Lai-Net: Local-Ancestry Inference with Neural Networks
Daniel Mas Montserrat,Carlos Bustamante,Alexander G. Ioannidis +2 more
- pp 1314-1318
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TLDR
The first neural network based LAI method, named LAI-Net, is developed, providing competitive accuracy with state-of-the-art methods and robustness to missing or noisy data, while having a small number of layers.Abstract:
Local-ancestry inference (LAI), also referred to as ancestry deconvolution, provides high-resolution ancestry estimation along the human genome. In both research and industry, LAI is emerging as a critical step in DNA sequence analysis with applications extending from polygenic risk scores (used to predict traits in embryos and disease risk in adults) to genome-wide association studies, and from pharmacogenomics to inference of human population history. While many LAI methods have been developed, advances in computing hardware (GPUs) combined with machine learning techniques, such as neural networks, are enabling the development of new methods that are fast, robust and easily shared and stored. In this paper we develop the first neural network based LAI method, named LAI-Net, providing competitive accuracy with state-of-the-art methods and robustness to missing or noisy data, while having a small number of layers.read more
Citations
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Iconographies supplémentaires de l'article : Case-control admixture mapping in Latino populations enriches for known asthma-associated genes
Dara G. Torgerson,Christopher R. Gignoux,Joshua Galanter,Katherine A. Drake,Lindsey A. Roth,Celeste Eng,Scott Huntsman,Raul Torres,Pedro C Avila,Rocio Chapela,Jean G. Ford,J.R. Rodriguez-Santana,William Rodríguez-Cintrón,Ryan D. Hernandez,E.G. Burchard +14 more
TL;DR: Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility.
Posted ContentDOI
Neural ADMIXTURE: rapid population clustering with autoencoders
Mantes Ad,Mantes Ad,Daniel Mas Montserrat,Carlos Bustamante,Xavier Giro-i-Nieto,Alexander G. Ioannidis +5 more
TL;DR: Neural ADMIXTURE as mentioned in this paper is a neural network autoencoder that follows the same modeling assumptions as ADMIXURE, providing similar (or better) clustering, while reducing the compute time by orders of magnitude.
Posted ContentDOI
XGMix: Local-Ancestry Inference With Stacked XGBoost
TL;DR: This work presents a method (XGMix) based on gradient boosted trees, which, while being accurate, is also simple to use, and fast to train, taking minutes on consumer-level laptops.
Posted ContentDOI
High Resolution Ancestry Deconvolution for Next Generation Genomic Data
Helgi Hilmarsson,Arvind Kumar,Richa Rastogi,Carlos Bustamante,Daniel Mas Montserrat,Alexander G. Ioannidis +5 more
TL;DR: In this paper, a set of algorithms that address each of these points, achieving higher accuracy and swifter computational performance than any existing LAI method, while also enabling portable models that are particularly useful when training data are not shareable due to privacy or other restrictions.
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TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
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Worldwide human relationships inferred from genome-wide patterns of variation.
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