Open AccessA Chromosome-Painting-Based Pipeline to Infer Local Ancestry under Limited Source Availability
Author(s) -
Ludovica Molinaro,
Davide Marnetto,
Mayukh Mondal,
Linda Ongaro,
Burak Yelmen,
Daniel J. Lawson,
Francesco Montinaro,
Luca Pagani
Publication year - 2021
Publication title -
genome biology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.702
H-Index - 74
ISSN - 1759-6653
DOI - 10.1093/gbe/evab025
Subject(s) - biology , evolutionary biology , genetic genealogy , population , pipeline (software) , 1000 genomes project , genome , genetic admixture , computational biology , genetics , computer science , gene , demography , genotype , sociology , single nucleotide polymorphism , programming language
Contemporary individuals are the combination of genetic fragments inherited from ancestors belonging to multiple populations, as the result of migration and admixture. Isolating and characterizing these layers are crucial to the understanding of the genetic history of a given population. Ancestry deconvolution approaches make use of a large amount of source individuals, therefore constraining the performance of Local Ancestry Inferences when only few genomes are available from a given population. Here we present WINC, a local ancestry framework derived from the combination of ChromoPainter and NNLS approaches, as a method to retrieve local genetic assignments when only a few reference individuals are available. The framework is aided by a score assignment based on source differentiation to maximize the amount of sequences retrieved and is capable of retrieving accurate ancestry assignments when only two individuals for source populations are used.