Log In Sign up
The largest database of trusted experimental protocols

Humancnv370

Manufactured by Illumina
Visit Supplier
Sourced in United States

The HumanCNV370 is a microarray-based laboratory instrument designed for the detection and analysis of copy number variations (CNVs) in human genomic samples. The core function of this product is to provide a high-throughput and cost-effective platform for researchers to study genetic variations associated with various human diseases and conditions.

Automatically generated - may contain errors

Lab products found in correlation

Humanhap300, by Illumina (4 mentions) Omniexpress, by Illumina (3 mentions) Omni2, by Illumina (3 mentions) Genome wide human snp array 6, by Thermo Fisher Scientific (2 mentions) Omni1, by Illumina (2 mentions) Humanexome 12, by Illumina (1 mentions) Hiseq 2000, by Illumina (1 mentions) Genome analyzer iix, by Illumina (1 mentions) Omniexpress beadchip, by Illumina (1 mentions) Humanhap660, by Illumina (1 mentions) Humanhap610, by Illumina (1 mentions) Humanomniexpress, by Illumina (1 mentions) Beadchip arrays, by Illumina (1 mentions)

Spelling variants of this product

Humancnv370-Duo BeadChip (3 citations) HumanCNV370-Quad BeadChip (2 citations) HumanCNV370-Quad v3.0 BeadChips (2 citations) HumanCNV370-Duo bead array (2 citations) HumanCNV370-Duo (2 citations)

6 protocols using humancnv370

1

Genome-Wide Genotyping and Imputation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Icelandic chip-typed samples were assayed using the Illumina HumanHap300, HumanCNV370, HumanHap610, HumanHap1M, HumanHap660, Omni-1, Omni 2.5 or Omni Express bead chips at deCODE genetics. SNPs were excluded if they had (i) yield less than 95%, (ii) minor allele frequency less than 1% in the population or (iii) significant deviation from Hardy-Weinberg equilibrium in the controls (P <0.001), (iv) if they produced an excessive inheritance error rate (over 0.001), or (v) if there was substantial difference in allele frequency between chip types (from just a single chip if that resolved all differences, but from all chips otherwise). All samples with a call rate below 97% were excluded from the analysis. For the HumanHap series of chips, 304,937 SNPs were used for long range phasing, whereas for the Omni series of chips 564,196 SNPs were included. The final set of SNPs used for long-range phasing was composed of 707,525 SNPs.
Genotyping of the Russian PTB cases and controls has been done using Affymetrix Genome-Wide Human SNP Array 6.0 and SNPs across the genome were imputed as described previously12 . Association analysis of the HLA SNPs rs557011, rs9271378 and rs9272785 has been done using PLINK38 (link).
Sveinbjornsson G., Gudbjartsson D.F., Halldorsson B.V., Kristinsson K.G., Gottfredsson M., Barrett J.C., Gudmundsson L.J., Blondal K., Gylfason A., Gudjonsson S.A., Helgadottir H.T., Jonasdottir A., Jonasdottir A., Karason A., Kardum L.B., Knežević J., Kristjansson H., Kristjansson M., Love A., Luo Y., Magnusson O.T., Sulem P., Kong A., Masson G., Thorsteinsdottir U., Dembic Z., Nejentsev S., Blondal T., Jonsdottir I, & Stefansson K. (2016). HLA class II sequence variants influence tuberculosis risk in populations of European ancestry. Nature genetics, 48(3), 318-322.
+ Open protocol
+ Expand
2

Genetic Variants in Aquaporin-4 Linked to Neurological Disorders

Check if the same lab product or an alternative is used in the 5 most similar protocols
Target AQP4 SNPs of interest were identified first based on SNPs that had previously been associated with altered outcomes in neurological disorders, including TBI and stroke [13] (link), [14] (link), [15] (link), [16] (link), and second based upon SNP coverage available within the gene array platform used with the present subjects' data set. Genome-wide SNP genotyping was performed through Illumina genome array platforms, including HumanExome-12, v1.0, HumanOmniExpressExome-8, HumanOmniExpressExome-8, Illumina 660, Illumina HumanCNV370, and Illumina OmniExpress. The final panel set consisted of five AQP4 SNPs: rs335929, rs3763043, rs3763040, rs9951307, and rs3875089. Those with one or two copies of the minor allele were identified as “carriers”, whereas homozygotes for the common major allele were classified as “noncarriers”. Participants carrying one or two copies of the minor allele were pooled for all SNPs because of the inadequate sample sizes of homozygous minor allele carriers in most genotyped SNPs.
Burfeind K.G., Murchison C.F., Westaway S.K., Simon M.J., Erten-Lyons D., Kaye J.A., Quinn J.F, & Iliff J.J. (2017). The effects of noncoding aquaporin-4 single-nucleotide polymorphisms on cognition and functional progression of Alzheimer's disease. Alzheimer's & Dementia : Translational Research & Clinical Interventions, 3(3), 348-359.
+ Open protocol
+ Expand
3

Whole-Genome Sequencing and Genotyping of Icelandic Samples

Cited 2 times
Check if the same lab product or an alternative is used in the 5 most similar protocols
Illumina BeadChip genotyping of Icelandic samples was performed on a HumanHap300, HumanCNV370, HumanHap610, HumanHap1M,, HumanHap660, Omnil, Omni2.5, or OmniExpress BeadChip at deCODE Genetics15 (link). Single-track genotyping using the Centaurus (Nanogen) platform38 (link) or Sanger sequencing was performed to validate and improve imputation of reported variants in Iceland and for association testing in other populations. Whole-genome sequencing was performed for 2,636 individuals selected for various conditions. All individuals were sequenced to a minimum depth of 10× (average of 22×)15 (link). Paired-end libraries for sequencing were prepared according to the manufacturer’s instructions (Illumina, TruSeq). Sequencing by synthesis was performed on Illumina Genome Analyzer IIx and/or HiSeq 2000 instruments, and reads were aligned to NCBI Build 36 of the human reference sequence using Burrows–Wheeler Aligner (BWA) 0.5.9 (ref. 39 (link)).
Helgadottir A., Gretarsdottir S., Thorleifsson G., Hjartarson E., Sigurdsson A., Magnusdottir A., Jonasdottir A., Kristjansson H., Sulem P., Oddsson A., Sveinbjornsson G., Steinthorsdottir V., Rafnar T., Masson G., Jonsdottir I., Olafsson I., Eyjolfsson G.I., Sigurdardottir O., Daneshpour M.S., Khalili D., Azizi F., Swinkels D.W., Kiemeney L., Quyyumi A.A., Levey A.I., Patel R.S., Hayek S.S., Gudmundsdottir I.J., Thorgeirsson G., Thorsteinsdottir U., Gudbjartsson D.F., Holm H, & Stefansson K. (2016). Variants with large effects on blood lipids and the role of cholesterol and triglycerides in coronary disease. Nature genetics, 48(6), 634-639.
+ Open protocol
+ Expand
4

Genomic Variation Catalog for Healthy Controls

Check if the same lab product or an alternative is used in the 5 most similar protocols
The Database of Genomic Variants (DGV; http://dgv.tcag.ca/, 6 June 2016, date last accessed) was used as a reference dataset to exclude benign polymorphisms. DGV holds information on common CNVs found in more than 20 000 healthy control samples and serves as a catalog of control data for correlating genomic variation with phenotypic data (MacDonald et al., 2013 (link)). In addition, genotype and phenotype information was drawn for the Estonian general population samples (n = 3188) from the EGCUT, previously subjected to SNP genotyping with HumanCNV370 (n = 489) and HumanOmniExpress (n = 2699) BeadChip arrays (Illumina, Inc., San Diego, CA, USA) to determine and exclude benign population-specific CNV regions. The derived EGCUT dataset represented control group of women with normal age at menopause, as the group included >41 years old pre- and post-menopausal women, but excluded potential POF cases.
Tšuiko O., Nõukas M., Žilina O., Hensen K., Tapanainen J.S., Mägi R., Kals M., Kivistik P.A., Haller-Kikkatalo K., Salumets A, & Kurg A. (2016). Copy number variation analysis detects novel candidate genes involved in follicular growth and oocyte maturation in a cohort of premature ovarian failure cases. Human Reproduction (Oxford, England), 31(8), 1913-1925.
+ Open protocol
+ Expand
5

Robust Genotype Filtering for GWAS

Check if the same lab product or an alternative is used in the 5 most similar protocols
Icelandic chip-typed samples were assayed using the Illumina HumanHap300, HumanCNV370, HumanHap610, HumanHap1M, HumanHap660, Omni-1, Omni 2.5 or Omni Express bead chips at deCODE genetics. SNPs were excluded if they had (i) yield <95%, (ii) MAF <1% in the population or (iii) significant deviation from Hardy–Weinberg equilibrium in the controls (P <0.001), (iv) if they produced an excessive inheritance error rate (over 0.001) or (v) if there was substantial difference in allele frequency between chip types (from just a single chip if that resolved all differences, but from all chips otherwise). All samples with a call rate below 97% were excluded from the analysis.
Gretarsdottir S., Helgason H., Helgadottir A., Sigurdsson A., Thorleifsson G., Magnusdottir A., Oddsson A., Steinthorsdottir V., Rafnar T., de Graaf J., Daneshpour M.S., Hedayati M., Azizi F., Grarup N., Jørgensen T., Vestergaard H., Hansen T., Eyjolfsson G., Sigurdardottir O., Olafsson I., Kiemeney L.A., Pedersen O., Sulem P., Thorgeirsson G., Gudbjartsson D.F., Holm H., Thorsteinsdottir U, & Stefansson K. (2015). A Splice Region Variant in LDLR Lowers Non-high Density Lipoprotein Cholesterol and Protects against Coronary Artery Disease. PLoS Genetics, 11(9), e1005379.
+ Open protocol
+ Expand
6

Genome-Wide Genotyping and Imputation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Icelandic chip-typed samples were assayed using the Illumina HumanHap300, HumanCNV370, HumanHap610, HumanHap1M, HumanHap660, Omni-1, Omni 2.5 or Omni Express bead chips at deCODE genetics. SNPs were excluded if they had (i) yield less than 95%, (ii) minor allele frequency less than 1% in the population or (iii) significant deviation from Hardy-Weinberg equilibrium in the controls (P <0.001), (iv) if they produced an excessive inheritance error rate (over 0.001), or (v) if there was substantial difference in allele frequency between chip types (from just a single chip if that resolved all differences, but from all chips otherwise). All samples with a call rate below 97% were excluded from the analysis. For the HumanHap series of chips, 304,937 SNPs were used for long range phasing, whereas for the Omni series of chips 564,196 SNPs were included. The final set of SNPs used for long-range phasing was composed of 707,525 SNPs.
Genotyping of the Russian PTB cases and controls has been done using Affymetrix Genome-Wide Human SNP Array 6.0 and SNPs across the genome were imputed as described previously12 . Association analysis of the HLA SNPs rs557011, rs9271378 and rs9272785 has been done using PLINK38 (link).
Sveinbjornsson G., Gudbjartsson D.F., Halldorsson B.V., Kristinsson K.G., Gottfredsson M., Barrett J.C., Gudmundsson L.J., Blondal K., Gylfason A., Gudjonsson S.A., Helgadottir H.T., Jonasdottir A., Jonasdottir A., Karason A., Kardum L.B., Knežević J., Kristjansson H., Kristjansson M., Love A., Luo Y., Magnusson O.T., Sulem P., Kong A., Masson G., Thorsteinsdottir U., Dembic Z., Nejentsev S., Blondal T., Jonsdottir I, & Stefansson K. (2016). HLA class II sequence variants influence tuberculosis risk in populations of European ancestry. Nature genetics, 48(3), 318-322.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!