GIMO_BostonGene Dataset

This dataset contains Whole Exome Sequencing (WES) and RNA sequencing (RNAseq) data from BostonGene orders for GIMO physicians. All raw data from MDACC orders were transferred to Genomic Medicine through Kenna Shaw’s team, with processing handled by Jianhua Zhang’s group. The GIMO patient data has been retrieved and transferred to the following location:

HPC storage: /rsrch9/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/GIMO_BostonGene/

The annotation results will be uploaded to Foundry in:

Foundry folder: /MDACC/Colorectal Cancer: LAB09-0373/09-Projects_with_Multiple_Tumor_Locations/BostonGene (not yet uploaded).

For access requests, please contact Kangyu Lin and cc Scott Kopetz.

Data statistics:

All GIMO orders by 2-11-2025 (Including failures):

Transfer 25Feb2025 and 03July2025:

	FASTQ					AddOn
Batch	RNASeq-tumor	WES-normal	WES-tumor	WES-tumor/normal_pair	RNA_WES_both	RNA_expression	Somatic Mutations	Copy_number
B001-B022	375	384	380	380	369	375	380	380
B023-B028	154	157	151	151	148

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This is the first transfer directly from BostonGene (the FASTQ files are also included in Transfer_25Feb2025):

The FASTQ files for RNAseq and WES data are transferred from BostonGene. Most samples include processed AddOn data: expression data (TPM) and somatic mutations.

Data were transferred to HPC: /rsrch5/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/GIMO_BostonGene/.

Sample information and AddOn data are available on Foundry under /MDACC/Colorectal Cancer: LAB09-0373/09-Projects_with_Multiple_Tumor_Locations/BostonGene.

Number of Data:

FASTQ				AddOn
RNASeq-tumor	WES-normal	WES-tumor	WES-tumor/normal_pair	Expressions	Somatic Mutations	Expressions_Somatic Mutations	MRN
241	246	244	244	281	295	277	291

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Last Updated: 07/03/2025