scholarly journals Genetic Analysis of colorectal carcinoma using high throughput SNP genotyping technique within the population of Jammu and Kashmir.

2021 ◽  
Author(s):  
Bhanu Sharma ◽  
Shabab Angurana ◽  
Amrita Bhat ◽  
Sonali Verma ◽  
Divya Bakshi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
High Throughput ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Colorectal Carcinogenesis ◽  
P Value ◽  
Jammu And Kashmir ◽  
Cost Effective Method ◽  
Underlying Causes ◽  
Multiple Samples

Abstract Background SNP genotyping has become increasingly more common place to understand the genetic basis of complex diseases like cancer. SNP-genotyping through massARRAY is a cost-effective method to quantitatively analyse the variation of gene expression in multiple samples, making it a potential tool to identify the underlying causes of colorectal carcinogenesis.Methods In the present study, SNP genotyping was carried out using Agena mass ARRAY, which is a cost-effective, robust, and sensitive method to analyse multiple SNPs simultaneously. We analysed 7 genes in 492 samples (100 cases and 392 controls) associated with CRC within the population of Jammu and Kashmir. These SNPs were selected based on their association with multiple cancers in literature.Results This is the first study to explore these SNPs with colorectal cancer within the J&K population.7 SNPs with a call rate of 90% were selected for the study. Out of these, one SNP i.e. rs2229080 of DCC was found to be significantly associated with the current study and 6 were non-significantly associated with CRC within the studied population. The allelic OR observed for the variant rs2229080 of DCC was 1.5 (1.1–2.3 at 95% CI), p value = 0.02.Conclusion This is the first study to find the relation of Genetic variants with the colorectal cancer within the studied population using high throughput mass ARRAY technology. It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

scholarly journals Genetic Analysis of colorectal carcinoma using high throughput SNP genotyping technique within the population of Jammu and Kashmir

2021 ◽  
Author(s):  
Bhanu Sharma ◽  
Shabab Angurana ◽  
Amrita Bhat ◽  
Sonali Verma ◽  
Divya Bakshi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
High Throughput ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Colorectal Carcinogenesis ◽  
P Value ◽  
Jammu And Kashmir ◽  
Cost Effective Method ◽  
Underlying Causes ◽  
Multiple Samples

Abstract Background SNP genotyping has become increasingly more common place to understand the genetic basis of complex diseases like cancer. SNP-genotyping through massARRAY is a cost-effective method to quantitatively analyse the variation of gene expression in multiple samples, making it a potential tool to identify the underlying causes of colorectal carcinogenesis. Methods In the present study, SNP genotyping was carried out using Agena mass ARRAY, which is a cost-effective, robust, and sensitive method to analyse multiple SNPs simultaneously. We analysed 7 genes in 492 samples (100 cases and 392 controls) associated with CRC within the population of Jammu and Kashmir. These SNPs were selected based on their association with multiple cancers in literature. Results This is the first study to explore these SNPs with colorectal cancer within the J&K population.7 SNPs with a call rate of 90% were selected for the study. Out of these, one SNP i.e. rs2229080 of DCC was found to be significantly associated with the current study and 6 were non-significantly associated with CRC within the studied population. The allelic OR observed for the variant rs2229080 of DCC was 1.5 (1.1–2.3 at 95% CI), p value = 0.02. Conclusion This is the first study to find the relation of Genetic variants with the colorectal cancer within the studied population using high throughput mass ARRAY technology. It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

scholarly journals MassARRAY-based single nucleotide polymorphism analysis in breast cancer of north Indian population

BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Divya Bakshi ◽  
Ashna Nagpal ◽  
Varun Sharma ◽  
Indu Sharma ◽  
Ruchi Shah ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Mutations ◽  
Cost Effective ◽  
P Value ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cost Effective Method ◽  
Common Genetic Variants ◽  
Underlying Causes

Abstract Background Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. Methods SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. Results The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08–2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136–5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123–0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46–0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. Conclusion It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

scholarly journals MassARRAY-based single nucleotide polymorphism analysis in breast cancer of North Indian Population.

2020 ◽  
Author(s):  
Divya Bakshi ◽  
Ashna Nagpal ◽  
Varun Sharma ◽  
Indu Sharma ◽  
Ruchi Shah ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Mutations ◽  
Cost Effective ◽  
P Value ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cost Effective Method ◽  
Common Genetic Variants ◽  
Underlying Causes

Abstract Background Breast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for the diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. Methods SNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. Results The SNPs were rs12190287 (TCF21) having OR 1.713 (1.08-2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136-5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123 -0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46-0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. Conclusion It is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

scholarly journals Single nucleotide polymorphism analysis in breast cancer using MassARRAY from Jammu and Kashmir, India

2020 ◽  
Author(s):  
Divya Bakshi ◽  
Ashna Nagpal ◽  
Varun Sharma ◽  
Indu Sharma ◽  
Ruchi Shah ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Mutations ◽  
Cost Effective ◽  
P Value ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Jammu And Kashmir ◽  
Cost Effective Method ◽  
Common Genetic Variants

Abstract BackgroundBreast Cancer (BC) is associated with inherited gene mutations. High throughput genotyping of BC samples has led to the identification and characterization of biomarkers for diagnosis of BC. The most common genetic variants studied are SNPs (Single Nucleotide Polymorphisms) that determine susceptibility to an array of diseases thus serving as a potential tool for identifying the underlying causes of breast carcinogenesis. MethodsSNP genotyping employing the Agena MassARRAY offers a robust, sensitive, cost-effective method to assess multiple SNPs and samples simultaneously. In this present study, we analyzed 15 SNPs of 14 genes in 550 samples (150 cases and 400 controls). We identified four SNPs of genes TCF21, SLC19A1, DCC, and ERCC1 showing significant association with BC in the population under study. ResultsThe SNPs were rs12190287 (TCF21) having OR 1.713 (1.08-2.716 at 95% CI) p-value 0.022 (dominant), rs1051266 (SLC19A1) having OR 3.461 (2.136-5.609 at 95% CI) p-value 0.000000466 (dominant), rs2229080 (DCC) having OR 0.6867 (0.5123 -0.9205 at 95% CI) p-value 0.0116 (allelic) and rs2298881 (ERCC1) having OR 0.669 (0.46-0.973 at 95% CI), p-value 0.035 (additive) respectively. The in-silico analysis was further used to fortify the above findings. ConclusionIt is further anticipated that the variants should be evaluated in other population groups that may aid in understanding the genetic complexity and bridge the missing heritability.

scholarly journals Molecularly Imprinted Nanoparticles Based Sensor for Cocaine Detection

Biosensors ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 22 ◽  
Author(s):  
Roberta D’Aurelio ◽  
Iva Chianella ◽  
Jack A. Goode ◽  
Ibtisam E. Tothill
Keyword(s):  
Electrochemical Impedance ◽  
Limit Of Detection ◽  
Solid Phase ◽  
Cost Effective ◽  
Cross Reactivity ◽  
P Value ◽  
Sensing Element ◽  
Molecularly Imprinted ◽  
Cost Effective Method ◽  
Cocaine Detection

The development of a sensor based on molecularly imprinted polymer nanoparticles (nanoMIPs) and electrochemical impedance spectroscopy (EIS) for the detection of trace levels of cocaine is described in this paper. NanoMIPs for cocaine detection, synthesized using a solid phase, were applied as the sensing element. The nanoMIPs were first characterized by Transmission Electron Microscopy (TEM) and Dynamic Light Scattering and found to be ~148.35 ± 24.69 nm in size, using TEM. The nanoMIPs were then covalently attached to gold screen-printed electrodes and a cocaine direct binding assay was developed and optimized, using EIS as the sensing principle. EIS was recorded at a potential of 0.12 V over the frequency range from 0.1 Hz to 50 kHz, with a modulation voltage of 10 mV. The nanoMIPs sensor was able to detect cocaine in a linear range between 100 pg mL−1 and 50 ng mL−1 (R2 = 0.984; p-value = 0.00001) and with a limit of detection of 0.24 ng mL−1 (0.70 nM). The sensor showed no cross-reactivity toward morphine and a negligible response toward levamisole after optimizing the sensor surface blocking and assay conditions. The developed sensor has the potential to offer a highly sensitive, portable and cost-effective method for cocaine detection.

scholarly journals Simple, Fast, and Cost-Effective Fabrication of Wafer-Scale Nanohole Arrays on Silicon for Antireflection

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Di Di ◽  
Xuezhong Wu ◽  
Peitao Dong ◽  
Chaoguang Wang ◽  
Jian Chen ◽  
...  
Keyword(s):  
High Throughput ◽  
Crystalline Silicon ◽  
Colloidal Crystal ◽  
Cost Effective ◽  
Wafer Scale ◽  
Crystalline Silicon Solar Cells ◽  
Cost Effective Method ◽  
Nanohole Arrays ◽  
Coating Method ◽  
Hole Arrays

A simple, fast, and cost-effective method was developed in this paper for the high-throughput fabrication of nanohole arrays on silicon (Si), which is utilized for antireflection. Wafer-scale polystyrene (PS) monolayer colloidal crystal was developed as templates by spin-coating method. Metallic shadow mask was prepared by lifting off the oxygen etched PS beads from the deposited chromium film. Nanohole arrays were fabricated by Si dry etching. A series of nanohole arrays were fabricated with the similar diameter but with different depth. It is found that the maximum depth of the Si-hole was determined by the diameter of the Cr-mask. The antireflection ability of these Si-hole arrays was investigated. The results show that the reflection decreases with the depth of the Si-hole. The deepest Si-hole arrays show the best antireflection ability (reflection < 9%) at long wavelengths (>600 nm), which was about 28 percent of the nonpatterned silicon wafer’s reflection. The proposed method has the potential for high-throughput fabrication of patterned Si wafer, and the low reflectivity allows the application of these wafers in crystalline silicon solar cells.

Rapid screening of SNPs in metastatic colorectal cancer (mCRC) utilizing multiplex sequencing technology (Sequenom).

2012 ◽  
Vol 30 (4_suppl) ◽  
pp. 418-418
Author(s):  
Radhashree Maitra ◽  
Jay B. Nayak ◽  
Atrayee Basu-Mallick ◽  
Arjun Sood ◽  
Titto A Augustine ◽  
...  
Keyword(s):  
High Throughput ◽  
Direct Sequencing ◽  
Cost Effective ◽  
Rapid Screening ◽  
Accurate Identification ◽  
Multiple Snps ◽  
Fast Screening ◽  
Effective Manner ◽  
Multiplex Sequencing ◽  
Multiple Samples

418 Background: Accurate and fast screening of mutations is essential for designing individualized therapy necessary and critical for efficient disease management and better patient outcome in mCRC. Detection of hotspots by gold standard direct sequencing (DS) is time consuming and cost ineffective. Pyrosequencing (PS) technique is rapid and precisely committed towards SNP detection. Recent introduction of high throughput multiplex PCR based extension on microarray (Sequenom, SEQ) offers a robust platform capable of detecting multiple SNPs simultaneously in a rapid and cost effective manner. The current study analyzes the concordance and efficacy of the cutting edge SEQ technique to the well established DS and PS methods. Methods: DNA isolated from 122 specimens from 76 mCRC patients were sequenced by all three methods. DS and PS were performed on 4 genes at 10 hotspots. SEQ multiplexing was performed on 31 hotspots in 19 genes by 4 multiplex reactions. Results: We were able to make "calls" for all samples by DS and PS. With the multiplex system, the “calls” rate was 97.8% of successful reactions. Using PS data as our standard in the assay we calculated the percent concordance of DS and SEQ. Futhermore SEQ offered a more accurate identification of the substituted nucleotide in Kras codon 12 as compared to PS. Conclusions: The multiplexing of PCR reactions offers an excellent advantage of high throughput with strong feasibility of analyzing several samples for multiple SNPs simultaneously. The concordance rate of > 90% when compared to PS along with the ability to analyze multiple samples/ hotspots plexed together in a time effective rapid mode provided a trifold advantage of the sequenom technology. It is therefore the next generation technology for rapid genetic evaluation of cancer patients. [Table: see text]

Wire mask assisted rolling as a cost-effective method for high-throughput surface micro-texturing

2020 ◽  
Vol 30 (7) ◽  
pp. 075010
Author(s):  
Anvesh Gaddam ◽  
Ashwin Prabhakaran ◽  
Amit Agrawal ◽  
Suhas S Joshi
Keyword(s):  
High Throughput ◽  
Cost Effective ◽  
Cost Effective Method

scholarly journals Detecting SARS-CoV-2 variants with SNP genotyping

2020 ◽  
Author(s):  
Helen Harper ◽  
Amanda J. Burridge ◽  
Mark Winfield ◽  
Adam Finn ◽  
Andrew D. Davidson ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Clinical Samples ◽  
Marker Panel ◽  
Qrt Pcr ◽  
Crucial Information ◽  
The Uk ◽  
Genotyping Panel

AbstractTracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020- and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 76% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with our marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.

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