Methods for analyzing genetic variation in modern and archaic

179 Pages·2017·25.12 MB·English

by  Laurits Skov

Methods for analyzing genetic variation in modern and archaic
humans
Laurits Skov
PhD Dissertation

Bioinformatics Research Center
Department of Computer Science
Aarhus University
Denmark
Methods for analyzing genetic variation in modern and archaic
humans

PhD Dissertation
Presented to the Faculty of Science and Technology
of Aarhus University
in Partial Fulfillment of the Requirements
for the PhD Degree

by
Laurits Skov
June 31, 2017

i
Preface
In this thesis, I will present work done at Aarhus University under the supervision of Prof. Mikkel Heide
Schierup and at the Welcome Trust Sanger Institute under the supervision of Dr. Ricard Durbin.
With a background in Nano-science, I did not know much about bioinformatics when I first started. I knew I
liked biological questions and programming, but that was it. I quickly developed an interest for working
with human data.
The first project that I was fortunately enough to be involved in was the Danish Pan Genome project. In this
project 150 genomes of Danish descent were de novo assembled and I got to work on the analysis of the Y
chromosome. Not knowing anything about the Y chromosome or de novo assemblies, this was a great
learning experience from me and my programming and analytical skills improved a lot. I investigated
evolutionary processes on the Y chromosome and found novel structural variants, which had never been
found before.
For my six months exchange I went to the Sanger Institute in Cambridge where Richard Durbin introduced
me to the field of ancient hominins. Having spent the first few months reading up on all the literature in the
field, I developed a method for identifying introgressed segments.
After I returned to Aarhus University, I was asked, if I wanted to do structural analysis on a newly
sequenced Neandertal. One of the things they were interested in was to see if we could get a better
catalogue of structural variants found in archaic humans. Having a good understanding of the field and
knowing how to genotype structural variants I joined the project and through it I learned a lot from the
people I worked with.
I have learned a lot during these past four years and I am looking much forward to learning more in the
years to come.

ii
Acknowledgements
During my studies, I have been into many different offices, asking many different questions from many
different people. I would like to thank all of them for taking their time to answer.
First, I would like to thank my main supervisor Mikkel Heide Schierup for all his help and valuable feedback.
He has always had the time to look at my figures, help me structure my research papers, discus my results
and sending me on missions to collect various great ape testicles. He has always been good at driving me
forward, motivating me and finding new ways to look at the data.
Second, I would also like to thank everyone I was involved with at the Sanger institute. Both people from
Richard Durbin’s group and Chris Tyler-Smiths’ group, including the two Gentlemen themselves.
Last, but not least, I would like to thank everyone at BiRC. A large reason why I have enjoyed my PhD
studies so much was because of the great workplace atmosphere at BiRC. From the Mols meetings,
Christmas dinners, Wednesday morning breakfast (I have actually been to some of them), annual BiRC
walks, everyday conversations over lunch and the occasional Friday bar. A special shout out to Jacob Malte
Jensen. It has been a pleasure attending workshops, conferences, missing breakfast at Mols and talking
about science with you.
iii
English résumé
Our knowledge of modern and archaic human genomes has increased dramatically over the last decade.
However, there are still many questions unanswered.
Traditional methods for calling structural variants in highly repetitive regions such as the Y chromosome
and using DNA reads from ancient DNA is pushing their limitations. Therefore, novel methods needs to be
developed.
We show that using a mix of traditional Next generation sequencing methods, de novo assemblies and k-
mer based variant genotyping that we are able to detect structural variation on the Y chromosome that was
previously undetectable, even in repetitive regions.
We also show that using this k-mer based genotyping we are able to detect around 200,000 structural
variants found in Neandertal that are also present in modern humans. 4,537 of these variants have a
putative effect and further investigation will likely reveal what functional impact they had in Neandertals
and in modern humans.
Finally, we developed a novel method for detecting archaic introgressing segments in modern humans. We
do this without relying on the Neandertal or Denisova reference genome and show that our novel approach
correctly identifies a large proportion of archaic segments.
iv
Dansk resumé
Vores viden vedrørende moderne og arkaiske mennesker er blevet forbedret utrolig meget over de sidste
årti. Men der er stadig mange ubesvarede spørgsmål.
Traditionelle metoder til at undersøge strukturel variation i komplekse regioner såsom Y kromosomet eller
ved at benytte gammelt DNA er ved at nå deres grænser. Derfor er det nødvendigt at udvikle nye metoder.
Vi viser at ved at bruge en kombination af traditionelle Next generation sequencing metoder, de novo
assemblies og k-mer baseret variant genotyping at vi er i stand til at detektere variation på y kromosomet
der tidligere ikke kunne findes, endda i komplekse regioner.
Vi viser at denne k-mer baseret måde at genotype på, er i stand til at finde omkring 200.000 strukturelle
varianter i Neandertalere som også findes i moderne mennesker. 4.537 af disse varianter formodes at have
en effekt og i fremtiden vil de sandsynligvis kunne hjælpe med at finde ud af hvilken funktion de har i
moderne og arkaiske mennesker.
Til slut, har vi udviklet in metode til at detektere områder i genomet der kommer fra Neandertalere. Vi
finder disse regioner uden at bruge reference Neandertal genomet eller reference Denisova genomet. Vi
viser at vores nye metode er i stand til at finde en stor andel af de arkaiske segmenter.

v
Outline
Reading guide
I divided this thesis into three three sections, each representing work I have done or am currently doing.
This is followed by four papers. In Each section I provide a bit of background for the project and give a short
description of the methods used in the field by other research groups. Then I discuss the questions we
wanted to answer in this project, my contribution to it the methods we developed to answer these
questions and the results we got. Each section ends with a discussion on what questions in this field I think
would find interesting to answer in the future.
Y chromosome
This section describes the background and work I did for the Danish Pan Genome project and for its
companion paper on the Y chromosome.
Identifying archaic introgression in modern humans
This section outlines the work that I started working on at the Sanger Institute and that I continued on at
BiRC.
Structural Variant calling in archaic populations
This section describes the work I did on calling structural variants in the newly sequenced Vindija genome.

After the method sections, I have attached four manuscripts. The first two, are the main paper from the
Danish pan genome project and my companion paper on the Y chromosome. The third is a paper still in
preparation. This is not the manuscript but rather a detailed list of all my results so far. The last paper is the
method section for the structural variant calling in the Vindija project. I do not have permission to attach
the main paper as it is currently under review.

vi
List of publications
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates
of gene conversion. Laurits Skov, The Danish Pan Genome Consortium, Mikkel Heide Schierup. Accepted for
publication in PLOSgenetics 2017.
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Lasse
Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits
Skov, Kirstine Belling, Christian Theil Have, Jose M. G. Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob
Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen Guo, Jihua Sun,
Hongzhi Cao, Chen Ye, Johan van Beusekom, Thomas Espeseth, Esben Flindt, Rune M. Friborg, Anders E.
Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter
Løngren, Thomas Mailund, Maria Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas
Sicheritz-Pontén, Patrick Sullivan, Ali Syed, DavidWestergaard, Rachita Yadav, Ning Li, Xun Xu, Torben
Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon
Rasmussen, Søren Besenbacher, Anders D. Børglum, JunWang, Hans Eiberg, Karsten Kristiansen, Søren
Brunak & Mikkel Heide Schierup. Accepted for publication in Nature. Schedule for publication the 3rd of
August 2017.
Identifying introgressed segment without using archaic reference genome. Laurits Skov, Richard Durbin. In
preparation.
A high-coverage Neandertal genome from Vindija Cave in Croatia. Kay Prüfer, Cesare de Filippo, Steffi
Grote, Fabrizio Mafessoni, Petra Korlević, Mateja Hajdinjak, Benjamin Vernot, Laurits Skov, Pinghsun Hsieh,
Stéphane Peyrégne, David Reher, Charlotte Hopfe, Sarah Nagel, Qiaomei Fu, Udo Stenzel, Christoph
Theunert, Rebekah Rogers, Pontus Skoglund, Manjusha Chintalapati, Michael Dannemann, Brad Nelson,
Felix M. Key, Pavao Rudan, Željko Kucan, Ivan Gušic, Liubov V. Golovanova, Vladimir B. Doronichev, Nick
Patterson, David Reich,Evan E. Eichler, Montgomery Slatkin, Mikkel H. Schierup, Aida Andrés, Janet Kelso,
Matthias Meyer, Svante Pääbo. Submitted to science 2017
vii
Contents
Preface…………………………………………………………………………………………………………………………………………………………………………ii
Acknowledgements……………………………………………………………………………………………………………………………………………………. iii
English Résumé……………………………………………..……………………………………………….………………………….…………………………….….iv
Dansk resumé……….…………………………………………………………………………………………………………………….…………………………….….v
Reading guide……….………………………………………………………………………………………………………………….…………………………….…...vi
List of publications……….………………………………………………………………………………………………………….…………………………….…...vii

1. Y chromosome ................................................................................................................................................................ 3
1. 1. Introduction ............................................................................................................................................................ 3
1. 2. What is known about the Y chromosome .............................................................................................................. 3
1.2.1. Structural variation .......................................................................................................................................... 4
1.2.2. Studying palindromes ...................................................................................................................................... 4
1.3. My contribution ....................................................................................................................................................... 5
1.3.1. Aim of study ..................................................................................................................................................... 5
1.3.2. My contribution ............................................................................................................................................... 5
1.3.3 Methods ............................................................................................................................................................ 5
1.4. Results ..................................................................................................................................................................... 7
1.5. Discussion and future studies .................................................................................................................................. 8
2. Identifying archaic introgression in modern humans ..................................................................................................... 9
2.1. Introduction ............................................................................................................................................................. 9
2.2. Evidence for archaic introgression ........................................................................................................................ 10
2.2.1 LD based methods S-star evolution ................................................................................................................ 11
2.2.2. HMM and conditional random field methods ............................................................................................... 14
2.3. My contribution ..................................................................................................................................................... 16
2.3.1. Aim of study ................................................................................................................................................... 16
2.3.2. My contribution ............................................................................................................................................. 16
2.3.3 Methods .......................................................................................................................................................... 16
2.4. Results ................................................................................................................................................................... 18
2.5. Discussion and future studies ................................................................................................................................ 19
3. Structural Variant calling in archaic populations .......................................................................................................... 20
3.1. Introduction ........................................................................................................................................................... 20
3.2. Calling indels in archaic hominins.......................................................................................................................... 21
3.3. My contribution ..................................................................................................................................................... 21
3.3.1. Aim of study ................................................................................................................................................... 21
1
3.3.2. My contribution ............................................................................................................................................. 22
3.3.3. Methods ......................................................................................................................................................... 22
3.4. Results ................................................................................................................................................................... 24
3.5. Discussion and future studies ................................................................................................................................ 26
References ........................................................................................................................................................................ 27

Manuscript I
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene
conversion.
Manuscript II
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference.
Manusctip III
Identifying introgressed segment without using archaic reference genome.
Manuscript IV
A high-coverage Neandertal genome from Vindija Cave in Croatia.

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