with this agreement or its subject matter or formation (including non-contractual disputes or claims). Nothing in this clause shall limit the right of University of Surrey to take proceedings against you in any other court of competent jurisdiction, nor shall the taking of proceedings in any one or more jurisdictions preclude the taking of proceedings in any other jurisdictions, whether concurrently or not, to the extent permitted by the law of such other jurisdiction.

14. Complaints

14.1       If you have any complaint, please contact Us. You can contact Us by telephoning or emailing the course administrator via k.rudomotkin@surrey.ac.uk.