SparSNP: fast and memory-efficient analysis of all SNPs for phenotype prediction.

BMC Bioinformatics
Gad AbrahamMichael Inouye

Abstract

A central goal of genomics is to predict phenotypic variation from genetic variation. Fitting predictive models to genome-wide and whole genome single nucleotide polymorphism (SNP) profiles allows us to estimate the predictive power of the SNPs and potentially develop diagnostic models for disease. However, many current datasets cannot be analysed with standard tools due to their large size. We introduce SparSNP, a tool for fitting lasso linear models for massive SNP datasets quickly and with very low memory requirements. In analysis on a large celiac disease case/control dataset, we show that SparSNP runs substantially faster than four other state-of-the-art tools for fitting large scale penalised models. SparSNP was one of only two tools that could successfully fit models to the entire celiac disease dataset, and it did so with superior performance. Compared with the other tools, the models generated by SparSNP had better than or equal to predictive performance in cross-validation. Genomic datasets are rapidly increasing in size, rendering existing approaches to model fitting impractical due to their prohibitive time or memory requirements. This study shows that SparSNP is an essential addition to the genomic analysis toolkit...Continue Reading

References

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Citations

Jul 27, 2015·Current Opinion in Genetics & Development·Gad Abraham, Michael Inouye
Mar 8, 2016·Genetic Epidemiology·Masao UekiUNKNOWN Alzheimer's Disease Neuroimaging Initiative
May 7, 2014·Genetic Epidemiology·Heather E WheelerHae Kyung Im
Oct 3, 2015·American Journal of Human Genetics·Bjarni J VilhjálmssonAlkes L Price
Aug 6, 2015·Genome Medicine·Gad AbrahamMichael Inouye
Apr 22, 2015·Autoimmunity Reviews·William John MartinIan P Wicks
Aug 10, 2013·Journal of Molecular Biology·Y Bromberg
Nov 14, 2014·PLoS Genetics·Sebastian OkserTero Aittokallio
Sep 7, 2017·Genetic Epidemiology·Kevin L KeysKenneth Lange
Oct 31, 2017·Current Diabetes Reports·Maria J RedondoAndrea K Steck
Feb 28, 2019·Genetics·Florian PrivéMichael G B Blum
Jan 1, 2012·ISRN Bioinformatics·Jarrett D Morrow, Brandon W Higgs
Jan 1, 2014·ISRN Bioinformatics·Giorgio Valentini
Jun 19, 2013·Nature Reviews. Genetics·Naomi R WrayPeter M Visscher
Nov 5, 2020·PloS One·Donia Macartney-CoxsonMiles C Benton
Sep 6, 2020·Annals of the Rheumatic Diseases·Rodrigo CánovasMichael Inouye
Sep 27, 2020·Computers in Biology and Medicine·Muhammad Khawar SanaMuhammad Haisum Maqsood
Nov 7, 2019·The Annals of Applied Statistics·Eugene Katsevich, Chiara Sabatti
May 9, 2021·American Journal of Human Genetics·Clara AlbiñanaBjarni J Vilhjálmsson

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Software Mentioned

Beagle
LIBSVM
Ubuntu Linux
glmnet
Hat Enterprise Linux Server
CDBLOCK
1000Genomes
IMPUTE
LIBLINEAR
Red

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