TARGET Project Experimental Methods

On this page researchers can find detailed information describing how TARGET data was generated by genomic platform, including protocols for establishing high-quality nucleic acid samples. 

*Note to users: Protocols are currently being added to this site, as a large portion of the data and metadata were recently released onto the TARGET Data Matrix. Please continue to check back in the coming weeks as updates are completed, and contact ocg@mail.nih.gov with any questions. 

TARGET Sample Naming 

TARGET samples are named using a coding system specific to OCG characterization programs. Please use the OCG Sample Codes document to properly discern the metadata reiterated within the sample name. PDF iconOCG Sample Codes_finalized 05 2017.pdf

 

Nucleic Acid Sample Processing

TARGET project teams use high-quality RNA and DNA from case-matched tumor and normal tissues to generate comprehensive genomics data. Below is a table outlining how each project team generated those samples.

General Methodology Sample Preparation Protocols
DNA/RNA Co-isolation with Qiagen AllPrep Kit (DNA/RNA) and mirVana (Total & Small RNAs) AML symbolAML , AML symbolAML-IF , Kidney tumor symbolCCSK , Kidney tumor symbolRT , Kidney tumor symbolWT , Osteosarcoma symbolOS , Neuroblastoma symbolNBL (after 2013)
DNA Isolation with Qiagen QIAamp DNA Minikit ALL symbolALL P1 , ALL symbolALL P2 , ALL symbolALL MDLS
DNA Isolation with Qiagen Genomic-Tips Neuroblastoma symbolNBL (prior to 2013) , Kidney tumor symbolWT
RNA Isolation with Invitrogen TRIzol ALL symbolALL P1 , ALL symbolALL P2 , ALL symbolALL MDLS
RNA Isolation with Invitrogen TRIzol and Qiagen RNAeasy Neuroblastoma symbolNBL (prior to 2013)
DNA/RNA Co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for AML

The protocol herein describes the procedures used by Fred Hutchinson Cancer Research Center to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA/RNA Co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for AML-IF

The protocol herein describes the procedures used by Fred Hutchinson Cancer Research Center to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA/RNA co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for CCSK

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA/RNA co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for RT

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA/RNA co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for WT

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA/RNA co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for OS

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

Some OS validation samples were extracted outside of Nationwide Children’s Hospital at either the National Cancer Institutes or international cancer centers to include Toronto SickKids (Ontario, Canada), Chiba Cancer Center (Japan) or the GRAACC Cancer Center in Sao Paulo, Brazil.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA/RNA co-isolation with Qiagen AllPrep kit (DNA/RNA) and mirVana (total & small RNAs) for NBL

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA Isolation with Qiagen QIAamp DNA Minikit for ALL P1

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA Isolation with Qiagen QIAamp DNA Minikit for ALL P2

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA Isolation with Qiagen QIAamp DNA Minikit for ALL MDLS

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA Isolation with Qiagen Genomic-Tips for NBL

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

DNA Isolation with Qiagen Genomic-Tips for WT

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

Some WT validation samples were extracted in the lab of Dr. Paul Grundy and were provided for TARGET through Ann & Robert H. Lurie Children’s Hospital.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

RNA Isolation with Invitrogen TRIzol for ALL P1

The protocol herein describes the procedures used by University of New Mexico to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

RNA Isolation with Invitrogen TRIzol for ALL P2

The protocol herein describes the procedures used by University of New Mexico to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

RNA Isolation with Invitrogen TRIzol for ALL MDLS

The protocol herein describes the procedures used by University of New Mexico to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

RNA Isolation with Invitrogen TRIzol and Qiagen RNAeasy for NBL

The protocol herein describes the procedures used by Nationwide Children’s Hospital to process disease tissues for RNA and/or DNA subsequently used for characterization in the NCI’s TARGET initiative.

All nucleic acid samples used in TARGET projects were quality tested for consistency using picogreen quantification and SSTR genotyping methods, regardless of where the nucleic acid was originally extracted.

Experimental Protocol

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