SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO
Breast cancer is commonly acknowledged as the primary type of cancer on a global scale, exerting a substantial influence on death rates, particularly in developing countries. The aforementioned discovery provides evidence in favor of the concept that genetic factors may contribute to the onset of br...
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Elsevier
2025-04-01
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| Series: | Data in Brief |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340925000757 |
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| author | Rafika Indah Paramita Sonar Soni Panigoro Fadilah Fadilah Septelia Inawati Wanandi Noorwati Sutandyo |
| author_facet | Rafika Indah Paramita Sonar Soni Panigoro Fadilah Fadilah Septelia Inawati Wanandi Noorwati Sutandyo |
| author_sort | Rafika Indah Paramita |
| collection | DOAJ |
| description | Breast cancer is commonly acknowledged as the primary type of cancer on a global scale, exerting a substantial influence on death rates, particularly in developing countries. The aforementioned discovery provides evidence in favor of the concept that genetic factors may contribute to the onset of breast cancer. This paper presents the unprocessed idat data containing single nucleotide polymorphisms (SNPs) acquired from breast cancer patients and a control group comprising of healthy women. The DNA was obtained from stored blood samples that were collected from a total of 48 female patients diagnosed with breast cancer at Cipto Mangunkusumo National Hospital Jakarta and Dharmais National Cancer Center Hospital Jakarta. Additionally, 24 healthy women were included as control subjects. Subsequently, the DNA samples were subjected to hybridization onto Infinium Asian Screening Array (ASA)’s beadchips. The chip was then subjected to fluorescence intensity measurements using an iScan machine manufactured by Illumina. The data output is produced in the form of a .idat file for each sample. Subsequently, further quality control measures and population stratification analysis were conducted using PLINK (v1.9). After the conclusion of the quality control procedure, 72 individuals and a dataset consisting of 424,285 genetic variants were selected for further analysis. The idat raw data files have been added to the Gene Expression Omnibus (GEO) with accession number: GSE245794 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245794). |
| format | Article |
| id | doaj-art-df0ef13c9612464e964cb070c159dc87 |
| institution | Kabale University |
| issn | 2352-3409 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj-art-df0ef13c9612464e964cb070c159dc872025-02-06T05:11:59ZengElsevierData in Brief2352-34092025-04-0159111343SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEORafika Indah Paramita0Sonar Soni Panigoro1Fadilah Fadilah2Septelia Inawati Wanandi3Noorwati Sutandyo4Doctoral Program in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta, 10430, IndonesiaMaster's Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Surgical Oncology Division, Department of Surgery, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta, 10430, Indonesia; Corresponding authors.Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta, 10430, Indonesia; Master's Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Corresponding authors.Master's Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, Indonesia; Molecular Biology and Proteomics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta, 10430, IndonesiaDepartment of Hematology and Medical Oncology, Dharmais National Cancer Center Hospital, Jalan Letjen S. Parman, Jakarta, 11420, Indonesia; Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta, 10430, IndonesiaBreast cancer is commonly acknowledged as the primary type of cancer on a global scale, exerting a substantial influence on death rates, particularly in developing countries. The aforementioned discovery provides evidence in favor of the concept that genetic factors may contribute to the onset of breast cancer. This paper presents the unprocessed idat data containing single nucleotide polymorphisms (SNPs) acquired from breast cancer patients and a control group comprising of healthy women. The DNA was obtained from stored blood samples that were collected from a total of 48 female patients diagnosed with breast cancer at Cipto Mangunkusumo National Hospital Jakarta and Dharmais National Cancer Center Hospital Jakarta. Additionally, 24 healthy women were included as control subjects. Subsequently, the DNA samples were subjected to hybridization onto Infinium Asian Screening Array (ASA)’s beadchips. The chip was then subjected to fluorescence intensity measurements using an iScan machine manufactured by Illumina. The data output is produced in the form of a .idat file for each sample. Subsequently, further quality control measures and population stratification analysis were conducted using PLINK (v1.9). After the conclusion of the quality control procedure, 72 individuals and a dataset consisting of 424,285 genetic variants were selected for further analysis. The idat raw data files have been added to the Gene Expression Omnibus (GEO) with accession number: GSE245794 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245794).http://www.sciencedirect.com/science/article/pii/S2352340925000757Breast cancerBlood DNA samplesGene Expression Omnibus (GEO)DNA mutationsSNP-array |
| spellingShingle | Rafika Indah Paramita Sonar Soni Panigoro Fadilah Fadilah Septelia Inawati Wanandi Noorwati Sutandyo SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO Data in Brief Breast cancer Blood DNA samples Gene Expression Omnibus (GEO) DNA mutations SNP-array |
| title | SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO |
| title_full | SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO |
| title_fullStr | SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO |
| title_full_unstemmed | SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO |
| title_short | SNP-array profiling data from breast cancer patients and healthy women's blood DNA samplesGEO |
| title_sort | snp array profiling data from breast cancer patients and healthy women s blood dna samplesgeo |
| topic | Breast cancer Blood DNA samples Gene Expression Omnibus (GEO) DNA mutations SNP-array |
| url | http://www.sciencedirect.com/science/article/pii/S2352340925000757 |
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