Can Deep Learning Improve Genomic Prediction of Complex Human Traits?

Genetics
Pau BellotMiguel Pérez-Enciso

Abstract

The genetic analysis of complex traits does not escape the current excitement around artificial intelligence, including a renewed interest in "deep learning" (DL) techniques such as Multilayer Perceptrons (MLPs) and Convolutional Neural Networks (CNNs). However, the performance of DL for genomic prediction of complex human traits has not been comprehensively tested. To provide an evaluation of MLPs and CNNs, we used data from distantly related white Caucasian individuals (n ∼100k individuals, m ∼500k SNPs, and k = 1000) of the interim release of the UK Biobank. We analyzed a total of five phenotypes: height, bone heel mineral density, body mass index, systolic blood pressure, and waist-hip ratio, with genomic heritabilities ranging from ∼0.20 to 0.70. After hyperparameter optimization using a genetic algorithm, we considered several configurations, from shallow to deep learners, and compared the predictive performance of MLPs and CNNs with that of Bayesian linear regressions across sets of SNPs (from 10k to 50k) that were preselected using single-marker regression analyses. For height, a highly heritable phenotype, all methods performed similarly, although CNNs were slightly but consistently worse. For the rest of the phenotype...Continue Reading

References

Apr 6, 2001·Genetics·T H MeuwissenM E Goddard
Aug 14, 2003·The Journal of Clinical Endocrinology and Metabolism·Tuan V NguyenJohn A Eisman
Oct 24, 2008·Journal of Dairy Science·P M VanRaden
Jun 22, 2010·Nature Genetics·Jian YangPeter M Visscher
Sep 8, 2010·American Journal of Human Genetics·Xiang WanWeichuan Yu
Nov 4, 2010·Nature Reviews. Genetics·Gustavo de los CamposDavid B Allison
Mar 8, 2011·American Journal of Human Genetics·Sang Hong LeePeter M Visscher
Mar 25, 2011·Genetics Research·Peter M VisscherJian Yang
May 9, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·J M González-CamachoJ Crossa
Jun 30, 2012·Genetics·Gustavo de Los CamposMario P L Calus
Jan 1, 2013·G3 : Genes - Genomes - Genetics·Paulino Pérez-RodríguezSusanne Dreisigacker
Jul 11, 2014·Genetics·Paulino Pérez, Gustavo de los Campos
Jan 1, 2013·Annual Review of Animal Biosciences·Theo MeuwissenMike Goddard
Feb 28, 2015·GigaScience·Christopher C ChangJames J Lee
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jul 28, 2015·Nature Biotechnology·Babak AlipanahiBrendan J Frey
Aug 25, 2015·Nature Methods·Jian Zhou, Olga G Troyanskaya
Mar 10, 2016·BMC Genomics·Juan Manuel González-CamachoDaniel Gianola
Aug 27, 2017·Genetics, Selection, Evolution : GSE·Natalia S FornerisMiguel Pérez-Enciso
Sep 13, 2017·Genetics·Hwasoon KimGustavo de Los Campos

❮ Previous
Next ❯

Citations

Dec 6, 2018·Molecular Biology and Evolution·Lex FlagelDaniel R Schrider
May 3, 2019·Human Genetics·Anne-Laure BoulesteixInke R König
Jul 25, 2019·Genes·Miguel Pérez-Enciso, Laura M Zingaretti
Sep 20, 2019·G3 : Genes - Genomes - Genetics·Christina B AzodiShin-Han Shiu
Nov 24, 2019·BMC Bioinformatics·Luis ToradaMatteo Fumagalli
Nov 14, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Qin WangXuehui Huang
Jun 1, 2020·Journal of Animal Science·Anderson Antonio Carvalho AlvesLucia Galvão de Albuquerque
Aug 20, 2020·Archives of Virology·Alexandr A Ezhov
Jun 6, 2020·Frontiers in Genetics·Roni Wilentzik Müller, Irit Gat-Viks
Mar 3, 2020·Frontiers in Genetics·Patrik WaldmannGábor Mészáros
Apr 26, 2020·Journal of Dairy Science·P M VanRaden
Mar 3, 2020·Frontiers in Plant Science·Laura M ZingarettiMiguel Pérez-Enciso
Feb 26, 2020·Genetics, Selection, Evolution : GSE·Rostam Abdollahi-ArpanahiFrancisco Peñagaricano
Oct 4, 2020·Journal of Human Genetics·Adrien BadréChongle Pan
Dec 2, 2020·Journal of Personalized Medicine·Christina VasilopoulouWilliam Duddy
Dec 8, 2020·Frontiers in Genetics·Torsten PookHenner Simianer
Dec 4, 2019·G3 : Genes - Genomes - Genetics·Sai Krishna ArojjuMarty J Faville
Jan 21, 2021·Frontiers in Plant Science·Karansher S SandhuArron H Carter
Jan 8, 2021·BMC Genomics·Osval Antonio Montesinos-LópezJosé Crossa
Jun 27, 2019·Trends in Biotechnology·Antoine L HarfoucheArie Altman
Apr 13, 2021·The Journal of Thoracic and Cardiovascular Surgery·Michael Domaratzki, Biniam Kidane
May 18, 2021·Frontiers in Plant Science·Rosangela M SimeãoJuarez C Machado
Jul 15, 2021·International Journal of Legal Medicine·Magdalena Kukla-BartoszekWojciech Branicki
Jul 5, 2021·Biological Chemistry·Nikoletta KatsaouniMarcel H Schulz
Jul 11, 2021·Trends in Genetics : TIG·Ying Ma, Xiang Zhou
Dec 10, 2021·Frontiers in Plant Science·Cathy C WesthuesTimothy M Beissinger

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Ali MohebbiMorten Morup
Archives of Internal Medicine
Arthur J Hartz, Alfred A Rimm
© 2022 Meta ULC. All rights reserved