Log In Sign up
The largest database of trusted experimental protocols

Foundationone platform

Manufactured by Foundation Medicine
Visit Supplier

The FoundationOne platform is a comprehensive genomic profiling assay that analyzes the key genes known to drive cancer growth and development. It is designed to detect genomic alterations in solid tumors and provide clinicians with actionable insights to guide patient treatment decisions.

Automatically generated - may contain errors

Lab products found in correlation

5 protocols using foundationone platform

1

Comprehensive Profiling of ALK Fusion Variants

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
ALK fusion variants were detected using the MGH fusion panel, which employs targeted RNA sequencing with anchored multiplex polymerase chain reaction (PCR) to detect fusion transcripts involving known oncogenes, including ALK;31 (link) the FoundationOne platform (Foundation Medicine, Inc., Cambridge, MA);32 (link) targeted NGS platforms at outside institutions as previously described;33 (link),34 (link) or reverse transcription PCR (commercial or as previously described35 (link)) and Sanger sequencing of complementary DNA (cDNA) (see Appendix; Appendix Fig. A1B).
Lin J.J., Zhu V.W., Yoda S., Yeap B.Y., Schrock A.B., Dagogo-Jack I., Jessop N.A., Jiang G.Y., Le L.P., Gowen K., Stephens P.J., Ross J.S., Ali S.M., Miller V.A., Johnson M.L., Lovly C.M., Hata A.N., Gainor J.F., Iafrate A.J., Shaw A.T, & Ou S.H. (2018). Impact of EML4-ALK Variant on Resistance Mechanisms and Clinical Outcomes in ALK-Positive Lung Cancer. Journal of Clinical Oncology, 36(12), 1199-1206.
+ Open protocol
+ Expand
2

FBXW7 Mutation Analysis Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

FBXW7 mutations were investigated in archival formalin-fixed, paraffin-embedded tissue blocks or material from fine needle aspiration biopsies obtained from diagnostic and/or therapeutic procedures. All histologies were centrally reviewed at MD Anderson. FBXW7 mutation analysis was performed in different Clinical Laboratory Improvement Amendment-certified laboratories as part of a gene panel analysis. These included 182 genes in targeted next-generation sequencing Foundation One platform (Foundation Medicine, Cambridge, MA), 46 genes in Ion Torrent next-generation sequencing (Baylor’s Cancer Genetics Laboratory, Houston, TX) and 53 genes in Sequenom Mass ARRAY platform (Knight Diagnostics,Portland, OR). Information about mutations in genes other than FBXW7 discovered in these multiplex panels was also registered.
Jardim D.L., Wheler J.J., Hess K., Tsimberidou A.M., Zinner R., Janku F., Subbiah V., Naing A., Piha-Paul S.A., Westin S.N., Roy-Chowdhuri S., Meric-Bernstam F, & Hong D.S. (2014). FBXW7 Mutations in Patients with Advanced Cancers: Clinical and Molecular Characteristics and Outcomes with mTOR Inhibitors. PLoS ONE, 9(2), e89388.
+ Open protocol
+ Expand
3

Genetic Profiling of p53 Mutations

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The p53 mutation status was determined by either polymerase chain reaction–based or next-generation sequencing in a Clinical Laboratory Improvement Amendments–certified laboratory, as previously described [23 (link)]. The next-generation sequencing included 182 genes in targeted next-generation sequencing Foundation One platform (Foundation Medicine, Cambridge, MA).
Said R., Ye Y., Hong D.S., Janku F., Fu S., Naing A., Wheler J.J., Kurzrock R., Thomas C., Palmer G.A., Hess K.R., Aldape K, & Tsimberidou A.M. (2014). Characteristics and survival of patients with advanced cancer and p53 mutations. Oncotarget, 5(11), 3871-3879.
+ Open protocol
+ Expand
4

Comprehensive Genomic Profiling of FFPE Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
Details on the sequencing methodology used in this study can be found in Frampton et al. (2013) (link). Routine formalin-fixed, paraffin-embedded (FFPE) tissue was sent to Foundation Medicine, Inc. for CGP using the CLIA-certified FoundationOne platform (Frampton et al. 2013 (link)). Targeted sequencing of the entire coding sequence was done for 236 genes and 47 introns of 19 genes involved in fusions at a depth of 500×–1000× (median exon depth of 792×; 100% of the baited region was sequenced at a depth of at least 100×; sequence alignment error of only 0.27%). The depth of variant call reads was 59×; these 59 chimeric reads equate to an independently validated variant calling method described in Frampton et al. (2013) (link). The depth of wild-type reads was 1155× (please see Supplemental Table S1).
Dhami J., Hirshfield K.M., Ganesan S., Hellmann M., Rojas V., Amorosa J.K., Riedlinger G.M., Zhong H., Ali S.M., Pavlick D., Elvin J.A, & Rodriguez-Rodriguez L. (2018). Comprehensive genomic profiling aids in treatment of a metastatic endometrial cancer. Cold Spring Harbor Molecular Case Studies, 4(2), a002089.
+ Open protocol
+ Expand
5

Molecular Profiling of NSCLC Progression

Check if the same lab product or an alternative is used in the 5 most similar protocols
A subset of the patients included in this study underwent repeat tumor or liquid biopsies at the time of progression on alectinib and prior to starting brigatinib, under IRB-approved protocols. Five patients underwent a tumor biopsy of the progressing lesion followed by targeted NGS using the commercially available FoundationOne platform (n = 2; Foundation Medicine, Inc.) or the MGH SNaPshot NGS platform (n = 3), as previously described.20 (link) Four patients underwent a liquid biopsy using either the commercially available Guardant360 cell-free DNA (Guardant Health, Inc.) or FoundationACT platform (Foundation Medicine, Inc.). Additionally, five patients underwent a tumor (FoundationOne, n = 2), liquid (Guardant360, n = 1; FoundationACT, n = 1), or both tumor and liquid (MGH SNaPshot NGS and Guardant360, n = 1) biopsy after progression on brigatinib.
Lin J.J., Zhu V.W., Schoenfeld A.J., Yeap B.Y., Saxena A., Ferris L.A., Dagogo-Jack I., Farago A.F., Taber A., Traynor A., Menon S., Gainor J.F., Lennerz J.K., Plodkowski A.J., Digumarthy S.R., Ou S.H., Shaw A.T, & Riely G.J. (2018). Brigatinib in Patients with Alectinib-Refractory ALK-Positive Non-Small Cell Lung Cancer: A Retrospective Study. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer, 13(10), 1530-1538.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!