Sequenom MassARRAY platform v1 (protocols.io.rq7d5zn)

Abstract Background We explored the association of leucine-rich repeats and calponin homology domain containing 1 (LRCH1) gene polymorphisms with genetic susceptibility to delayed encephalopathy after acute carbon monoxide poisoning (DEACMP), which might provide a theoretical basis for the pathogenesis, diagnosis, and prognosis research of DEACMP. Methods Four single nucleotide polymorphisms, rs1539177 (G/A), rs17068697 (G/A), rs9534475 (A/C), and rs2236592 (T/C), of LRCH1, selected as candidate genes through genome-wide association analysis, were genotyped in 661 patients (DEACMP group: 235 cases; ACMP group: 426 cases) using Sequenom Massarray®. The association analysis of four SNPs and LRCH1 was performed under different genetic models. Results LRCH1 polymorphisms (rs1539177, rs17068697, rs9534475) under additive and dominant genetic models were significantly associated with an increased risk of DEACMP, but no significant association under allele and recessive models was found. The LRCH1 rs2236592 polymorphism was susceptible to DEACMP only under the dominant model (TT/TC + CC, OR = 1.616, 95% CI: 1.092–2.390, P = 0.015784). In addition, the A allele gene of rs9534475 polymorphism in LRCH1 might increase the risk for DEACMP (OR = 1.273, 95% CI: 1.013–1.601, P = 0.038445). Conclusions We found a significant association between the four LRCH1 polymorphisms and DEACMP. The allelic A of rs9534475 polymorphism in LRCH1 might be a risk factor for DEACMP.

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Abstract 4713: High-throughput multiplex Sequenom MassARRAY clinical diagnostic assay for the identification of actionable genetic variants in hematologic malignancies

10.1158/1538-7445.am2014-4713 ◽

2014 ◽

Author(s):

Mahadeo A. Sukhai ◽

Mariam Thomas ◽

Tong Zhang ◽

Cuihong Wei ◽

Suzanne Trudel ◽

...

Keyword(s):

High Throughput ◽

Genetic Variants ◽

Hematologic Malignancies ◽

Diagnostic Assay ◽

Sequenom Massarray ◽

Clinical Diagnostic

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Correction to: Assessment of intratumor immune-microenvironment in colorectal cancers with extranodal extension of nodal metastases

Cancer Cell International ◽

10.1186/s12935-019-0966-z ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Matteo Fassan ◽

Luca Vianello ◽

Diana Sacchi ◽

Giuseppe N. Fanelli ◽

Giada Munari ◽

...

Keyword(s):

Colorectal Cancers ◽

Nodal Metastases ◽

Immune Microenvironment ◽

Sequenom Massarray ◽

Extranodal Extension

Following publication of the original article [1], it has been brought to our attention that an incorrect Sequenom MassArray trace and an incorrect nomenclature were used to represent the PIK3CA p.E545A mutation in Fig. 2b. The correct Fig. 2b is shown in this erratum. The authors apologize for the confusion.

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Prospective study of genetic mutations in matched tumor and plasma specimens in colorectal cancer patients.

Journal of Clinical Oncology ◽

10.1200/jco.2011.29.4_suppl.356 ◽

2011 ◽

Vol 29 (4_suppl) ◽

pp. 356-356

Author(s):

G. Perkins ◽

J. Dukes ◽

T. A. Yap ◽

R. Riisnaes ◽

L. Pope ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Patients ◽

The Other ◽

Amplification Refractory Mutation System ◽

Advanced Cancer Patients ◽

Assay Sensitivity ◽

Sequenom Massarray ◽

Pik3ca Mutations ◽

Ffpe Tumor ◽

Colorectal Cancer Patients

356 Background: Circulating free DNA (cfDNA) represents a minimally-invasive resource for detecting mutations in advanced cancer patients. The primary objective of this study was to determine if cfDNA is representative of tumor tissue for multiplex mutation detection utilizing Sequenom MassARRAY. Methods: Samples were spiked with dilutions (10ng/μl to 0.01ng/μl) of HCT116 DNA containing KRAS G13D mutations to determine assay sensitivity and specificity. Metastatic colorectal cancer patients referred to the Drug Development Unit at the Royal Marsden Hospital between 9/09-8/10 gave their consent to provide DNA from matched archival formalin fixed paraffin-embedded (FFPE) tumor and plasma. Samples had ∼200 described gene mutations genotyped using Sequenom MassARRAY (OncoCarta Panel). Results: Serial dilution spiking experiments revealed that the KRAS G13D mutation was reproducibly detectable to 40ng/mL of HCT116 DNA; 26 patient samples were then analyzed. KRAS, BRAF and PIK3CA mutations were detected in 8 (31%), 3 (12%) and 3 (12%) tumor specimens respectively; 100% concordance for KRAS status was observed between multiple FFPE biopsies from the same patient and analysis by Amplification Refractory Mutation System (ARMS)-Scorpion PCR. The median quantity of cfDNA was 353ng/ml (range 106-4603). Concordance between matched FFPE and cfDNA was 88% for KRAS and 100% for BRAF mutations. No patients with wildtype KRAS or BRAF tumor genotypes had mutations in their respective cfDNA confirming the high specificity of cfDNA analysis. Three patients had detectable PIK3CA mutations; 1 patient had a E346K mutation detected in both FFPE tissue and plasma; 1 patient had E545K detected only in FFPE and the other had E542K detected in a liver metastasis but not in the colorectal primary or plasma. The recently reported oncogenic AKT1 E17K mutation was detected in 1 patient in tissue and plasma. No mutations in any of the other tested oncogenes studied were detected. Conclusions: A high concordance in detected mutations was observed between FFPE tumor and matched cfDNA. cfDNA is representative of tumor DNA and may be used for the prospective selection of cancer patients for treatment with targeted therapeutics. No significant financial relationships to disclose.

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SNP Genotyping using Sequenom MassARRAY 7K Platform

Current Protocols in Human Genetics ◽

10.1002/0471142905.hg0212s42 ◽

2004 ◽

Vol 42 (1) ◽

Cited By ~ 10

Author(s):

Stacey Gabriel ◽

Liuda Ziaugra

Keyword(s):

Snp Genotyping ◽

Sequenom Massarray

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Sequenom MassARRAY Technology for the Analysis of DNA Methylation

Epigenetic Biomarkers and Diagnostics ◽

10.1016/b978-0-12-801899-6.00007-3 ◽

2016 ◽

pp. 137-153

Author(s):

Enrique J. Busó ◽

Marisa Iborra

Keyword(s):

Dna Methylation ◽

Sequenom Massarray

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Genes of different molecular classes and their relationship with type 1 diabetes an age of manifestation

Nauchno-prakticheskii zhurnal «Medicinskaia genetika» ◽

10.25557/2073-7998.2020.05.89-91 ◽

2020 ◽

pp. 89-91

Author(s):

Н.В. Тарасенко ◽

И.А. Гончарова ◽

А.В. Марков ◽

Е.И. Кондратьева ◽

Л.В. Спирина ◽

...

Keyword(s):

Mass Spectrometry ◽

Immune Response ◽

Type 1 Diabetes ◽

Genetic Variants ◽

Metabolic Pathways ◽

Age Of Onset ◽

Healthy Population ◽

Sequenom Massarray ◽

Different Ages

В работе изучена генетическая составляющая возраста манифестации сахарного диабета 1-го типа (СД1). В общей группе больных СД1 (n=330), а также в подгруппах с разным возрастом манифестации СД1 (до 30 лет, n=269, с 31 года, n=61) и популяционной выборке (n=289) изучено 58 однонуклеотидных полиморфизмов (SNPs), локализованных в 47 генах, продукты которых участвуют в различных метаболических путях и вовлечены в процессы фиброгенеза, эндотелиальную дисфункцию, иммунный ответ и воспаление. Генотипирование выполнено методом масс-спектрометрии на приборе «Sequenom MassARRAY» (США). В результате выявлена ассоциация с возрастом манифестации СД1 до 30 лет rs1007856 гена ITGB5 (генотип TT, р=0,02), rs3765124 гена ADAMDEC1 (генотип AA, р=0,01). При сравнении подгрупп СД1 с разным возрастом манифестации отличия получены для rs1107946 гена COL1A1 (генотип AA, р=0,03) и rs514921 гена MMP1 (генотип AA, р=0,03). Гены, SNPs которых показали ассоциацию с возрастом манифестации СД1, кодируют белковые продукты, вовлеченные в метаболизм экстрацеллюлярного матрикса и коллагена. Данные варианты могут рассматриваться в качестве маркеров возраста дебюта СД1. We have studied the genetic component of the age of onset of type 1 diabetes (T1D). We examined a group of patients with T1D (n = 330), which was divided into subgroups with different ages of manifestation of T1D (up to 30 years, n = 269, from 31 years old, n=61). A total of 289 healthy population individuals were enrolled in this study. We studied 58 SNPs of 47 genes whose products are involved in various metabolic pathways as well as fibrogenesis, endothelial dysfunction, the immune response and inflammation. We performed genotyping by mass spectrometry using a Sequenom MassARRAY (USA). As a result, we identified an association with the manifestation age of T1D up to 30 years for rs1007856 of the gene ITGB5 (genotype TT, p=0,02), rs3765124 of the gene ADAMDEC1 (genotype AA, p=0,01). Differences received when comparing subgroups of T1D with different ages of manifestation: for rs1107946 of the gene COL1A1 (genotype AA, p=0,03) and rs514921 of the gene MMP1 (genotype AA, p=0,03). Genes whose SNPs have been associated with an age of manifestation of T1D are involved in the metabolism of extracellular matrix and collagen. Identified genetic variants can be considered as markers of the age of onset of T1D.

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