Molecular profiling data based patient stratification plays a key role in clinical decision making, such as identification of disease subgroups and prediction of treatment responses of individual subjects. Many existing knowledge management systems like tranSMART enable scientists to do such analysis. But in the big data era, molecular profiling data size increases sharply due to new biological techniques, such as next generation sequencing. None of the existing storage systems work well while considering the three ”V” features of big data (Volume, Variety, and Velocity). New Key Value data stores like Apache HBase and Google Bigtable can provide high speed queries by the Key. These databases can be modeled as Distributed Ordered Table (DOT), which horizontally partitions a table into regions and distributes regions to region servers by the Key. However, none of existing data models work well for DOT. A Collaborative Genomic Data Model (CGDM) has been designed to solve all these is- sues. CGDM creates three Collaborative Global Clustering Index Tables to improve the data query velocity. Microarray implementation of CGDM on HBase performed up to 246, 7 and 20 times faster than the relational data model on HBase, MySQL Cluster and MongoDB. Single nucleotide polymorphism implementation of CGDM on HBase outperformed the relational model on HBase and MySQL Cluster by up to 351 and 9 times. Raw sequence implementation of CGDM on HBase gains up to 440-fold and 22-fold speedup, compared to the sequence alignment map format implemented in HBase and a binary alignment map server. The integration into tranSMART shows up to 7-fold speedup in the data export function. In addition, a popular hierarchical clustering algorithm in tranSMART has been used as an application to indicate how CGDM can influence the velocity of the algorithm. The optimized method using CGDM performs more than 7 times faster than the same method using the relational model implemented in MySQL Cluster.