• Advanced Courses in Life Sciences

    Header of Genetics and Genomics at Transmitting Science

Online Course – 1st Edition

Introduction to Palaeogenomics – concepts, methods and applications of ancient human and non-human DNA data

May 17th-21st, 2021

Genetics and Genomics

Genetics and Genomics

This course will be delivered live online

25 hours of online live lessons

Course Introduction to Palaeogenomics – concepts, methods and applications of ancient human and non-human DNA data

Course Overview

Ancient DNA (aDNA) research, defined as the retrieval and analysis of DNA sequences from various degraded biological materials, has been evolving as a research field for four decades. Through advances in DNA isolation and amplification techniques, sequencing technologies and data analysis pipelines, the field has revolutionized and transitioned to what we now know as palaeogenomics. DNA extracted from archaeological samples, and museum specimens has proven useful to study species and life on earth from the genomic perspective. It has made it possible to measure changes in genetic diversity through time, test hypotheses about the association of environmental phenomena and genetic changes in natural populations, and to resolve long-standing questions about the evolutionary relationships between species.

In a combination of interactive lectures and hands-on practical sessions, this course will provide a theoretical overview of molecular biology laboratory techniques for the retrieval of aDNA from ancient samples from different species and an introduction to the bioinformatic pipelines for the analysis of palaeogenomic data. Students will be introduced to the standard bioinformatic methods often used in palaeogenomic projects for the analysis of aDNA data from human and non-human samples. We will also review the history and developments of the field to understand how it came to be what it is today, and consider and discuss the practical problems of ancient DNA recovery, the theoretical problems associated with the interpretation of palaeogenomic data, and the ethical implications embedded in this type of research.

At the end of the course, students will have gained a general understanding of common key methods and tools used in palaeogenomics projects: from the basics in the field to the interpretation of the results, as well as ethical and responsibility aspects and implications of aDNA research.

Requirements

Graduate or postgraduate degree in Life sciences discipline. Basic knowledge and experience on linux command line and bash scripting.

All participants must have a personal laptop and access to a stable internet connection.

Contact

haris.saslis@transmittingscience.com

Dates

May 17th-21st, 2021

Schedule and Course length

Online live sessions from Monday 17th to Friday 21st of May from 16:00 to 21:00 (GMT+2, Madrid time zone).

25 hours live online.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

Language

English

Places

Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Marcela Sandoval Velasco instructor for Transmitting Science

Dr. Marcela Sandoval Velsaco
University of Copenhagen
Denmark

Jazmín Ramos-Madrigal instructor for Transmitting Science

Dr. Jazmín Ramos-Madrigal
University of Copenhagen
Denmark

Program

  1. Introduction to ancient DNA and palaeogenomics – History and development of the field. Contamination and degradation of DNA. Best practices and sampling strategies. Ethical implications of aDNA research
  2. Laboratory methods – DNA extraction. Library preparation methods (ds, ss, BEST, BEMT, SC). Sequencing strategies. Best practices.
  3. Data preprocessing, particularities of ancient DNA data and basic data quality statistics.
  4. Standard and alternative mapping strategies. Overview of palaeogenomics analysis pipelines (e.g. paleomix and eager). Selection of reference genome. Reference bias and strategies to overcome it.
  5. aDNA authentication. Damage, error rates and contamination analysis.
  6. Analysis of low coverage data using Angsd (potential strategies using genotype likelihoods and pseudo-haploid data)
  7. Broad ancestry estimation using NGS tools. Clustering strategies (PCA, Admixture). Phylogenomics (Treemix)
  8. Introduction to F-statistics (D-statistics, F3) and Admixture graphs.

Fees

  • Course Fee
  • Early bird (until April 30th, 2021):
  • 485 € *

    (388 € for Ambassador Institutions)

  • Regular (after April 30th, 2021):
  • 585 € *

    (468 € for Ambassador Institutions)

  • Prices are VAT included.
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com

Funding

Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Registration

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