A genome-wide scan of 850,000 tag SNPs (Infinium CytoSNP-850k BeadChip, Illumina, San Diego, CA, United States) was performed at INGEMM, in the majority of the patients, but three (analyzed by array-CGH at ECEMC). They were analyzed by using the Chromosome Viewer tool contained in the Genome Studio package (Illumina). In Chromosome Viewer, gene call scores <0.15 at any locus were considered “no calls.” In addition, an allele frequency analysis was applied for all SNPs. All genomic positions were established according to the 2009 human genome build 19 (GRCh37/NCBI build 37.1). Deletion sizes were plotted on the genome browser (Figure 2 and Supplementary Data ) using the University of California at Santa Cruz Genome Browser1 .
Infinium cytosnp 850k beadchip
Manufactured by Illumina
Sourced in United States
The Infinium CytoSNP-850K BeadChip is a high-density single nucleotide polymorphism (SNP) array designed for cytogenetic analysis. It contains probes for approximately 850,000 genetic markers across the human genome.
Automatically generated - may contain errors
Lab products found in correlation
Chromosome viewer tool, by Illumina (3 mentions)
Genome studio package, by Illumina (2 mentions)
Iscan system, by Illumina (2 mentions)
Cytoscan 750k array, by Thermo Fisher Scientific (2 mentions)
Chromosome analysis suite chas software, by Thermo Fisher Scientific (2 mentions)
Bluefuse multi software, by Illumina (2 mentions)
Cytoscan hd array, by Illumina (1 mentions)
Genomestudio, by Illumina (1 mentions)
Gentra puregene kit, by Qiagen (1 mentions)
Bluefuse multi software v4, by Illumina (1 mentions)
Chromosome analysis suite chas, by Thermo Fisher Scientific (1 mentions)
Bluefuse multi 4, by Illumina (1 mentions)
16 protocols using infinium cytosnp 850k beadchip
1
Genome-wide SNP Analysis of Patients
2
Genomic DNA Analysis of IGF1 Gene
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Genomic DNA was isolated using the Chemagen automated DNA isolation work station (Janus Chemagic 360, Perkin Elmer). Single nucleotide variation and copy number variation (CNV) analysis of the IGF1 gene (NM_000618.5) was performed using Sanger sequencing and multiplex ligation-dependent probe amplification (SALSA MLPA Probemix P262 GHI, MRC Holland) according to standard procedures (details available upon request). Single nucleotide variation and CNV classification was performed using ACMG/AMP criteria [34, 35, 44] . Genome-wide CNV analysis was performed using Affymetrix CytoScan HD array, Illumina Infinium CytoSNP-850K BeadChip or Illumina Infinium GSA+MD-24 v1.0 Beadchip according to standard procedures (details available upon request).
3
Chromosomal Microarray Analysis Protocol
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The chromosomal microarray analysis was performed using the Infinium CytoSNP-850K BeadChip (SNP-array, Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Array scanning data were generated on the Illumina iScan system, and the results were analyzed by Bluefuse Multi 4.4 software. Each detected copy number variant was evaluated considering its frequency on the healthy human population (DGV, Database of Genomic Variant), gene content, and scientific literature.
4
Genome-Wide SNP Microarray Analysis in Tumor Samples
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Genome‐wide SNP microarray analysis was performed on genomic DNA extracted from the tumor samples using the Illumina Infinium CytoSNP‐850K BeadChip (Illumina, San Diego, CA) according to our standard protocol (5 ). The chip contains approximately 850 000 empirically selected single nucleotide polymorphisms (SNPs) spanning the entire genome with enriched coverage for 3262 genes of known cytogenetics relevance in both constitutional and cancer applications as defined by the International Collaboration for Clinical Genomics (ICCG) and the Cancer Genomics Consortium (CGC). The data were analyzed using CNV Workshop (7 ) and vendor provided analysis software (GenomeStudio). Deletions of ≥ 200Kb, duplications of ≥ 1Mb in a genomic region, loss of heterozygosity (LOH) of ≥ 5Mb or any changes below criteria but deemed to be clinically significant was reported.
5
Genome-wide SNP Profiling with Arrays
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Genomic DNA samples were extracted from peripheral blood cells or saliva following standard procedures. SNP-array experiments were performed using the Illumina Infinium CytoSNP 850 K BeadChip (Illumina, San Diego, USA), except for 810 cases which were carried out using the Affymetrix CytoScan 750 K Array (Affymetrix, Santa Clara, USA). Data were analyzed using either the BlueFuse™ Multi Analysis (Illumina, San Diego, USA) or the Chromosome Analysis Suite—ChAS Software (Affymetrix, Santa Clara, USA). Log2 ratio and B Allele Frequency (BAF) values were plotted along chromosomal coordinates, allowing the detection of both copy number changes and copy neutral regions of homozygosity (ROH).
6
Comprehensive Genomic Profiling with Array-CGH and CytoSNP
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All patients were analysed using an Array-CGH 4x180K (Agilent Technologies, Santa Clara, CA, USA) or Infinium CytoSNP-850K BeadChip (Illumina, San Diego, CA, USA) platform. Confirmation and segregation tests on patient’s and parents’ DNA were performed by fluorescence in situ hybridisation (FISH) analysis.
7
Genome-Wide SNP Array Analysis
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Single nucleotide polymorphism-array (SNP-array) analysis was performed on DNA of proband 1 and his parents using Infinium CytoSNP-850 K BeadChip (Illumina, San Diego, CA, USA) and in accordance with the manufacturer’s instructions. Array scanning data were generated by iScan system (Illumina, San Diego, CA, USA) and the results were analysed by Bluefuse Multi software (v 4.4).
8
Genome-wide SNP Genotyping Analysis
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A genome-wide scan of 850,000 tag SNPs (Illumina Infinium CytoSNP-850k BeadChip) in most of the patients at INGEMM. They were analyzed by using the Chromosome Viewer tool contained in the Genome Studio package (Illumina, San Diego, CA, USA) using the manufacturer’s instructions. All genomic positions were based upon NCBI Build 37 (dbSNP version 130), and genomic coordinates were established according to the 2009 human genome build 19 (GRCh37/NCBI build 37.1). Deletion sizes were plotted on the genome browser using the University of California at Santa Cruz Genome Browser (http://genome.ucsc.edu/ , accesed on 20 June 2022).
9
Genome-wide SNP Profiling and Array-CGH Analysis
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A genome‐wide scan of 850,00 tag SNPs was conducted on three patients, using the Illumina Infinium CytoSNP‐850 k BeadChip according to the manufacturer's specifications (Illumina). GenCall scores <0.15 at any locus were considered ‘no calls. Image data were analysed using the Chromosome Viewer tool contained in Genome Studio (Illumina). In addition, an allele frequency analysis was applied for all SNPs. All genomic positions were based upon NCBI Build 37 (dbSNP version 130). In patient number 3 used array‐CGH KaryoNim Prenatal 60 K was performed.
10
Genetic Analysis of Macular Dystrophy
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DNA was extracted from lymphocytes, and array comparative genomic hybridization analysis (Illumina Infinium CytoSNP-850K BeadChip, San Diego, CA) was performed to look for copy number variants, with manual analysis of MCDR1 and MCDR3. Whole blood was collected from the patient in an Ethylenediaminetetraacetic acid (EDTA) tube and DNA extracted using a standard automated method (QIAsymphony® AS instrument, Qiagen, Hombrechtikon,Switzerland) as recommended by the manufacturer. Sanger sequencing of the PRDM13 gene and the NCMD mutation hotspot 13 kb was performed by Molecular Vision Laboratory (Hillsboro, OR). Informed written consent was obtained from the family for genetic testing and for publication purpose. [6 (link)].
The research was conducted in accordance with the Declaration of Helsinki, and local institutional ethical requirements were met. The research, which adhered to ethical principles of medical research involving human subjects, was conducted in accordance with the Declaration of Helsinki, and local institutional ethical requirements were met.
The research was conducted in accordance with the Declaration of Helsinki, and local institutional ethical requirements were met. The research, which adhered to ethical principles of medical research involving human subjects, was conducted in accordance with the Declaration of Helsinki, and local institutional ethical requirements were met.
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