Hm450k

Manufactured by Illumina

Sourced in United States

The HM450K is a DNA methylation microarray manufactured by Illumina. It is designed to analyze the methylation status of over 450,000 CpG sites across the human genome. The HM450K provides a comprehensive and high-throughput solution for genome-wide DNA methylation profiling.

Automatically generated - may contain errors

Lab products found in correlation

Infinium humanmethylation450 beadchip array hm450k, by Illumina (1 mentions) Humanmethylation450 beadchip, by Illumina (1 mentions) Methylationepic beadchip, by Illumina (1 mentions) High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

HM450K array (9 citations) HM450K BeadChip (8 citations) Infinium HumanMethylation450 BeadChip (HM450K) (7 citations) Infinium HumanMethylation450 BeadChip Array (HM450K) (5 citations) HumanMethylation450 BeadChip (HM450K) (5 citations) Infinium HumanMethylation450K array (HM450K; (2 citations) HM450K assay (2 citations)

3 protocols using hm450k

TCGA Head and Neck Cancer Methylation Analysis

Cited 3 times

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

The TCGA database of head and neck cancers was accessed for publically available methylation data assessed by the Infinium HumanMethylation450 beadchip array (HM450K, Illumina inc., San Diego, US).
Methylation data from Level 1 raw IDAT files were obtained from the heterogeneous TCGA HNSCC samples (http://cancergenome.nih.gov/; HM450K download date 24 June 2013; clinical data download date 22 July 2013). Utilizing R software (version 3.0.1; http://cran.r-project.org/), background correction and probe specific correction with SWAN normalization was performed utilizing Methylumi and Minfi packages found in Bioconductor [112 (link)–114 (link)]. Probes mapping to common variant SNPs or non-unique mappings were removed from the analysis, leaving 330,557 probes for the downstream analysis [115 (link)]. Our MS-HRM amplicons interrogating the APC, BRCA1, CDH1, CDH13 and MLH1 genes, overlapped with CpG probes assessed by the HM450K. For the seven genes (ABO, ATM, DAPK1, RASSF1A, MGMT, ERCC1 and RUNX3) that did not have overlapping CpGs on the HM450K, the two probes immediately flanking upstream and downstream of our MS-HRM amplicon were assessed. A β-value greater than 0.2 was used to define the presence of significant methylation [116 (link)].

Lim A.M., Candiloro I.L., Wong N., Collins M., Do H., Takano E.A., Angel C., Young R.J., Corry J., Wiesenfeld D., Kleid S., Sigston E., Lyons B., Rischin D., Solomon B, & Dobrovic A. (2014). Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome. Clinical Epigenetics, 6, 22.

+ Open protocol

+ Expand

DNA methylation profiling in cohorts

Cited 1 time

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

In Cohort 1, DNAm for the discovery sample was profiled by using the Illumina Infinium HumanMethylation450 Beadchip (Illumina HM450K) (San Diego, CA, USA). DNAm for the replication sample was assessed by using the Illumina Infinium MethylationEPIC Beadchip (Illumina EPIC) (San Diego, CA, USA). In Cohort 2, DNAm was measured by using Illumina HM450K. All samples in Cohorts 1 and 2 were processed at the Yale Center for Genomic Analysis [14 (link)]. After QC (details in Supplementary Information), in Cohort 1, a total of 437,722 CpGs from 450K array remained in the discovery sample and 846,604 CpGs from EPIC array remained for the replication sample. A total of 48.26% common CpGs (408,583) were analyzed in meta-analyses. In Cohort 2, we applied the same QC criteria. A total of 437,722 CpGs remained for analysis.

Liang X., Justice A.C., So-Armah K., Krystal J.H., Sinha R, & Xu K. (2020). DNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations. Molecular Psychiatry, 26(6), 2238-2253.

+ Open protocol

+ Expand

Multimodal Epigenomic and Transcriptomic Analysis of Lung Cancer

Cited 2 times

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

DNA extraction, modification, and methylation analysis using Combined Bisulfite Modification and Restriction Analysis (CoBRA), Methylation-Specific PCR (MSP), and (for sputum samples) Nested MSP assays were conducted as described.^{20 (link)–22 (link)} The primer sequences and amplification conditions are shown in supplementary Tables S1 and S2. Genome-wide methylation of lung tumor-normal pairs was quantified using HM450K (Illumina, San Diego, CA).^{12 (link)} Methylation data for lung tumor-normal pairs evaluated by TCGA was obtained from https://tcga-data.nci.nih.gov/tcga/.
Gene expression analysis was conducted using RNA isolated from lung tumor-CFLT pairs and cell lines as described.^{23 (link)} Briefly, 1 μg total RNA was reverse transcribed using the High Capacity cDNA Reverse Transcription Kit from Applied Biosystems (Foster City, CA) according to the manufacturer’s protocol. Expression of CCDC37, MAP1B, and BETA-ACTIN was quantified using Hs00403623_m1, Hs00195485_m1, and 4310881E TaqMan assays (Applied Biosystems), respectively, as described.^{24 (link),25 (link)} All samples were analyzed at least twice in duplicate and expression levels were calculated using ΔΔCT method.^{26 (link)}

Tessema M., Yingling C.M., Picchi M.A., Wu G., Liu Y., Weissfeld J.L., Siegfried J.M., Tesfaigzi Y, & Belinsky S.A. (2015). Epigenetic Repression of CCDC37 and MAP1B Links Chronic Obstructive Pulmonary Disease to Lung Cancer. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer, 10(8), 1181-1188.

+ 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?

Revolutionizing how scientists
search and build protocols!