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Ancestry specific association mapping in admixed populations [article]

Line Skotte, Emil Joersboe, Thorfinn Sand S Korneliussen, Ida Moltke, Anders Albrechtsen
2015 bioRxiv   pre-print
These results are all in line with the conclusions about causality drawn in Moltke et al. (2014) .  ...  A recent GWAS in the Greenlandic population (Moltke et al. 2014) led to the identification of a variant in the gene TDB1D4 which confers type 2 diabetes.  ... 
doi:10.1101/014001 fatcat:w4prwt6cwjbjdeewd7it6ltm5u

Archaic adaptive introgression in TBX15/WARS2 [article]

Fernando Racimo, David Gokhman, Matteo Fumagalli, Amy Ko, Torben Hansen, Ida Moltke, Anders Albrechtsen, Liran Carmel, Emilia Huerta-Sanchez, Rasmus Nielsen
2015 bioRxiv   pre-print
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using SNP chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue
more » ... erentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
doi:10.1101/033928 fatcat:gkt2r7qmfngl5gq5d67zbm4nxu

NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

Thorfinn Sand Korneliussen, Ida Moltke
2015 Bioinformatics  
Motivation: Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty. Results: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype
more » ... ihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods.
doi:10.1093/bioinformatics/btv509 pmid:26323718 pmcid:PMC4673978 fatcat:bu6ombrxczgjrlu4sg273tigmm

Diabetes in Population Isolates: Lessons from Greenland

Niels Grarup, Ida Moltke, Anders Albrechtsen, Torben Hansen
2015 The Review of Diabetic Studies  
Type 2 diabetes (T2D) is an increasing health problem worldwide with particularly high occurrence in specific subpopulations and ancestry groups. The high prevalence of T2D is caused both by changes in lifestyle and genetic predisposition. A large number of studies have sought to identify the genetic determinants of T2D in large, open populations such as Europeans and Asians. However, studies of T2D in population isolates are gaining attention as they provide several advantages over open
more » ... ions in genetic disease studies, including increased linkage disequilibrium, homogeneous environmental exposure, and increased allele frequency. We recently performed a study in the small, historically isolated Greenlandic population, in which the prevalence of T2D has increased to more than 10%. In this study, we identified a common nonsense variant in TBC1D4, which has a population-wide impact on glucose-stimulated plasma glucose, serum insulin levels, and T2D. The variant defines a specific subtype of non-autoimmune diabetes characterized by decreased post-prandial glucose uptake and muscular insulin resistance. These and other recent findings in population isolates illustrate the value of performing medical genetic studies in genetically isolated populations. In this review, we describe some of the advantages of performing genetic studies of T2D and related cardio-metabolic traits in a population isolate like the Greenlandic, and we discuss potentials and perspectives for future research into T2D in this population.
doi:10.1900/rds.2015.12.320 pmid:27111118 pmcid:PMC5275757 fatcat:lsc24a6cjbc33otn6nu37lwcoa

Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data [article]

Ryan K Waples, Anders Albrechtsen, Ida Moltke
2018 bioRxiv   pre-print
Knowledge of how individuals are related is important in many areas of research and numerous methods for inferring pairwise relatedness from genetic data have been developed. However, the majority of these methods were not developed for situations where data is limited. Specifically, most methods rely on the availability of population allele frequencies, the relative genomic position of variants, and accurate genotype data. But in studies of non-model organisms or ancient human samples, such
more » ... a is not always available. Motivated by this, we present a new method for pairwise relatedness inference, which requires neither allele frequency information nor information on genomic position. Furthermore, it can be applied not only to accurate genotype data but also to low-depth sequencing data from which genotypes cannot be accurately called. We evaluate it using data from a range of human populations and show that it can be used to infer close familial relationships with a similar accuracy as a widely used method that relies on population allele frequencies. Additionally, we show that our method is robust to SNP ascertainment and applicable to low-depth sequencing data generated using different strategies, including resequencing and RADseq, which is important for application to a diverse range of populations and species.
doi:10.1101/260497 fatcat:ozamjgtwj5bmbjqam56ygheb3a

Natural Selection and the Distribution of Identity-by-Descent in the Human Genome

Anders Albrechtsen, Ida Moltke, Rasmus Nielsen
2010 Genetics  
Moltke and Rasmus Nielsen Copyright Ó 2010 by the Genetics Society of America DOI: 10.1534/genetics.110.113977 GENETICS TABLE S1 Table of S1of the HapMap phase 3 TABLE S2 Table of S2of the IBD  ...  LITERATURE CITED Supporting Information http://www.genetics.org/cgi/content/full/genetics.110.113977/DC1 Natural Selection and the Distribution of Identity-by-Descent in the Human Genome Anders Albrechtsen, Ida  ... 
doi:10.1534/genetics.110.113977 pmid:20592267 pmcid:PMC2940294 fatcat:uxrfwt2qvzfirp3xmnnobvsbvu

A Probabilistic Model of RNA Conformational Space

Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck, Paul Gardner
2009 PLoS Computational Biology  
The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling procedure. Both are only partly solved problems. Here, we focus on the problem of conformational sampling. The current state of the art solution is based on fragment assembly methods, which construct
more » ... lausible conformations by stringing together short fragments obtained from experimental structures. However, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.
doi:10.1371/journal.pcbi.1000406 pmid:19543381 pmcid:PMC2691987 fatcat:fex7t7phwjfirmtf3eoxkxjmvi

NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data [article]

Anne Krogh Nøhr, Kristian Hanghøj, Genis Garcia Erill, Ida Moltke, Anders Albrechtsen
2020 bioRxiv   pre-print
Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here we present a software tool, NGSremix, for maximum likelihood estimation of
more » ... between pairs of admixed individuals from low depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix .
doi:10.1101/2020.10.20.347500 fatcat:usn3smpnjze2fogaimf2qox67i

Archaic adaptive introgression in TBX15/WARS2

Fernando Racimo, David Gokhman, Matteo Fumagalli, Amy Ko, Torben Hansen, Ida Moltke, Anders Albrechtsen, Liran Carmel, Emilia Huerta-Sánchez, Rasmus Nielsen
2016 Molecular biology and evolution  
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been
more » ... ed with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
doi:10.1093/molbev/msw283 pmid:28007980 pmcid:PMC5430617 fatcat:k7kksuzninbrbi5ie4rg2ik7aq

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

Kristian Hanghøj, Ida Moltke, Philip Alstrup Andersen, Andrea Manica, Thorfinn Sand Korneliussen
2019 GigaScience  
In the absence of inbreeding our model reduces to the work in Korneliussen and Moltke [11] .  ...  This approach is similar to the previous approach in Korneliussen and Moltke [11] , which J 1 J 2 J 3 J 4 J 5 J 6 J 7 J 8 J 9 A i A i A i A i p i p 2 i p 2 i p 3 i p 2 i p 3 i p 2 i p 3 i p 4 i A i  ...  The optimization follows the approach described in Korneliussen and Moltke [11] .  ... 
doi:10.1093/gigascience/giz034 pmid:31042285 pmcid:PMC6488770 fatcat:odw6hrzswfdlxoc7sumqkanwoy

Allele frequency-free inference of close familial relationships from genotypes or low-depth sequencing data

Ryan K. Waples, Anders Albrechtsen, Ida Moltke
2019 Molecular Ecology  
Waples https://orcid.org/0000-0003-0526-6425 O RCI D Anders Albrechtsen https://orcid.org/0000-0001-7306-031X Ida Moltke https://orcid.org/0000-0001-7052-8554  ...  methods have been developed, for example, Thompson (1975) , Lee (2003 ), Purcell et al. (2007 , Albrechtsen et al. (2009) , Manichaikul et al. (2010) , Stevens et al. (2011) , Korneliussen and Moltke  ... 
doi:10.1111/mec.14954 pmid:30462358 fatcat:mmiorgeutfdk5etjrarukvoz3q

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

Troels T. Marstrand, Jes Frellsen, Ida Moltke, Martin Thiim, Eivind Valen, Dorota Retelska, Anders Krogh, Richard Copley
2008 PLoS ONE  
Citation: Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, et al (2008) Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites. PLoS ONE 3(2): e1623.  ... 
doi:10.1371/journal.pone.0001623 pmid:18286180 pmcid:PMC2229843 fatcat:7ux6pnbg6nfrvlsisjwuzh2l6q

Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull)

Ida Moltke, Thorfinn Sand Korneliussen, Andaine Seguin-Orlando, J. Víctor Moreno-Mayar, Ernie LaPointe, William Billeck, Eske Willerslev
2021 Science Advances  
[Figure: see text].
doi:10.1126/sciadv.abh2013 pmid:34705496 pmcid:PMC8550246 fatcat:uteo3am3tfdc5hxwzj46lpvn34

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data

Thorfinn Sand Korneliussen, Ida Moltke, Anders Albrechtsen, Rasmus Nielsen
2013 BMC Bioinformatics  
A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima's D. These statistics are now often being applied in the analysis of Next Generation Sequencing (NGS) data. However, estimates of frequency spectra from NGS data are strongly affected by low sequencing coverage; the inherent technology dependent variation in sequencing depth causes systematic differences in the
more » ... e of the statistic among genomic regions. Results: We have developed an approach that accommodates the uncertainty of the data when calculating site frequency based neutrality test statistics. A salient feature of this approach is that it implicitly solves the problems of varying sequencing depth, missing data and avoids the need to infer variable sites for the analysis and thereby avoids ascertainment problems introduced by a SNP discovery process. Conclusion: Using an empirical Bayes approach for fast computations, we show that this method produces results for low-coverage NGS data comparable to those achieved when the genotypes are known without uncertainty. We also validate the method in an analysis of data from the 1000 genomes project. The method is implemented in a fast framework which enables researchers to perform these neutrality tests on a genome-wide scale.
doi:10.1186/1471-2105-14-289 pmid:24088262 pmcid:PMC4015034 fatcat:oo6nkdzrjfb27dkklewntkivne

New evidence for hybrid zones of forest and savanna elephants in Central and West Africa

Samrat Mondol, Ida Moltke, John Hart, Michael Keigwin, Lisa Brown, Matthew Stephens, Samuel K. Wasser
2015 Molecular Ecology  
The African elephant consists of forest and savanna subspecies. Both subspecies are highly endangered due to severe poaching and habitat loss, and knowledge of their population structure is vital to their conservation. Previous studies have demonstrated marked genetic and morphological differences between forest and savanna elephants, and despite extensive sampling, genetic evidence of hybridization between them has been restricted largely to a few hybrids in the Garamba region of northeastern
more » ... emocratic Republic of Congo (DRC). Here, we present new genetic data on hybridization from previously unsampled areas of Africa. Novel statistical methods applied to these data identify 46 hybrid samplesmany more than have been previously identifiedonly two of which are from the Garamba region. The remaining 44 are from three other geographically distinct locations: a major hybrid zone along the border of the DRC and Uganda, a second potential hybrid zone in Central African Republic and a smaller fraction of hybrids in the Pendjari-Arli complex of West Africa. Most of the hybrids show evidence of interbreeding over more than one generation, demonstrating that hybrids are fertile. Mitochondrial and Y chromosome data demonstrate that the hybridization is bidirectional, involving males and females from both subspecies. We hypothesize that the hybrid zones may have been facilitated by poaching and habitat modification. The localized geography and rarity of hybrid zones, their possible facilitation from human pressures, and the high divergence and genetic distinctness of forest and savanna elephants throughout their ranges, are consistent with calls for separate species classification.
doi:10.1111/mec.13472 pmid:26577954 fatcat:56okndv7rfchzkefde7pttb3ya
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