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Infinium omni2 5exome 8 v1 3 or v1

Manufactured by Thermo Fisher Scientific
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The Infinium Omni2.5Exome-8 v1.3 or v1.4 is a high-density genotyping array designed for comprehensive genetic analysis. It contains over 2.5 million markers, including exome-focused content, to provide a broad overview of genetic variation. The array is intended for use in large-scale genomic studies and can be processed in a 96-well plate format.

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Lab products found in correlation

Snp 6.0 array, by Thermo Fisher Scientific (2 mentions)

2 protocols using infinium omni2 5exome 8 v1 3 or v1

1

Comprehensive Genomic Profiling Protocol

Cited 3 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
Each model underwent analysis using the Illumina Infinium Omni2.5Exome-8 v1.3 or v1.4 or the Affymetrix SNP 6.0 array. These samples were processed according to PDXnet specifications1 (link) using the tumor-only procedure outlined by recommendations in ASCAT62 (link). To account for median-centered differences between the Affymetrix and Illumina chip, we calculated platform-specific thresholds for amplifications and deletions (0.9 and −0.9 for Affymetrix CN ratios and 0.6 and −0.6 for Illumina CN ratios; Extended Data Fig. 5). The gene set chosen for Fig. 1a was curated from a set of four breast cancer or pan-cancer publications63 (link),64 (link) as well as sentinel genes, that is, genes that represent a larger genomic region, from public and commercial sources, including FoundationOne, cBioPortal and Ambry Genetics Corporation. These extra genes include FGF3, CDK12, NOTCH2, H3P6, SIPA1L3, ADCY9, FAM72C, SDK2, CDK18, STX4, TNFRSF10C, NKX3-1, LYN, JAK1, JAK2, CD274, PDCD1LG2, ERBB4, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A, MUTYH, NBN, NP1, PALB2, RAD50, RAD51C and RAD51D.
Guillen K.P., Fujita M., Butterfield A.J., Scherer S.D., Bailey M.H., Chu Z., DeRose Y.S., Zhao L., Cortes-Sanchez E., Yang C.H., Toner J., Wang G., Qiao Y., Huang X., Greenland J.A., Vahrenkamp J.M., Lum D.H., Factor R.E., Nelson E.W., Matsen C.B., Poretta J.M., Rosenthal R., Beck A.C., Buys S.S., Vaklavas C., Ward J.H., Jensen R.L., Jones K.B., Li Z., Oesterreich S., Dobrolecki L.E., Pathi S.S., Woo X.Y., Berrett K.C., Wadsworth M.E., Chuang J.H., Lewis M.T., Marth G.T., Gertz J., Varley K.E., Welm B.E, & Welm A.L. (2022). A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nature Cancer, 3(2), 232-250.
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2

Comprehensive Genomic Profiling of PDX Models

Cited 3 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
Each model underwent analysis using the Illumina Infinium Omni2.5Exome-8 v1.3 or v1.4 or the Affymetrix SNP 6.0 array. These samples were processed according to PDXnet specifications1 (link) using the tumor-only procedure outlined by recommendations in ASCAT62 (link). To account for median-centered differences between the Affymetrix and Illumina chip we calculated platform specific thresholds for amplifications and deletions (0.9 and −0.9 for Affymetrix CN ratios, and 0.6 and −0.6 for Illumina CN ratios; ED Figure 3). The gene set chosen for Figure 1a was curated from a set of four breast cancer or pan-cancer publications63 (link),64 (link) as well as sentinel genes, i.e., genes that represent a larger genomic region, from public and commercial sources including FoundationOne, cBioPortal, and Ambry Genetics Corporation. These extra genes include FGF3, CDK12, NOTCH2, H3P6, SIPA1L3, ADCY9, FAM72C, SDK2, CDK18, STX4, TNFRSF10C, NKX3–1, LYN, JAK1, JAK2, CD274, PDCD1LG2, ERBB4, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A, MUTYH, NBN, NP1, PALB2, RAD50, RAD51C, and RAD51D.
Guillen K.P., Fujita M., Butterfield A.J., Scherer S.D., Bailey M.H., Chu Z., DeRose Y.S., Zhao L., Cortes-Sanchez E., Yang C.H., Toner J., Wang G., Qiao Y., Huang X., Greenland J.A., Vahrenkamp J.M., Lum D.H., Factor R.E., Nelson E.W., Matsen C.B., Poretta J.M., Rosenthal R., Beck A.C., Buys S.S., Vaklavas C., Ward J.H., Jensen R.L., Jones K.B., Li Z., Oesterreich S., Dobrolecki L.E., Pathi S.S., Woo X.Y., Berrett K.C., Wadsworth M.E., Chuang J.H., Lewis M.T., Marth G.T., Gertz J., Varley K.E., Welm B.E, & Welm A.L. (2022). A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nature Cancer, 3(2), 232-250.
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