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).
Genome studio package
Manufactured by Illumina
Sourced in United States
The Genome Studio package is a suite of software tools and hardware components designed for the analysis and interpretation of genomic data. It provides a comprehensive platform for processing, visualizing, and managing data generated from Illumina's next-generation sequencing (NGS) instruments. The Genome Studio package offers core functionalities for the analysis of gene expression, genotyping, and other genomic applications.
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6 protocols using genome studio package
1
Genome-wide SNP Genotyping Analysis
2
Genome-wide SNP Analysis of Patients
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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 .
3
Family-based Genetic Segregation Analysis
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In addition to the study of the probands, the analysis of all available first-degree relatives of the index cases was completed. Samples were obtained from the parents of the proband and siblings and the genetic segregation study was performed by sanger sequencing.
In patient 2, we performed a SNP array to confirm the deletion detected in the proband and her relatives. For this purpose, a SNP array study was carried out using the Infinium OmniExpressExome 8 v1.6 platform (Illumina). Image data were analyzed using the Chromosome Viewer tool contained in the Genome Studio package (Illumina, San Diego, CA, USA). In Chromosome Viewer, gene call scores < 0.15 at any locus were considered “no calls”. In addition, allele frequency analysis was applied for all SNPs. All genomic coodinates 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 os California at Santa Cruz Genome Browser (http://genome.ucsc.edu/ , accessed on 25 June 2021).
In unaffected carriers, a complete and specific diagnostic follow-up was performed in order to rule out the disease.
In patient 2, we performed a SNP array to confirm the deletion detected in the proband and her relatives. For this purpose, a SNP array study was carried out using the Infinium OmniExpressExome 8 v1.6 platform (Illumina). Image data were analyzed using the Chromosome Viewer tool contained in the Genome Studio package (Illumina, San Diego, CA, USA). In Chromosome Viewer, gene call scores < 0.15 at any locus were considered “no calls”. In addition, allele frequency analysis was applied for all SNPs. All genomic coodinates 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 os California at Santa Cruz Genome Browser (
In unaffected carriers, a complete and specific diagnostic follow-up was performed in order to rule out the disease.
4
Genotyping 384 SNPs in Aphid Genes
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Target SNPs were identified in control, chemosensory and detoxification genes in the capture sequencing data set. To design our custom set of 384 SNPs, flanking sequences of 100 bp to either side of target SNPs were processed using the Illumina Assay Design Tool (ADT) in order to confirm their suitability for the assay, and the finalized panel of 384 SNPs was ordered from Illumina (Illumina, San Diego, CA, USA). The final 384 SNPs comprised 222 in chemosensory genes, 71 in nonchemosensory genes of interest (P450s, PS and Rad51C) and 91 in control genes. One hundred and twenty‐seven target SNPs were in genes identified as having a significant excess of outlier SNPs in the capture sequencing data set. SNP IDs, chromosome positions and flanking sequences for the panel of 384 SNPs are available in Table S1 (Supporting information).
SNP data were analysed from each plate in turn using the Genotyping module of Illumina's GenomeStudio package (Illumina). SNPs were filtered for quality using standard thresholds, SNPs with no polymorphism, SNPs with no heterozygotes and SNPs with indication of copy number variation were also removed. This left 179 high‐quality SNPs for further analysis (Table S2, Supporting information). Aphids with more than 12 null SNP calls were removed from the data set, leaving data for 373 aphids.
SNP data were analysed from each plate in turn using the Genotyping module of Illumina's GenomeStudio package (Illumina). SNPs were filtered for quality using standard thresholds, SNPs with no polymorphism, SNPs with no heterozygotes and SNPs with indication of copy number variation were also removed. This left 179 high‐quality SNPs for further analysis (Table S2, Supporting information). Aphids with more than 12 null SNP calls were removed from the data set, leaving data for 373 aphids.
5
High-Throughput Genotyping for Genetic Variance
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Following genotyping, five DNA samples per each wild-type (WT), Neo/+, WT/−, Neo/Neo, and Neo/− groups were sent to GeneSeek Inc. (a NeoGene company, Lincoln, Nebraska USA). DNA samples were run on the GigaMuga mouse genotyping chips (Illumina), for a total of 143,000 SNPs. After quality control and removal of the X and Y chromosomes, we performed analyses using 133,559 SNPs on each of 17 samples, 4–5 per group. QC and SNP calls were done using the GenomeStudio Package (Illumina) by GeneSeek. Further analysis was performed using the SNPRelate Package in R to calculate the SNP frequencies and the relative inbreeding69 (link). The SNP frequencies were used to calculate the additive genetic variance70 .
6
Characterizing Genomic Variants via Microarray
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Saliva-derived genomic DNA from the index case was quantified using Nanodrop1000 spectrophotomer (Thermofisher) and Qubit (Thermofisher). Chromosomal microarray analysis was performed with the genome-wide scan of 850,000 tag SNPs (Illumina Infinum CutoSNP-850k BeadChIP) following standard laboratory procedures. Copy-number variations were determined using the Chromosome Viewer tool contained in the Genome Studio package (Illumina). In Chromosome Viewer, gene call score <0.15 at a locus were considered "no calls". In addition, all allele frequency analysis was applied for all SNPs.
Long-range PCR PCR products were generated from DNA samples of the KOS14 index case using Immolase DNA Taq polymerase (Bioline) and staggered PCR primers. An amplicon was obtained using C4F-ACCGGAGTTCCTTTCAGAGACA and TR3-GGTTCAGGCAGGGTACAGGACAT. The resulting PCR product was subject to Sanger sequencing in both directions using BigDye Terminator v3.1 kit (Thermofisher) and run on ABI 3730 DNA 48-capillary sequencer. The resulting electropherograms were analysed in Sequencher and subject to BLAST in the UCSC genome browser.
Long-range PCR PCR products were generated from DNA samples of the KOS14 index case using Immolase DNA Taq polymerase (Bioline) and staggered PCR primers. An amplicon was obtained using C4F-ACCGGAGTTCCTTTCAGAGACA and TR3-GGTTCAGGCAGGGTACAGGACAT. The resulting PCR product was subject to Sanger sequencing in both directions using BigDye Terminator v3.1 kit (Thermofisher) and run on ABI 3730 DNA 48-capillary sequencer. The resulting electropherograms were analysed in Sequencher and subject to BLAST in the UCSC genome browser.
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