Humancytosnp 12

Manufactured by Illumina

Sourced in United States

The HumanCytoSNP-12 is a microarray platform designed for cytogenomic analysis. It provides comprehensive coverage of genomic regions associated with constitutional chromosomal abnormalities. The HumanCytoSNP-12 is capable of detecting copy number variations, loss of heterozygosity, and regions of homozygosity across the human genome.

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Lab products found in correlation

Bluefuse multi v4, by Illumina (2 mentions) 24sure, by Illumina (2 mentions) Human karyomapping beadarray, by Illumina (2 mentions) Nexus copy number software, by BioDiscovery (1 mentions) Hiseq 2500, by Illumina (1 mentions) Sureselect whole exome v6, by Agilent Technologies (1 mentions) Cytoscan 750k, by Thermo Fisher Scientific (1 mentions) Infinium coreexome 24, by Illumina (1 mentions) Genome wide human snp array 6, by Thermo Fisher Scientific (1 mentions) Axiom genome wide ceu 1 array, by Thermo Fisher Scientific (1 mentions) Karyostudio, by Illumina (1 mentions) Omniexpressexome, by Illumina (1 mentions) Goldengate assay, by Illumina (1 mentions)

Spelling variants of this product

HumanCytoSNP-12 BeadChip (23 citations) HumanCytoSNP-12 BeadChip platform (10 citations) HumanCytoSNP-12 DNA Analysis BeadChip (5 citations) HumanCytoSNP-12 v2.1 BeadChip kit (4 citations) HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (4 citations) HumanCytoSNP-12 v2.1 chips (3 citations) Infinium II SNP array (HumanCytoSNP-12 v2.1 DNA Analysis BeadChip, (3 citations) HumanCytoSNP-12 v2·1 microarrays (2 citations) Infinium HumanCytoSNP-12 BeadChip (2 citations) Infinium HumanCytoSNP-12 (2 citations)

15 protocols using humancytosnp 12

Single-cell DNA analysis protocols

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For array CGH analysis, 4 μl aliquots of Sureplex single cell amplified DNA Products (PB1, PB2, oocyte or blastomere) were processed on microarray slides (24Sure; Illumina, USA). The data was imported and analysed using dedicated software (BlueFuse Multi v 4.0; Illumina, USA).
For SNP genotyping, 400 ng of genomic DNA or 8 μl of WGA products from the single cell and embryo samples (PB1, PB2, oocyte, single blastomere or whole embryo) were processed on a SNP genotyping beadarray (Human CytoSNP-12 or Human Karyomapping beadarray; Illumina, San Diego, CA, USA) for ~300K SNPs, using a shortened protocol and the genotype data analysed using a dedicated software programme for karyomapping (BlueFuse Multi v 4.0; Illumina, San Diego, CA, USA) or exported as a text file for analysis in Micrsoft Excel¹².

Ottolini C.S., Newnham L., Capalbo A., Natesan S.A., Joshi H.A., Cimadomo D., Griffin D.K., Sage K., Summers M.C., Thornhill A.R., Housworth E., Herbert A.D., Rienzi L., Ubaldi F.M., Handyside A.H, & Hoffmann E.R. (2015). “Genome-wide recombination and chromosome segregation in human oocytes and embryos reveal selection for maternal recombination rates”. Nature genetics, 47(7), 727-735.

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Identifying Recessive Skin Disorder Genes

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Genomic DNA was extracted from peripheral blood or saliva samples with standard methods. Homozygosity mapping was performed in samples of index patients using HumanCytoSNP‐12 (Illumina, San Diego, CA, USA), following the manufacturer's instructions. Generated data were analyzed with Nexus Copy Number™ software (BioDiscovery, Hawthorne CA, USA). The longest regions of homozygosity were extracted for each index case and compared to the locations of known ARCI genes.

Lima Cunha D., Alakloby O.M., Gruber R., Kakar N., Ahmad J., Alawbathani S., Plank R., Eckl K., Krabichler B., Altmüller J., Nürnberg P., Zschocke J., Borck G., Schmuth M., Alabdulkareem A.S., Abdulaziz Alnutaifi K, & Hennies H.C. (2019). Unknown mutations and genotype/phenotype correlations of autosomal recessive congenital ichthyosis in patients from Saudi Arabia and Pakistan. Molecular Genetics & Genomic Medicine, 7(3), e539.

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Genome-wide SNP Analysis for Rare Disorder

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Genome-wide SNP (single nucleotide polymorphism) array was performed using Illumina HumanCytoSNP 12 in Patient 1, Patient 2 and both parents to search for regions of homozygosity by descent that might contain the mutated gene.

Shahni R., Cale C.M., Anderson G., Osellame L.D., Hambleton S., Jacques T.S., Wedatilake Y., Taanman J.W., Chan E., Qasim W., Plagnol V., Chalasani A., Duchen M.R., Gilmour K.C, & Rahman S. (2015). Signal transducer and activator of transcription 2 deficiency is a novel disorder of mitochondrial fission. Brain, 138(10), 2834-2846.

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SNP Genotyping for Karyomapping

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For SNP genotyping, 400-ng samples of parental and reference genomic DNA or 8 μl of MDA product from the embryo samples were processed according to the standard protocol, modified to reduce the initial whole-genome amplification and hybridization steps so that genotyping on a 300K SNP bead array (Human CytoSNP-12; Illumina, San Diego, CA) could be completed in less than 24 h, over a period of 2 days. Bead array data were then imported directly into dedicated software for karyomapping (BlueFuse Multi, Version 4.0; Illumina). With genomic DNA samples, call rates of >98% were generally achieved. With MDA products from single blastomeres and multiple-cell trophectoderm samples, call rates were significantly lower, in the 75–95% range. However, karyomap analysis of these samples was highly consistent, indicating few genotyping errors (excluding ADO). Samples with call rates of <60% (for euploid samples), indicating failure of amplification, had a high incidence of erroneous heterozygous calls, which prevented reliable karyomap analysis. These samples were excluded from further analysis.

Natesan S.A., Bladon A.J., Coskun S., Qubbaj W., Prates R., Munne S., Coonen E., Dreesen J.C., Stevens S.J., Paulussen A.D., Stock-Myer S.E., Wilton L.J., Jaroudi S., Wells D., Brown A.P, & Handyside A.H. (2014). Genome-wide karyomapping accurately identifies the inheritance of single-gene defects in human preimplantation embryos in vitro. Genetics in Medicine, 16(11), 838-845.

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Single-cell DNA analysis protocols

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Comprehensive Embryo Evaluation and Prenatal Diagnosis

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Embryos undergo ranking based on both PGT‐M results and morphology grading, which is carried out by geneticists, embryologists, and gynecologists. Following this process, embryos are carefully selected for post‐resuscitation intrauterine transfer. A clinical pregnancy is considered to have occurred when female human chorionic gonadotropin (HCG) levels increase and gestational sac formation is confirmed via B‐ultrasound on day 19 after transplantation. Amniocentesis prenatal diagnosis is typically performed during the 16–18th weeks of gestation. Fetal chromosomal analysis is carried out using the Human cytoSNP‐12 (Illumina, USA) chip and conventional karyotype. Additionally, mutations are assessed by Gap‐PCR for deletional α‐Thal, Sanger sequencing for rare monogenic disorders (RMD), and RDB‐PCR for β‐thalassemia (β‐Thal).

Huang P., Lan Y., Zhou H., Lin L., Shu J., Wang C., Zhao X., Liang L., He S., Mou J., Zhang X., Qiu Q, & Wei H. (2023). Comprehensive application of multiple molecular diagnostic techniques in pre‐implantation genetic testing for monogenic. Molecular Genetics & Genomic Medicine, 12(1), e2293.

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Chromosomal Microarray Analysis in Siblings

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EDTA blood samples were collected from P1, P2, and both parents after obtaining written informed consent. Chromosomal microarray was performed using Illumina HumanCytoSNP-12 on DNA obtained from peripheral blood samples of both affected siblings. The genome-wide resolution of this array is ~30kb.

Upadhyai P., Amiri E.F., Guleria V.S., Bielas S.L., Girisha K.M, & Shukla A. (2020). Recurrent 1q21.1 Deletion Syndrome: Report on Variable Expression, Non-Penetrance and Review of Literature. Clinical dysmorphology, 29(3), 127-131.

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Comprehensive Genetic Screening and Embryo Selection

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The case.12 was conducted with long-acting GnRH agonist long protocol in follicular phase and the other eleven female patients were treated with a long luteal phase stimulation protocol for controlled ovarian stimulation (COS). Oocytes were observed closely after ICSI, and all embryos were transferred into equilibrated medium and cultured at 37°Cin a CO₂ incubator. The embryos were scored on Day3 and Day5/6 according to the criterion thatembryos on Day3 that scored ≥6 C-II were considered high-quality embryos, andblastocysts on Day5/6 that scored ≥3BB were considered high-quality blastocysts.
Case.8 performed blastomeres biopsied on Day3, and the others were biopsied at blastocyst stage on Day5/6. Two to five cells were biopsied, and comprehensive gene amplification was performed. Next, these biopsied cells were assessed by single nucleotide polymorphism microarray (SNP microarray) (HumanCytoSNP-12, Illumina company, resolution about 5-10 M) or next generation sequencing (NGS) (Hiseq2500, Illumina company, resolution about 4 M) technology. Then, vitrification was performed, and embryos identified as euploidy were subjected to frozen-thawed embryo transfer.

Li G., Shi W., Niu W., Xu J., Guo Y., Su Y, & Sun Y. (2020). The influence of balanced complex chromosomal rearrangements on preimplantation embryonic development potential and molecular karyotype. BMC Genomics, 21, 326.

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Genetic Insights into SNIP1-Related Disorder in Old Order Amish

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We identified a total of 51 individuals of Old Order Amish descent affected with SNIP1-related disorder through clinics who provide care for the Amish communities (The Community Health Clinic; Indiana, New Leaf Center; Ohio, Center for Special Children; Wisconsin, Clinic for Special Children; Pennsylvania). We conducted a historical review of clinical information and undertook physical examination and a parent survey for 35 of the affected children available for evaluation considering geographical restrictions. Blood/buccal samples were obtained for DNA extraction using standard techniques from affected individuals, their parents and unaffected siblings with informed consent. Single-nucleotide polymorphism (SNP) genotyping was performed using HumanCytoSNP-12 (v2.1 beadchip array, Illumina). WES (BGI Seq) involved: Agilent Sureselect Whole Exome v6 targeting, read alignment (BWA-MEM (v0.7.17), mate-pairs fixed and duplicates removed (Picard v2.15.0), InDel realignment/base quality recalibration (GATK v3.7.0), single-nucleotide variant (SNV)/InDel detection (GATK HaplotypeCaller), annotation (Alamut v1.10) and read depth (GATK DepthOfCoverage). Copy number variants (CNVs) were detected using both ExomeDepth (https://cran.r-project.org/web/packages/ExomeDepth) and SavvyCNV [33 ]. Dideoxy sequencing was undertaken using standard techniques.

Ammous Z., Rawlins L.E., Jones H., Leslie J.S., Wenger O., Scott E., Deline J., Herr T., Evans R., Scheid A., Kennedy J., Chioza B.A., Ames R.M., Cross H.E., Puffenberger E.G., Harries L., Baple E.L, & Crosby A.H. (2021). A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PLoS Genetics, 17(9), e1009803.

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Confirmatory Testing for High-Risk GW-NIPS Results

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Pre-and postnatal confirmatory testing options were available to couples and were taken up at their discretion. Uptake of these options varied depending on the personal preferences of each couple. For all high risk gw-NIPS results, confirmatory diagnostic testing was recommended. For low risk results, diagnostic testing was available and ultrasound surveillance was recommended. Samples for prenatal diagnosis were obtained via CVS or amniocentesis. Postnatal samples for study included umbilical cord, newborn blood, and saliva. Diagnostic testing was performed using single-nucleotide polymorphism (SNP) microarray (HumanCytoSNP-12 or Infinium CoreExome-24, Illumina Inc., or CytoScan 750 K, Affymetrix, Santa Clara, CA, USA), or by using conventional karyotyping.
Pregnancy outcome data were obtained through records of pre-or postnatal diagnostic testing, or by a member of the VCGS NIPS genetics counseling team confirming with the patient's referring practitioner, or with the patient themselves, that there had been a normal newborn physical exam following a low risk gw-NIPS result. Newborn physical exams were performed by an experienced obstetrician or pediatrician. A normal newborn physical exam was considered to support a low risk NIPS result. The type of pregnancy outcome data collected for each case is listed in Tables 1 and2.

Flowers N.J., Burgess T., Giouzeppos O., Shi G., Love C.J., Hunt C.E., Scarff K.L., Archibald A.D, & Pertile M.D. (2020). Genome-wide noninvasive prenatal screening for carriers of balanced reciprocal translocations. Genetics in medicine : official journal of the American College of Medical Genetics, 22(12).

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