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Genomestudio data analysis software v2011

Manufactured by Illumina
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GenomeStudio data analysis software v2011.1 is a bioinformatics tool designed for the visualization and analysis of genomic data generated by Illumina's sequencing platforms. It provides a comprehensive suite of tools for data processing, quality control, and variant calling.

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Lab products found in correlation

Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Veracode technology, by Illumina (2 mentions) Qiaamp 96 spin blood kit, by Qiagen (2 mentions) Goldengate genotyping assay system, by Illumina (2 mentions) Beadxpress reader, by Illumina (2 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Nexus copy number v9, by BioDiscovery (1 mentions) Infinium ffpe qc kit, by Illumina (1 mentions) Infinium hd ffpe dna restoration kit, by Illumina (1 mentions)

4 protocols using genomestudio data analysis software v2011

1

Genome-wide SNP Profiling of FFPE Tumor Samples

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FFPE tissues were sectioned. Archived hematoxylin and eosin-stained tissue slides were evaluated by a pathologist for the area with at least 70% tumor cells for manual macrodissection using a needle tip or scalpel. A minimum amount of 200 ng of DNA extracted from each FFPE tissue was quantified by the Qubit® 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and qualified using the Infinium FFPE QC Kit before being processed with the Infinium HD FFPE DNA Restoration Kit (Illumina, San Diego, CA), all according to the manufacturers’ protocols.
SNP array was performed with the HumanCytoSNP FFPE-12 v2.1 DNA Analysis BeadChip (Illumina, San Diego, CA), according to the manufacturer’s instructions. This array contains approximately 299,140 SNP markers spanning the entire genome with an average probe spacing of 72 kb. The data were analyzed with GenomeStudio Data Analysis Software v. 2011.1 (Illumina, San Diego, CA) and Nexus Copy Number v9.0 (BioDiscovery, Inc., El Segundo, CA) using the reference human genome (hg19/GRCh37).
Sunpaweravong S., Bunbanjerdsuk S., Pongrujikorn T., Naktang C., Sunpaweravong P., Nitiruangjaras A., Dechaphankul T, & Jinawath N. (2019). Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysis. BMC Cancer, 19, 1174.
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2

Genotyping HIV+ and HIV- Blood Samples

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DNA was extracted from 200 μl of packed blood pellets from HIV+ patients and whole-blood samples from HIV− donors using the QIAamp 96 spin blood kit (QIAGEN, Valencia, CA). DNA concentrations were measured using Qubit® Fluorometer (Invitrogen, Carlsbad, CA). SNPs were genotyped using Illumina’s GoldenGate® genotyping assay system combined with VeraCode® Technology (Illumina Inc., San Diego, CA). Allelic discrimination was performed using a BeadXpress® Reader (Illumina) according to the manufacturer’s instructions.
The genotype data were uploaded and filtered using the GenomeStudio data analysis software v2011.1 (Illumina Inc., San Diego, CA). SNPs were filtered by genotype call frequency (<0.9, n = 1) and replicate errors (n = 2). Samples with genotype call frequency <0.9 were excluded (n = 4). Subsequently, SNPs were excluded from analysis if genotypic distribution among HIV− donors, stratified by race, deviated from the Hardy-Weinberg equilibrium (HWE) with a significant cutoff value of P ≤ 0.001 (n = 1). Thus, in the final analysis, 41 SNPs, as listed in Supplementary Table A, were examined in a total of 276 subjects (HIV+, n = 180; HIV−, n = 96).
Willie B., Hall N., Stein C., Jurevic R., Weinberg A., Mehlotra R, & Zimmerman P. (2014). Association of toll-like receptor polymorphisms with HIV status in North Americans. Genes and immunity, 15(8), 569-577.
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3

Detecting Trisomy X using SNP Intensity

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Trisomy X (47,XXX) for each individual was detected through examining the fluorescence intensity of the B allele across all SNPs in X chromosome. Genome Studio data analysis software V.2011.1 (Illumina) was used to quantify the intensity of B allele for SNPs. Scatter plots of B allele intensity were then generated for each individual, with x-axis indicating SNPs across X chromosome and y-axis indicating the intensity of B allele for the SNP. For a SNP with BB homozygous genotype, the expected intensity is 100% in the scatter plot, while the expected intensity is 0% for a SNP with AA homozygosity. In addition, the expectation is 50% for a SNP with AB heterozygosity.
Thus, for females who carried two copies of X chromosome (46,XX), we expected to observe ‘three-band’ pattern in the scatter plot, indicating three groups of the SNPs with different genotypes (AA, AB and BB). However, for females with trisomy X (47,XXX), they have three alleles for each SNP, resulting in four possible genotypes (AAA, AAB, ABB, BBB) in the X chromosome. In this case, we expected to observe four bands in the scatter plot, indicating 0%, 33%, 66% and 100% of intensisty of B allele (online supplemental figure S2).
Tangtanatakul P., Lei Y., Jaiwan K., Yang W., Boonbangyang M., Kunhapan P., Sodsai P., Mahasirimongkol S., Pisitkun P., Yang Y., Eu-Ahsunthornwattana J., Aekplakorn W., Jinawath N., Neelapaichit N., Hirankarn N, & Wang Y.F. (2024). Association of genetic variation on X chromosome with systemic lupus erythematosus in both Thai and Chinese populations. Lupus Science & Medicine, 11(1), e001061.
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4

Genotyping HIV+ and HIV- Blood Samples

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DNA was extracted from 200 μl of packed blood pellets from HIV+ patients and whole-blood samples from HIV− donors using the QIAamp 96 spin blood kit (QIAGEN, Valencia, CA). DNA concentrations were measured using Qubit® Fluorometer (Invitrogen, Carlsbad, CA). SNPs were genotyped using Illumina’s GoldenGate® genotyping assay system combined with VeraCode® Technology (Illumina Inc., San Diego, CA). Allelic discrimination was performed using a BeadXpress® Reader (Illumina) according to the manufacturer’s instructions.
The genotype data were uploaded and filtered using the GenomeStudio data analysis software v2011.1 (Illumina Inc., San Diego, CA). SNPs were filtered by genotype call frequency (<0.9, n = 1) and replicate errors (n = 2). Samples with genotype call frequency <0.9 were excluded (n = 4). Subsequently, SNPs were excluded from analysis if genotypic distribution among HIV− donors, stratified by race, deviated from the Hardy-Weinberg equilibrium (HWE) with a significant cutoff value of P ≤ 0.001 (n = 1). Thus, in the final analysis, 41 SNPs, as listed in Supplementary Table A, were examined in a total of 276 subjects (HIV+, n = 180; HIV−, n = 96).
Willie B., Hall N., Stein C., Jurevic R., Weinberg A., Mehlotra R, & Zimmerman P. (2014). Association of toll-like receptor polymorphisms with HIV status in North Americans. Genes and immunity, 15(8), 569-577.
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