scholarly journals Optimizing Polymerase Chain Reaction (PCR) using Machine Learning

2021 ◽  
Author(s):  
Nicholas J. Cordaro ◽  
Andrew J. Kavran ◽  
Michael Smallegan ◽  
Megan Palacio ◽  
Nickolaus Lammer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Polymerase Chain Reaction ◽  
Similar Data ◽  
Success Rates ◽  
Chain Reaction ◽  
Data Set ◽  
Machine Learning Model ◽  
Crowdsourced Data ◽  
Polymerase Chain ◽  
Active Research

Despite substantial standardization, polymerase chain reaction (PCR) experiments frequently fail. Troubleshooting failed PCRs can be costly in both time and money. Using a crowdsourced data set spanning 290 real PCRs from six active research laboratories, we investigate the degree to which PCR success rates can be improved by machine learning. While human designed PCRs succeed at a rate of 55-64%, we find that a machine learning model can accurately predict reaction outcome 81% of the time. We validate this level of improvement by then using the model to guide the design and predict the outcome of 39 new PCR experiments. In addition to improving outcomes, the model identifies 15 features of PCRs that researchers did not optimize well compared to the learned model. These results suggest that PCR success rates can easily be improved by 17-26%, potentially saving millions of dollars and thousands of hours of researcher time each year across the scientific community. Other common laboratory methods may benefit from similar data-driven optimization effort.

scholarly journals Machine Learning Prediction of SARS-CoV-2 Polymerase Chain Reaction Results with Routine Blood Tests

2020 ◽  
Author(s):  
Thomas Tschoellitsch ◽  
Martin Dünser ◽  
Carl Böck ◽  
Karin Schwarzbauer ◽  
Jens Meier
Keyword(s):  
Machine Learning ◽  
Polymerase Chain Reaction ◽  
Characteristic Curve ◽  
Cohort Analysis ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Blood Tests ◽  
Routine Blood ◽  
Machine Learning Model ◽  
Polymerase Chain

Abstract Objective The diagnosis of COVID-19 is based on the detection of SARS-CoV-2 in respiratory secretions, blood, or stool. Currently, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used method to test for SARS-CoV-2. Methods In this retrospective cohort analysis, we evaluated whether machine learning could exclude SARS-CoV-2 infection using routinely available laboratory values. A Random Forests algorithm with 1353 unique features was trained to predict the RT-PCR results. Results Out of 12,848 patients undergoing SARS-CoV-2 testing, routine blood tests were simultaneously performed in 1528 patients. The machine learning model could predict SARS-CoV-2 test results with an accuracy of 86% and an area under the receiver operating characteristic curve of 0.90. Conclusion Machine learning methods can reliably predict a negative SARS-CoV-2 RT-PCR test result using standard blood tests.

scholarly journals Influence of SARS-CoV-2 Virus Infection on the Course of Psoriasis during Treatment with Biological Drugs

Medicina ◽  
2021 ◽  
Vol 57 (9) ◽  
pp. 881
Author(s):  
Magdalena Mroz ◽  
Szymon Mućka ◽  
Martyna Miodońska ◽  
Dominika Ziolkowska ◽  
Ewa Hadas ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Biological Treatment ◽  
Systemic Treatment ◽  
Control Group ◽  
Similar Data ◽  
Chain Reaction ◽  
Positive Real ◽  
Psoriasis Area Severity Index ◽  
Polymerase Chain ◽  
The Impact

Background and objectives: Biological treatment is an important and effective therapy for psoriasis. During the COVID-19 pandemic, it remains unclear whether this type of therapy affects the course of SARS-CoV-2 infection. The aim of the study was to observe patients with psoriasis undergoing biological or other systemic treatment in relation to the impact of SARS-CoV-2 infection on the course of psoriasis and the COVID-19 disease itself. Materials and methods: A one-year observational study included 57 patients with diagnosed psoriasis who qualified for biological treatment and a group of 68 similar patients who were administered a different systemic treatment. Patients were analyzed monthly for psoriasis (including Psoriasis Area Severity Index (PASI) assessment) and constantly for SARS-CoV-2 infection (telephone contact). Cases of COVID-19 were confirmed by Polymerase Chain Reaction (PCR) at the study center. Results: SARS-CoV-2 infection was confirmed by a positive Real Time Polymerase Chain Reaction (RT-PCR) test in eight patients (14.0%) with psoriasis on biological therapy. None of the cases in this group required hospitalization for COVID-19. Similar data were obtained in the control group. Specifically, 11 (16%) patients were confirmed to be infected with SARS-CoV-2. These results were statistically comparable (p > 0.05). In the group of patients undergoing biological treatment, six (75%) of eight patients developed an exacerbation of psoriasis during SARS-CoV-2 infection, and similar results were noted in the control group, with eight (72%) patients experiencing an exacerbation of psoriasis. Conclusions: Patients with psoriasis who were administered biological treatment or other systemic therapy may experience a mild course of SARS-CoV-2 infection but might also experience a temporary exacerbation of skin lesions.

scholarly journals Elevated AQP1 Expression Is Associated With Unfavorable Oncologic Outcome in Patients With Hilar Cholangiocarcinoma

2016 ◽  
Vol 16 (4) ◽  
pp. 421-427 ◽  
Author(s):  
Chunxiang Li ◽  
Xiaofu Li ◽  
Linfeng Wu ◽  
Zheng Jiang
Keyword(s):  
Polymerase Chain Reaction ◽  
Messenger Rna ◽  
Hilar Cholangiocarcinoma ◽  
Quantitative Polymerase Chain Reaction ◽  
Rank Test ◽  
Chain Reaction ◽  
Data Set ◽  
Aquaporin 1 ◽  
Tumor Node Metastasis Stage ◽  
Polymerase Chain

Background: Hilar cholangiocarcinomas are malignant tumors with a poor prognosis. An early prediction of prognosis for patients may help us determine treatment strategies. Aquaporin 1 is a cell membrane channel involved in water transport, cell motility, and proliferation. Increasing evidences showed that aquaporin 1 played a role in tumor prognosis and diagnosis. The purpose of this study is to evaluate the role of aquaporin 1 in hilar cholangiocarcinoma. Methods: Here, we analyzed messenger RNA expression data of genes function as bile secretion in a data set of 169 samples using the R2 bioinformatic platform ( http://r2.amc.nl ). Quantitative polymerase chain reaction was performed to verify the gene expression in 17 hilar cholangiocarcinoma samples. Immunohistochemistry was also performed in a series of specimens from 62 hilar cholangiocarcinoma tissues, and its clinical significance was assessed by clinical correlation and Kaplan-Meier analyses. Results: All data were analyzed using the R2 web application, aquaporin 1 was selected for further analysis. The significant expression variation of aquaporin 1 among 17 cases with cholangiocarcinoma was also found using quantitative polymerase chain reaction. The expression level of aquaporin 1 protein significantly correlated with tumor-node-metastasis stage ( P = .002) and overall survival time ( P = .010). Higher aquaporin 1 expression indicated poor prognostic outcomes ( P <.05, log-rank test). Multivariate analysis also showed strong aquaporin 1 protein expression was an independent adverse prognosticator in hilar cholangiocarcinoma ( P = .002). Conclusion: This study highlighted the prognostic value of aquaporin 1 in hilar cholangiocarcinoma. Strong aquaporin 1 expression predicts poor survival, regardless of pathological features. Immunohistochemical detection of aquaporin 1, as a prognostic marker, may contribute to predicting clinical outcome for patients with hilar cholangiocarcinoma.

High performance Nanogold™-in situ hybridzation and its use in the detection of hybridized and PCR-amplified microscopical preparations

1996 ◽  
Vol 54 ◽  
pp. 896-897
Author(s):  
G. W. Hacker ◽  
I. Zehbe ◽  
J. Hainfeld ◽  
A.-H. Graf ◽  
C. Hauser-Kronberger ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Messenger Rna ◽  
High Performance ◽  
Detection System ◽  
Direct Methods ◽  
Genetic Alterations ◽  
Chain Reaction ◽  
Protein Encoding ◽  
Polymerase Chain

In situ hybridization (ISH) with biotin-labeled probes is increasingly used in histology, histopathology and molecular biology, to detect genetic nucleic acid sequences of interest, such as viruses, genetic alterations and peptide-/protein-encoding messenger RNA (mRNA). In situ polymerase chain reaction (PCR) (PCR in situ hybridization = PISH) and the new in situ self-sustained sequence replication-based amplification (3SR) method even allow the detection of single copies of DNA or RNA in cytological and histological material. However, there is a number of considerable problems with the in situ PCR methods available today: False positives due to mis-priming of DNA breakdown products contained in several types of cells causing non-specific incorporation of label in direct methods, and re-diffusion artefacts of amplicons into previously negative cells have been observed. To avoid these problems, super-sensitive ISH procedures can be used, and it is well known that the sensitivity and outcome of these methods partially depend on the detection system used.

1504: Molecular Diagnosis and Staging of Prostate Cancer Using Clusterin in Real Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

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