Stepwise Distributed Open Innovation Contests for Software Development: Acceleration of Genome-Wide Association Analysis.
The association of differing genotypes with disease-related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low-cost genotyping and sequencing has made collecting large-scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies is being used to capture numerous new and complex phenotypic descriptors. As a result, genotype and phenotype datasets have grown exponentially. Genome-wide association studies associate genotypes and phenotypes using methods such as logistic regression. As existing tools for association analysis limit the efficiency by which value can be extracted from increasing volumes of data, there is a pressing need for new software tools that can accelerate association analyses on large genotype-phenotype datasets.



Using open innovation (OI) and contest-based crowdsourcing, the logistic regression analysis in a leading, community-standard genetics software package (PLINK 1.07) was substantially accelerated. OI allowed us to do this in <6 months by providing rapid access to highly skilled programmers with specialized, difficult-to-find skill sets. Through a crowd-based contest a combination of computational, numeric, and algorithmic approaches was identified that accelerated the logistic regression in PLINK 1.07 by 18- to 45-fold. Combining contest-derived logistic regression code with coarse-grained parallelization, multithreading, and associated changes to data initialization code further developed through distributed innovation, we achieved an end-to-end speedup of 591-fold for a data set size of 6678 subjects by 645 863 variants, compared to PLINK 1.07's logistic regression. This represents a reduction in run time from 4.8 hours to 29 seconds. Accelerated logistic regression code developed in this project has been incorporated into the PLINK2 project.



Using iterative competition-based OI, we have developed a new, faster implementation of logistic regression for genome-wide association studies analysis. We present lessons learned and recommendations on running a successful OI process for bioinformatics.
Research Business Technology, Pfizer Research, 1 Portland Street, Cambridge, Massachusetts, 02139 USA.
Andrew
A
Hill
Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.|Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts, 02142 USA.
Po-Ru
PR
Loh
Babbage Analytic and Innovation, Boston Massachusetts, USA.|Current affiliation, Nyrasta LLC.
Ragu B
RB
Bharadwaj
Current affiliation, Criteo Labs, 32 Rue Blanche, 75009, Paris, France.
Pascal
P
Pons
Current affiliation, Computer Science Department, University of Illinois at Urbana-Champaign 201 N Goodwin Ave, Urbana, Illinois, USA.
Jingbo
J
Shang
Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts, 02215, USA.|Harvard Business School, Boston, Massachusetts, 02163 USA.
Eva
E
Guinan
Babbage Analytic and Innovation, Boston Massachusetts, USA.|Harvard Business School, Boston, Massachusetts, 02163 USA.|Harvard-NASA Tournament Lab, Institute for Quantitative Social Science 1737 Cambridge Street, Cambridge Massachusetts, 02138, USA.
Karim
K
Lakhani
Department of Inflammation and Immunology, Pfizer Research, 1 Portland Street, Cambridge, Massachusetts, 02139, USA.
Iain
I
Kilty
Department of Inflammation and Immunology, Pfizer Research, 1 Portland Street, Cambridge, Massachusetts, 02139, USA.
Scott A
SA
Jelinsky
D063045:Crowdsourcing; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D062069:Inventions; D016015:Logistic Models; D010641:Phenotype; D012984:Software
Crowdsourcing; Genome-wide association study; Logistic regression; Open innovation; PLINK