Infinium array

Manufactured by Illumina

Sourced in United States

The Infinium array is a high-throughput genotyping platform developed by Illumina. It is designed to analyze genetic variations across the human genome. The Infinium array provides a comprehensive solution for genetic research, enabling the simultaneous interrogation of thousands of genetic markers.

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31 protocols using infinium array

MicroRNA-related SNP Selection and Genotyping

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A total of 2,169 miRSNPs within the 3′ UTRs of the cancer associated genes were selected for genotyping. A SNP was selected if differential miRNA binding potential for the alternative alleles was predicted by at least two of four algorithms: 1. Mirsnpscore (29 (link)); 2. Miranda and 3. Sanger (both available through SNPinfo) (28 (link)); and 4. MicroSNiPer (30 (link)). Genotyping was performed using a custom Illumina Infinium array that included 211,115 SNPs (the iCOGS chip) (4 (link)). Genotypes were called using Illumina’s proprietary GenCall algorithm. SNPs were excluded from further analysis if the call rate was <95%, deviated from Hardy-Weinberg Equilibrium (HWE) in controls at P<10⁻⁷, or if genotypes were discrepant in more than 2% of duplicate samples.

Stegeman S., Amankwah E., Klein K., O’Mara T.A., Kim D., Lin H.Y., Permuth-Wey J., Sellers T.A., Srinivasan S., Eeles R., Easton D., Kote-Jarai Z., Olama A.A., Benlloch S., Muir K., Giles G.G., Wiklund F., Gronberg H., Haiman C.A., Schleutker J., Nordestgaard B.G., Travis R.C., Neal D., Pharoah P., Khaw K.T., Stanford J.L., Blot W.J., Thibodeau S., Maier C., Kibel A.S., Cybulski C., Cannon-Albright L., Brenner H., Kaneva R., Teixeira M.R., Consortium P., Spurdle A.B., Clements J.A., Park J.Y, & Batra J. (2015). A large scale analysis of genetic variants within putative miRNA binding sites in prostate cancer. Cancer discovery, 5(4), 368-379.

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Maize Pan-Genome SNP Discovery

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One hundred one bp Illumina paired-end reads from a set of 23 maize inbred lines were aligned to the B73/F2 pan-genome to discover SNPs in B73/F2 shared regions as well as in F2-specific regions. This set of lines was provided by the Cornfed program (A. Charcosset, personal communication) and had been chosen to maximize the genetic diversity of American and European temperate maize (Additional file 1: Table S7) [54 (link)]. B73 and F2 reads used previously (sampled to 20X) were also included as controls. Reads were aligned against the B73/F2 pan-genome sequence using Stampy v1.0.21 [72 (link)] and PCR duplicates were removed using SAMtools rmdup v0.1.18 [73 (link)]. SNPs were detected using SAMtools mpileup (-B) and VarScan v 2.3.6 (−-min-coverage 3 --min-avg-qual 30 --min-var-freq 0.9 --p-value 0.05) [74 (link)]. SNPs corresponding to Ns were discarded. For B73/F2 shared regions, SNPs with a different call between the B73 reference sequence and B73 Illumina reads were also discarded. For F2 novel regions, SNPs showing a different call in F2 reference and F2 Illumina reads were discarded, as well as SNPs covered by B73 reads. Our SNP discovery pipeline was tested using genotyping from a 50 k Illumina Infinium array [75 (link)], and showed a high agreement rate (> 99%).

Darracq A., Vitte C., Nicolas S., Duarte J., Pichon J.P., Mary-Huard T., Chevalier C., Bérard A., Le Paslier M.C., Rogowsky P., Charcosset A, & Joets J. (2018). Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, 19, 119.

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Chicken Genotyping and SNP Analysis

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All hens were genotyped for 57,636 single nucleotide polymorphisms (SNPs) using the Illumina Infinium array. The genotyping was performed by the SNP&SEQ Technology Platform (Uppsala University, Sweden). We aligned the sequences flanking the SNPs against the GRCg6a chicken reference genome to determine the physical positions of the SNPs. One hundred and eighty-eight SNPs were removed because of their very low representation in the population and 21,230 were monomorphic in the analysed sample, leaving 36,218 SNPs for GWAS.

Sallam M., Wilson P.W., Andersson B., Schmutz M., Benavides C., Dominguez‑Gasca N., Sanchez‑Rodriguez E., Rodriguez‑Navarro A.B., Dunn I.C., De Koning D, & Johnsson M. (2023). Genetic markers associated with bone composition in Rhode Island Red laying hens. Genetics, Selection, Evolution : GSE, 55, 44.

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Lifting SNP loci from Matina v1.1 to Pound 7

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The SNP loci previously genotyped with an Illumina Infinium array^{17 (link)} were lifted over from their original positions on Matina v1.1 to the Pound 7 contigs using blat and other UCSC tools^{37 (link)}. The alleles from the Pound 7 contigs were then checked for consistency against the Pound 7 genotypes called on the chip array.

Morrissey J., Stack J.C., Valls R, & Motamayor J.C. (2019). Low-cost assembly of a cacao crop genome is able to resolve complex heterozygous bubbles. Horticulture Research, 6, 44.

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Heterotic Pattern for Hybrid Wheat Breeding

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A genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding was investigated, and the study was based on 135 advanced elite winter wheat lines^{27 (link)}. A set of 1604 wheat hybrids produced from crosses among the 15 male lines and 120 female lines were then evaluated for grain yield (YLD) (Mg/ha) in 11 environments. Grain yield data for all

C_{2}^{135} = 9045

unique hybrids were predicted based on those of the phenotyped individuals. For the genotype data, the 135 lines were fingerprinted by using a 90,000 SNP array based on an Illumina Infinium array. After quality tests, 17,372 high-quality SNP markers were retained.
To study optimal designs for GS, 2556 hybrid combinations, produced by the half diallel mating design on 72 lines selected from the original 135 elite wheat lines, were analyzed in the article^{2 (link)}. An optimal training population with 600 individuals, determined by the r-score criterion^{28 (link)}, was used in the current study to build the GBLUP model for the performance evaluation on the 2556 hybrid combinations.

Chen S.P., Tung C.W., Wang P.H, & Liao C.T. (2023). A statistical package for evaluation of hybrid performance in plant breeding via genomic selection. Scientific Reports, 13, 12204.

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Genotyping of Prostate Cancer Loci

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Detailed information relating to the custom iCOGS Illumina Infinium array can be found in Eeles et al., 2013 [7] (link). With respect to the HOXB locus, 747 SNPs spanning the interval chr17:46201311–47382559 were genotyped on the iCOGS array, submitted by a combination of the PRACTICAL and OCAC consortia (Supplementary Figure S1).
To boost imputation performance, additional genotyping of 677 PrCa cases from the UK was conducted using the Illumina (San Diego, CA, USA) OMNI2.5 BeadChip according to the manufacturer's instructions. Further genotyping of the rs138213197 variant was carried out by Taqman assay (Applied Biosystems Inc., Foster City, CA, USA) for 2476 cases and 2198 controls from the UK and by MassARRAY iPLEX (Sequenom Inc., San Diego, CA, USA) for 3024 cases and 2725 controls from Sweden.

Saunders E.J., Dadaev T., Leongamornlert D.A., Jugurnauth-Little S., Tymrakiewicz M., Wiklund F., Al Olama A.A., Benlloch S., Neal D.E., Hamdy F.C., Donovan J.L., Giles G.G., Severi G., Gronberg H., Aly M., Haiman C.A., Schumacher F., Henderson B.E., Lindstrom S., Kraft P., Hunter D.J., Gapstur S., Chanock S., Berndt S.I., Albanes D., Andriole G., Schleutker J., Weischer M., Nordestgaard B.G., Canzian F., Campa D., Riboli E., Key T.J., Travis R.C., Ingles S.A., John E.M., Hayes R.B., Pharoah P., Khaw K.T., Stanford J.L., Ostrander E.A., Signorello L.B., Thibodeau S.N., Schaid D., Maier C., Kibel A.S., Cybulski C., Cannon-Albright L., Brenner H., Park J.Y., Kaneva R., Batra J., Clements J.A., Teixeira M.R., Xu J., Mikropoulos C., Goh C., Govindasami K., Guy M., Wilkinson R.A., Sawyer E.J., Morgan A., Easton D.F., Muir K., Eeles R.A, & Kote-Jarai Z. (2014). Fine-Mapping the HOXB Region Detects Common Variants Tagging a Rare Coding Allele: Evidence for Synthetic Association in Prostate Cancer. PLoS Genetics, 10(2), e1004129.

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Genotyping and Homozygosity Mapping

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DNAs of studied individuals were genotyped at the iGE3 Platform of the University of Geneva, Switzerland, using an Illumina Infinium array (San Diego, CA, USA; GSAMD-24v2.0). Genotype values were obtained with GenomeStudio (Illumina). Homozygosity mapping was obtained by the use of the PLINK software. Due to the high degree of consanguinity, SNP genotyping was chosen as a complementary analysis to narrow down homozygous regions and reduce the number of candidate variants.

Salmaninejad A., Bedoni N., Ravesh Z., Quinodoz M., Shoeibi N., Mojarrad M., Pasdar A, & Rivolta C. (2020). Whole exome sequencing and homozygosity mapping reveals genetic defects in consanguineous Iranian families with inherited retinal dystrophies. Scientific Reports, 10, 19413.

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Genotyping with Illumina Infinium Array

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Genotyping was conducted using the custom Illumina Infinium array (iCOGS) (14 (link)). DNA samples containing each of the variants were included in iCOGS genotyping as positive controls and were used to inform genotype calling. Genotypes were called with the GenCall algorithm. Descriptions of sample and genotype quality control have been published (14 (link), 16 (link)). Cluster plots for rare variants for this study were manually evaluated relative to positive control samples.

Shimelis H., Mesman R.L., Von Nicolai C., Ehlen A., Guidugli L., Martin C., Calléja F.M., Meeks H., Hallberg E., Hinton J., Lilyquist J., Hu C., Aalfs C.M., Aittomäki K., Andrulis I., Anton-Culver H., Arndt V., Beckmann M.W., Benitez J., Bogdanova N.V., Bojesen S.E., Bolla M.K., Borresen-Dale A.L., Brauch H., Brennan P., Brenner H., Broeks A., Brouwers B., Brüning T., Burwinkel B., Chang-Claude J., Chenevix-Trench G., Cheng C.Y., Choi J.Y., Collée M., Cox A., Cross S.S., Czene K., Darabi H., Dennis J., Dörk T., dos-Santos-Silva I., Dunning A.M., Fasching P.A., Figueroa J., Flyger H., García-Closas M., Giles G.G., Glendon G., Guénel P., Haiman C.A., Hall P., Hamann U., Hartman M., Hogervorst F.B., Hollestelle A., Hopper J.L., Ito H., Jakubowska A., Kang D., Kosma V.M., Kristensen V., Collaborators F.N., Lai K.N., Lambrechts D., Le Marchand L., Li J., Lindblom A., Lophatananon A., Lubinski J., Machackova E., Mannermaa A., Margolin S., Marme F., Matsuo K., Miao H., Michailidou K., Milne R.L., Muir K., Neuhausen S.L., Nevanlinna H., Olson J.E., Olswold C., Oosterwijk J.J., Osorio A., Peterlongo P., Peto J., Pharoah P.D., Pylkäs K., Radice P., Rashid M.U., Rhenius V., Rudolph A., Sangrajrang S., Sawyer E.J., Schmidt M.K., Schoemaker M.J., Seynaeve C., Shah M., Shen C.Y., Shrubsole M., Shu X.O., Slager S., Southey M.C., Stram D.O., Swerdlow A., Teo S.H., Tomlinson I., Torres D., Truong T., van Asperen C.J., van der Kolk L.E., Wang Q., Winqvist R., Wu A.H., Yu J.C., Zheng W., Zheng Y., Leary J., Walker L., Foretova L., Fostira F., Claes K.B., Varesco L., Moghadasi S., Easton D.F., Spurdle A., Devilee P., Vrieling H., Monteiro A.N., Goldgar D.E., Carreira A., Vreeswijk M.P, & Couch F.J. (2017). BRCA2 hypomorphic missense variants confer moderate risks of breast cancer. Cancer research, 77(11), 2789-2799.

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Genetic Variants in Small GTPases and Ovarian Cancer Risk

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We studied 18,736 EOC patients (10,316 of serous histology) and 26,138 controls who participated in Ovarian Cancer Association Consortium studies; all participants were of European ancestry.[11 (link)] This included participants from the GWAS which was used for variant selection (described above)[10 (link)] and an additional 10,243 patients and 16,932 controls. Genotyping used a custom Illumina Infinium array. [11 (link)] SNPs were excluded according to the following criteria: no genotype call; monomorphism; call rate less than 95% and minor allele frequency > 0.05 or call rate less than 99% with minor allele frequency < 0.05; evidence of deviation of genotype frequencies from Hardy-Weinberg equilibrium (p < 10⁻⁷); greater than 2% discordance in duplicate pairs. Overall, 322 small GTPase gene SNPs were genotyped and passed QC; numbers of participants with data for each SNP vary, as some DNA samples failed QC for particular SNPs. This study was reviewed and approved by the Mayo Clinic Institutional Review Board as protocol 1367–05.

Earp M., Tyrer J.P., Winham S.J., Lin H.Y., Chornokur G., Dennis J., Aben K.K., Anton‐Culver H., Antonenkova N., Bandera E.V., Bean Y.T., Beckmann M.W., Bjorge L., Bogdanova N., Brinton L.A., Brooks-Wilson A., Bruinsma F., Bunker C.H., Butzow R., Campbell I.G., Carty K., Chang-Claude J., Cook L.S., Cramer D.W., Cunningham J.M., Cybulski C., Dansonka-Mieszkowska A., Despierre E., Doherty J.A., Dörk T., du Bois A., Dürst M., Easton D.F., Eccles D.M., Edwards R.P., Ekici A.B., Fasching P.A., Fridley B.L., Gentry-Maharaj A., Giles G.G., Glasspool R., Goodman M.T., Gronwald J., Harter P., Hein A., Heitz F., Hildebrandt M.A., Hillemanns P., Hogdall C.K., Høgdall E., Hosono S., Iversen E.S., Jakubowska A., Jensen A., Ji B.T., Jung A.Y., Karlan B.Y., Kellar M., Kiemeney L.A., Kiong Lim B., Kjaer S.K., Krakstad C., Kupryjanczyk J., Lambrechts D., Lambrechts S., Le N.D., Lele S., Lester J., Levine D.A., Li Z., Liang D., Lissowska J., Lu K., Lubinski J., Lundvall L., Massuger L.F., Matsuo K., McGuire V., McLaughlin J.R., McNeish I., Menon U., Milne R.L., Modugno F., Moysich K.B., Ness R.B., Nevanlinna H., Odunsi K., Olson S.H., Orlow I., Orsulic S., Paul J., Pejovic T., Pelttari L.M., Permuth J.B., Pike M.C., Poole E.M., Rosen B., Rossing M.A., Rothstein J.H., Runnebaum I.B., Rzepecka I.K., Schernhammer E., Schwaab I., Shu X.O., Shvetsov Y.B., Siddiqui N., Sieh W., Song H., Southey M.C., Spiewankiewicz B., Sucheston-Campbell L., Tangen I.L., Teo S.H., Terry K.L., Thompson P.J., Thomsen L., Tworoger S.S., van Altena A.M., Vergote I., Vestrheim Thomsen L.C., Vierkant R.A., Walsh C.S., Wang-Gohrke S., Wentzensen N., Whittemore A.S., Wicklund K.G., Wilkens L.R., Woo Y.L., Wu A.H., Wu X., Xiang Y.B., Yang H., Zheng W., Ziogas A., Lee A.W., Pearce C.L., Berchuck A., Schildkraut J.M., Ramus S.J., Monteiro A.N., Narod S.A., Sellers T.A., Gayther S.A., Kelemen L.E., Chenevix-Trench G., Risch H.A., Pharoah P.D., Goode E.L, & Phelan C.M. (2018). Variants in genes encoding small GTPases and association with epithelial ovarian cancer susceptibility. PLoS ONE, 13(7), e0197561.

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Development of CottonSNP80K Genotyping Array

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To develop the genome-wide CottonSNP80K chip, an Illumina Infinium array, as well as intraspecific SNPs data from sequencing of the allotetraploid cotton G. hirsutum acc. TM-1 [22 (link)] and re-sequencing of 100 different cultivars in G. hirsutum with 5× coverage on average [27 (link)] were used. In total, 1,372,195 putative intraspecific SNPs with MAF > 0.1 were detected and chosen for inclusion on the array. When designing the array, subsequent filtering steps included the following: (1) genotype accuracy was required to be >99.12%; (2) SNPs in repeat regions were filtered; (3) no other SNPs or InDels were permitted in the 50 bp flanking the SNP site; (4) heterozygosity rates were required to be <15%; (5) SNP cluster analysis was carried out. After these filters were applied, 175,192 SNPs remained and were submitted through the Illumina Assay Design Tool to determine array design scores for each marker. SNPs in gene regions with Illumina design scores >0.7, and SNPs in intergenic regions with Illumina design scores >0.9 remained. Further, the inter-marker distance flanking the SNPs was >2100 bp. The remaining 82,259 SNP markers were used for the manufacture of the CottonSNP80K array by Illumina (Additional file 6: Table S5). The scheme of CottonSNP80K development is shown in Additional file 1: Figure S1.

Cai C., Zhu G., Zhang T, & Guo W. (2017). High-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis. BMC Genomics, 18, 654.

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