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Sequenom platform

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The Sequenom platform is a genetic analysis system designed for high-throughput DNA sequencing. It utilizes mass spectrometry technology to detect and analyze genetic variations with a high degree of accuracy and sensitivity. The core function of the Sequenom platform is to enable efficient and reliable genetic analysis, facilitating various applications in research and diagnostics.

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Lab products found in correlation

Taqman, by Thermo Fisher Scientific (4 mentions) Paxgene blood dna kit, by Qiagen (3 mentions) Vantage, by Labcorp (2 mentions) Iplex application guide, by Labcorp (2 mentions) Exome array, by Illumina (1 mentions) Sequenom massarray system, by Agena (1 mentions) Massarray platform, by Labcorp (1 mentions) M csf, by Fujifilm (1 mentions) Genome wide human snp array 6, by Thermo Fisher Scientific (1 mentions) Massarray assay design 3, by Labcorp (1 mentions) Wizard genomic dna purification kit, by Promega (1 mentions)

41 protocols using sequenom platform

1

Genetic Variants in Colorectal Cancer Pathway Genes

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Using a tagSNP approach, the genetic variants were retrieved from a set of common SNPs in the Caucasian population of HapMap project (CEU). The Genome Variation Server (version 7.00) was used to recover tagSNPs capturing variations (1) with a minor allele frequency equal or superior to 15%; (2) within the coding region of the genes plus 2 Kb upstream and downstream and (3) with a r2 superior to 0.8. A total of 140 tagSNPs were captured: 6, 15, 31 and 88 tagSNPs in COX-2, HPGD, SLCO2A1 and ABCC4 genes, respectively. We further selected SNPs with high likelihood of genotyping success using the Sequenom platform, (Sequenom, San Diego, CA). Briefly, tagSNPs were prioritized as follows: first, all non-singletons tagSNPs or singletons with expected functional repercussion (FuncPred software) were tested. TagSNPs with low genotyping scores were replaced with representative variants; and finally the non-significant singletons were included in the array design. A total of 55 SNPs were successfully converted to the Sequenom platform.
Furthermore, we also included polymorphisms that were previously associated with colorectal tumors development and had a minor allele frequency equal or superior to 15% that failed to converted to the Sequenom platform: rs20417, rs689466 and rs5275 in COX-2 and rs2612656 and rs2555639 in HPGD genes.
Pereira C., Queirós S., Galaghar A., Sousa H., Pimentel-Nunes P., Brandão C., Moreira-Dias L., Medeiros R, & Dinis-Ribeiro M. (2014). Genetic Variability in Key Genes in Prostaglandin E2 Pathway (COX-2, HPGD, ABCC4 and SLCO2A1) and Their Involvement in Colorectal Cancer Development. PLoS ONE, 9(4), e92000.
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2

Genetic Variants Associated with Gestational Diabetes

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We genotyped 34 SNPs that included: 18 SNPs for loci that had been
significantly associated (P < 5x10−8) with T2DM or
fasting glucose in two or more genome wide association studies (GWAS) in the
general population, 6 SNPs previously associated with GDM or glycemic traits in
pregnancy, and 10 SNPs previously associated with both T2DM/fasting glucose in
the general population and GDM/glycemic traits in pregnant women (Supplement Table S1). The
selected SNPs were from studies in the general population published up to 2013,
from two large-meta-analysis of GDM,7 (link), 8 (link) and from one GWAS
of glycemic traits in pregnant women.15 (link) If two or more variants were in linkage disequilibrium
(r2>0.5), we selected the variant that was directly
associated with GDM or tag variants. Genotyping was performed by the Vanderbilt
Technologies for Advance Genomics (VANTAGE) at Vanderbilt University Medical
Center according to standard protocols using the Sequenom platform. SNPs that
failed or did not pool well in Sequenom were genotyped using TaqMan assays. For
quality control, we required genotyping call rates above 90%. We
examined significant departures from Hardy-Weinberg equilibrium (HWE) in
controls using a threshold of P < 0.001.
Kawai V.K., Levinson R.T., Adefurin A., Kurnik D., Collier S.P., Conway D, & Stein C.M. (2017). A genetic risk score that includes common type 2 diabetes risk variants is associated with gestational diabetes. Clinical endocrinology, 87(2), 149-155.
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3

Genotyping 78 MS-associated SNPs

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Genomic DNA was isolated from peripheral blood cell pellets using standard laboratory techniques. Isolated DNA was resuspended in Tris-EDTA (pH = 7.5) buffer and stored at −20°C. Genotyping was performed using the Illumina 610K Quad array (Illumina, San Diego, CA) or Sequenom platform (on both platforms, genotyping was performed in 1 run according to good laboratory practice following the manufacturers' protocol) for 78 MS-associated risk SNPs at the Erasmus MC4 (link),5 (link) (table e-1 at Neurology.org/nn). All SNPs were in the Hardy-Weinberg equilibrium (all p values >0.30).
Kreft K.L., Van Nierop G.P., Scherbeijn S.M., Janssen M., Verjans G.M, & Hintzen R.Q. (2017). Elevated EBNA-1 IgG in MS is associated with genetic MS risk variants. Neurology® Neuroimmunology & Neuroinflammation, 4(6), e406.
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4

APOL1 Genotyping for DDKT Outcomes

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Two single nucleotide polymorphisms (SNPs) in the APOL1 G1 nephropathy risk allele (rs73885319; rs60910145) and an insertion/deletion for the G2 risk allele (rs71785313) were genotyped using a custom assay designed at WFSM on the Sequenom platform (San Diego, California).(10 (link)) G1 and G2 genotype calls were visually inspected for quality control. Genotyping of three blind duplicates resulted in a concordance rate of 100% and the genotyping efficiency for the three SNPs was >99% in both cohorts. As analyses assessed the clinical impact of APOL1 G1 and G2, and African ancestry outside of APOL1 did not significantly impact DDKT outcomes in our initial report, ancestry informative markers were not genotyped. This approach was intentional because the clinical application of APOL1 genotyping in DDKT requires rapid turnaround and ease of interpretation.
Freedman B.I., Julian B.A., Pastan S.O., Israni A.K., Schladt D., Gautreaux M.D., Hauptfeld V., Bray R.A., Gebel H.M., Kirk A.D., Gaston R.S., Rogers J., Farney A.C., Orlando G., Stratta R.J., Mohan S., Ma L., Langefeld C.D., Hicks P.J., Palmer N.D., Adams P.L., Palanisamy A., Reeves-Daniel A.M, & Divers J. (2015). Apolipoprotein L1 gene variants in deceased organ donors are associated with renal allograft failure. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, 15(6), 1615-1622.
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5

Vitamin D Status and Genetic Risk Factors

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Vitamin D status was assessed using serum 25(OH)D obtained during routine clinical care from the EHR. For patients with ≥ 2 time points of measurement, we examined change in vitamin D between initial and subsequent assessment and defined normalization as initially insufficient levels (< 30ng/mL) subsequent achieving sufficiency (≥30ng/mL). Patients were genotyped for four vitamin D risk alleles previously described to influence serum levels in healthy adults39 (link), 40 (link). These vitamin D risk alleles were described in Caucasian populations. These included a locus each at the cytochrome P450 2R1 (CYP2R1) (rs10741657; chromosome 11, position 14893332), cytochrome P450 24A1 (rs6013897; chromosome 20, position 54125940), nicotinamide adenine dinucleotide synthetase 1 (NADSYN1) (rs2060793; chromosome 11, position 14893764) and 7-dehydrocholesterol reductase (DHCR7) (rs12785878; chromosome 11, 71456403). Genotyping was performed on a Sequenom platform (Sequenom Inc, San Diego, CA) at the Broad Institute in a single batch. In addition to analyzing each locus separately, a vitamin D genetic risk score defined as the sum of risk alleles for all four loci was calculated (range 0-8). Weighting was not performed for this score given similar effect sizes for all four loci.
Ananthakrishnan A.N., Cagan A., Cai T., Gainer V.S., Shaw S.Y., Churchill S., Karlson E.W., Murphy S.N., Kohane I., Liao K.P, & Xavier R.J. (2015). Common genetic variants influence circulating vitamin D levels in inflammatory bowel diseases. Inflammatory bowel diseases, 21(11), 2507-2514.
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6

Mitochondrial SNP Genotyping and Analysis

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Mitochondrial SNPs were genotyped using the Sequenom platform (n = 186 mtSNPs) [44 (link)] and the Illumina Exome array [45 (link)] (n = 240 mtSNPs). The 2,723 cases and 3,260 controls were shared between the two genotyping platforms with an average call rate of 99.83%. Forty mtSNPs were common in both genotyping platforms with a concordance rate of 99.3%. Of the 386 unique mtSNPs across the two genotyping platforms, we excluded 72 mtSNPs with MAF<0.1% among the overall sample, resulting in 314 mtSNPs that were distributed across 13 mtDNA genes, comprising four complexes of the OXPHOS pathway, and the tRNA and rRNA subunits (19 mtSNPs per kb).
Li Y., Giorgi E.E., Beckman K.B., Caberto C., Kazma R., Lum-Jones A., Haiman C.A., Marchand L.L., Stram D.O., Saxena R, & Cheng I. (2019). Association between mitochondrial genetic variation and breast cancer risk: The Multiethnic Cohort. PLoS ONE, 14(10), e0222284.
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7

APOL1 Genotyping for Renal Risk

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Two single nucleotide polymorphisms (SNPs) in the APOL1 G1-renal-risk allele (rs73885319; rs60910145) and an insertion/deletion for the G2-renal-risk allele (rs143830837) were genotyped using a custom assay designed at WFSM on the Sequenom platform (San Diego, California). Genotype calls were visually inspected for quality control.(3 ,14 (link)) Genotyping of 15 blind duplicates resulted in a concordance rate of 100% and the genotyping efficiency for the three SNPs was >99% in all 1153 DDKTs.
Freedman B.I., Pastan S.O., Israni A.K., Schladt D., Julian B.A., Gautreaux M.D., Hauptfeld V., Bray R.A., Gebel H.M., Kirk A.D., Gaston R.S., Rogers J., Farney A.C., Orlando G., Stratta R.J., Mohan S., Ma L., Langefeld C.D., Bowden D.W., Hicks P.J., Palmer N.D., Palanisamy A., Reeves-Daniel A.M., Brown W.M, & Divers J. (2016). APOL1 genotype and kidney transplantation outcomes from deceased African American donors. Transplantation, 100(1), 194-202.
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8

Genetic Analysis of Neurodegenerative Disorders

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Frozen cerebellar tissue was used to extract DNA. Sequencing of all GBA exons was performed as described previously[9 (link)]. Sequencing of all exons of HEXA, SMPD1 and MCOLN1 was also performed. Details of PCR and sequencing primers are available upon request. APOE genotyping was performed by MALDI-TOF mass spectrometry on the Sequenom platform as described previously[11 (link)].
Clark L.N., Chan R., Cheng R., Liu X., Park N., Parmalee N., Kisselev S., Cortes E., Torres P.A., Pastores G.M., Vonsattel J.P., Alcalay R., Marder K., Honig L.L., Fahn S., Mayeux R., Shelanski M., Di Paolo G, & Lee J.H. (2015). Gene-Wise Association of Variants in Four Lysosomal Storage Disorder Genes in Neuropathologically Confirmed Lewy Body Disease. PLoS ONE, 10(5), e0125204.
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9

Innate Immune Responses in Crohn's Disease

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Informed consent was obtained per protocol approved by the institutional review board at Yale University. Healthy individuals had no personal or family history of autoimmune/inflammatory disease, including psoriasis, systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, type 1 diabetes mellitus, Crohn's disease and UC, or a history of HIV. Given the limitation in peripheral cell numbers and the range of innate responses we sought to examine, two separate cohorts of 100 and 98 European ancestry individuals were recruited for NOD2/Toll-like receptor (TLR)2 dose–response studies in MDMs and MDDCs, and NOD2/TLR synergy studies in MDDCs, respectively. We further ascertained a separate cohort of 24 patients with Crohn's disease based on TPL2 genotype (see online supplementary table S1). We genotyped polymorphisms by TaqMan (Applied Biosystems, Foster City, California, USA) or Sequenom platform (Sequenom, San Diego, California, USA).
Hedl M, & Abraham C. (2015). A TPL2 (MAP3K8) disease-risk polymorphism increases TPL2 expression thereby leading to increased pattern recognition receptor-initiated caspase-1 and caspase-8 activation, signalling and cytokine secretion. Gut, 65(11), 1799-1811.
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10

SNP Validation in Crossbred Cattle

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As the crossbred population used to validate SNPs and perform association tests included animals from Angus, Hereford and Limousin (pure or crossbred), only some of the SNPs detected in the re-sequencing stage were considered for further validation. In other words, many of the SNPs detected by re-sequencing showed no variation in the Taurine breeds and were not considered, since they would probably show no variation in the crossbred population. For this reason, additional SNPs were selected from dbSNP [14 ] to have a better covering of the length of the genes using markers with proven variation in Taurine breeds. At this stage, the addition of another candidate gene was decided, and SNPs in the RXRA gene were also selected from dbSNP to be validated and tested for associations. Genotyping was performed by the Neogen genotyping service (USA) using the Sequenom platform [15 ].
Goszczynski D.E., Mazzucco J.P., Ripoli M.V., Villarreal E.L., Rogberg-Muñoz A., Mezzadra C.A., Melucci L.M, & Giovambattista G. (2016). Genetic characterisation of PPARG, CEBPA and RXRA, and their influence on meat quality traits in cattle. Journal of Animal Science and Technology, 58, 14.
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