Clinical application of high-throughput genomic technologies for treatment selection in breast cancer

Hansen, Aaron R; Bedard, Philippe L

doi:10.1186/bcr3558

Table 3 Selected national or institutional molecular screening programs in breast cancer or advanced solid tumors

From: Clinical application of high-throughput genomic technologies for treatment selection in breast cancer

Institution or national program	Platform	Cancer(s)	Archival versus	Additional details
			biopsy
Princess Margaret Cancer Centre, Canada	MiSeq and Sequenom	Breast, CRC, ovarian, NSCLC, pancreatobiliary, GU, upper aerodigestive and phase I	Archival	Customized Sequenom panel (279 mutations, 23 genes). TSACP 48 genes, >770 mutations. NCT01505400
Massachusetts General Hospital	SNaP Shot	NSCLC, CRC, melanoma, breast	Archival	Breast cancer: 130 mutations, 15 oncogenes.
Dana Farber Cancer Institute	Sequenom	All solid tumors	Archival	OncoMap ~470 mutations in 41 genes.
MD Anderson Cancer Center	IMPACT trial [12]	All solid tumors	Archival	Umbrella protocol (NCT00851032)
	T9 Program: Sequenom	All solid tumors	Archival	Customized Sequenom panel (40+ genes) with Sanger confirmation.
	Clearing House Protocol	All solid tumors	NS	200-gene panel
Vanderbilt-Ingram Cancer Center	SNaPshot	Melanoma, NSCLC, CRC, and breast cancer	Archival	Personalized Cancer Medicine Initiative: Custom breast panel: HER2 (FISH), PTEN (IHC), PIK3CA, AKT1
University of Michigan Comprehensive Cancer Center	WGS and multi-gene sequencing - Illumina HiSeq	All solid tumors	Fresh biopsies	PARADIGM (University of Michigan Health system joint venture with ICGC)
University of Michigan Comprehensive Cancer Center	WGS and multi-gene sequencing - Illumina HiSeq	All solid tumors	Fresh biopsies	To be conducted in CLIA-certified lab
Memorial Sloan-Kettering Cancer Center	Clinical and Research Assays: Sequenom and MiSeq	All solid tumors	Archival	275 genes
Memorial Sloan-Kettering Cancer Center	Clinical and Research Assays: Sequenom and MiSeq	All solid tumors	Archival	NCT01775072
Mayo Clinic Cancer Center	Whole-genome sequencing (platform NS)	Breast	Fresh biopsies and surgical specimens	BEAUTY Breast Cancer Genome Guided Therapy study
Mayo Clinic Cancer Center	Whole-genome sequencing (platform NS)	Breast	Fresh biopsies and surgical specimens	Sequence patients with pCR. Tumor samples before neoadjuvant chemotherapy and during chemotherapy and surgical resection.
Institut Gustav Roussy, France	aCGH and DNA sequencing	Breast, phase I	Biopsy	MOSCATO (phase I) and SAFIR (breast). SEQCan 46 genes, 739 hotspot mutations
Institut Curie, Institut National du Cancer (French National Cancer Institute)	AmpliSeq panel and Ion Torrent PGM	All solid tumors	Fresh biopsies (FFPE and frozen)	SHIVA Phase II trial: NCT01771458. PMID: 23161020. Mutations and amplifications in 46 genes. Multiple eligible targeted therapies
Institut National du Cancer (French National Cancer Institute)	Platform NS	GIST, melanoma, CRC, NSCLC, and stomach and breast cancer	NS	Nationwide. HER2 amplification, mutations in KIT, PDGFR, KRAS, BRAF, EGFR, HER2, PIK3CA, ALK translocation
Cancer Research UK - Stratified Medicine Programme	Targeted sequencing of select genes	Breast, melanoma, prostate, ovarian, CRC, and NSCLC	Archival	Breast panel includes sequencing PIK3CA (exons 9 and 20), TP53 (exons 4-9), PTEN (exons 2-10, LOH)
The Netherlands: CPCT	Targeted sequencing (platform NS)	Solid tumors	Biopsy	Nested therapeutic clinical trials and basic sciences research. More than 1,200 genes to be sequenced
Norway Nationwide program	Whole-genome sequencing (platform NS)	Solid tumors	Fresh and archival samples	Norwegian Cancer Genomics consortium
Norway Nationwide program	Whole-genome sequencing (platform NS)	Solid tumors	Fresh and archival samples	In its three-year pilot phase: sequence 1,000 tumor genomes and 3,000 archival samples
Lunds Universetit, Sweden	Whole-transcriptome sequencing	Breast cancer	Archival	South Sweden Cancerome Analysis Network -Breast

aCGH, array comparative genome hybridization; CLIA, Clinical Laboratory Improvement Amendments; CPCT, Centre for Personalized Cancer Treatment; CRC, colorectal cancer, FFPE, formalin-fixed and paraffin-embedded; FISH, fluorescence in situ hybridization; GIST, gastrointestinal stromal tumor; GU, genitourinary; ICGC, International Cancer Genome Consortium; IHC, immunohistochemistry; IMPACT, IMmunotherapy Prostate AdenoCarcinoma Treatment; LOH, loss of heterozygosity; NS, not stipulated, NSCLC, Non-small cell lung cancer; pCR, pathological complete response; PGM, Personal Genome Machine; TSACP, Truseq amplicon cancer panel; WGS, whole-genome sequencing.

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