Overview of a Queensland study which set out to ascertain the prevalence of HIV amongst MSM attending gay saunas and other recreational venues; determine the level of undiagnosed HIV infection within a community setting; and to identify sexual risk behaviour associated with HIV positive and negative serostatus. This presentation was given at the AFAO AGM workshops November 2007.
AGBT 2013: Home Brewed Personalized Genomics - The Quest for Meaningful Analy...Golden Helix Inc
Personalized genomics may be moving into a new era with whole-exome and whole-genome sequencing becoming affordable and available to consumers. 23andMe recently piloted a more affordable 80x exome to their existing customers. But it remains to be seen whether this wealth of raw genomic data can be analyzed to provide meaningful results for both healthy and symptomatic individuals.
By acquiring 23andMe exomes on his family, Gabe puts himself in the position of a bioinformatically inclined consumer, but non-clinician, to approach this question with his own analysis. His trio consists of a healthy father and son, and a mother with clinically-diagnosed idiopathic rheumatoid arthritis.
The following goals were set for the analysis: 1) How accurate are variant calls from direct-to-consumer NGS services? 2) How useful and durable is the list of risk variants provided by 23andMe? 3) Can a healthy individual's exome provide additional risk information over standard genotype-array-based risk prediction? and 4) Can the state of our current understanding of the complex genomic architecture of autoimmune diseases be enough to to find potential driver variants and genes to explain the diagnosis of a single case?
Here Gabe presents his findings of this analysis and discuss how individualized genomics might change in the world of affordable sequencing.
We travel the world - meet people with a vision and brands with a purpose.
Project by CoolBrands
CBNWS #CBNWS #ATW80B
Authors: Anouk Pappers and Maarten Schäfer
Overview of a Queensland study which set out to ascertain the prevalence of HIV amongst MSM attending gay saunas and other recreational venues; determine the level of undiagnosed HIV infection within a community setting; and to identify sexual risk behaviour associated with HIV positive and negative serostatus. This presentation was given at the AFAO AGM workshops November 2007.
AGBT 2013: Home Brewed Personalized Genomics - The Quest for Meaningful Analy...Golden Helix Inc
Personalized genomics may be moving into a new era with whole-exome and whole-genome sequencing becoming affordable and available to consumers. 23andMe recently piloted a more affordable 80x exome to their existing customers. But it remains to be seen whether this wealth of raw genomic data can be analyzed to provide meaningful results for both healthy and symptomatic individuals.
By acquiring 23andMe exomes on his family, Gabe puts himself in the position of a bioinformatically inclined consumer, but non-clinician, to approach this question with his own analysis. His trio consists of a healthy father and son, and a mother with clinically-diagnosed idiopathic rheumatoid arthritis.
The following goals were set for the analysis: 1) How accurate are variant calls from direct-to-consumer NGS services? 2) How useful and durable is the list of risk variants provided by 23andMe? 3) Can a healthy individual's exome provide additional risk information over standard genotype-array-based risk prediction? and 4) Can the state of our current understanding of the complex genomic architecture of autoimmune diseases be enough to to find potential driver variants and genes to explain the diagnosis of a single case?
Here Gabe presents his findings of this analysis and discuss how individualized genomics might change in the world of affordable sequencing.
We travel the world - meet people with a vision and brands with a purpose.
Project by CoolBrands
CBNWS #CBNWS #ATW80B
Authors: Anouk Pappers and Maarten Schäfer
Validation of anti niv igm capture elisa version#1krishgen
NiV is a negative-sense, non-segmented RNA virus that was first isolated from cerebrospinal fluid of human patients and classified in the family Paramyxoviridae under the new genus
Henipavirus. Its genome encodes six structural proteins: the nucleocapsid (N) protein,
phosphoprotein (P), matrix (M) protein, fusion (F) protein, glycoprotein (G), and large (L)
protein.
Nipah virus glycoprotein G has a globular head domain formed of a six-bladed beta sheet propeller, connected via a flexible stalk domain to a transmembrane anchor. The G binds to the cellular receptors ephrin B2 are ephrin B3, mediating viral attachment. Following attachment Nipah Virus glycoprotein G undergoes a conformational change that leads to triggering of glycoprotein F which leads to membrane fusion (Biering et al, 2012).
The Nipah virus glycoprotein G is a recombinant protein expressed in mammalian HEK293 cells. It is presented as a fusion protein with a mouse Fc tag linked to the C-terminus of glycoprotein G, amino acids 71-602.
We established preliminary specifications defining acceptable ranges for the parameters indicated herein below for our Anti Nipah Virus IgM Capture ELISA kit. These parameters were tracked day-to-day, run-to-run, and operator-to-operator, over a schedule defined inhouse.
Recommended assay characteristics included absorbance of a zero concentration standard; factors which describe the calibration for each standard and statistical description of the calibration curve such as coefficient of correlation, slope and/or intercept; and recovery of results on control samples. It is important to be able to relate the specifications for a parameter to expected reliability of the result. Our in-house standard defined was r=0.990.
1.A new diagnostic test has been developed to Diagnose Disease.docxmansonagnus
1.
A new diagnostic test has been developed to Diagnose Disease Y. The new test was compared to the standard diagnostic test (“the gold standard”) on the same set of patients, and the following data were obtained:
Number of patients diagnosed by the new test as having Disease Y, who actually had Disease Y = 3,252
Number of patients in the group who were diagnosed by the standard test as having Disease Y = 4,579
Number of patients diagnosed by the new test as not having Disease Y = 4, 737
Number of patients diagnosed by the new test as having Disease Y, who actually do not have Disease Y= 784
The standard diagnostic test is a tissue biopsy, and therefore, is considered to be 100% sensitive for diagnosing Disease Y.
a.
Create the 2x2 table that shows this data
b.
Calculate:
i.
The sensitivity of the new test
ii.
The specificity of the new test
iii.
The false positive rate of the new test
iv.
The false negative rate of the new test
v.
The positive predictive value of the new test
vi.
The negative predictive value of the new test
vii.
The likelihood ratio positive for the new test
viii.
The likelihood ratio negative for the new test
2.
Two new tests have been developed to diagnose Condition Z. One test (Test A) measures a metabolite “Metabolite A” in the serum. The other test (Test B) measures a different metabolite, “Metabolite B” in the urine. After appropriate preliminary testing, human trials are conducted. Following informed consent, the two tests were run on a group of patients with each patient getting both tests, as well as the “gold standard” test for diagnosing Condition Z. The following data were obtained:
Important!!!!
Since some answers depend on the results you obtained in previous sections of the problem, it is important for you that you show *all* work, since I will give partial credit if your analysis and set up are correct, even if your numerical result is incorrect.
Serum level (metabolite A)
# of patients
Disease positive
Disease negative
(mg / ml)
(by gold standard)
(by gold standard)
0 – 1.99
25
22
3
2.0 – 3.99
273
201
72
4.0 – 5.99
584
572
12
6.0 – 7.99
538
529
9
8.0 – 9.99
175
170
5
>10.0
14
14
0
Urine level (metabolite B)
(ng/ml)
0 – 2.99
30
5
25
3.0 – 5.99
245
46
199
6.0 – 8.99
423
400
23
9.0 – 11.99
628
620
8
12.0 – 14.99
175
169
6
15.0 – 17.99
99
95
4
>18.0
9
9
0
a)
For test A, a cutoff value of 4.0 mg / ml of metabolite A is chosen as the boundary between a negative and a positive test result (i.e., values below 4.0 mg / ml
are considered “negative” and values of 4.0 mg / ml or greater are considered “positive”).
For test B, a cutoff value of 6.0 ng / ml for metabolite B is chosen as the boundary between a negative and a positive test result (i.e., values below 6.0 ng / ml are considered “negative” and values of 6.0 ng / ml or greater are considered.
Ab find, an antibody test after covid 19 vaccination by meril lifeYashChopra43
Meril Life has created ABFind, India's first post-covid-19 vaccine antibody test kit. Here's where you can learn about home testing for fast neutralising antibodies.
Accuracy report of Healgen IgG/IgM Rapid Test kits AntibodyHK HuZef
1. Accuracy
1.1 Purpose
To evaluate the equivalence of COVID-19 IgG/IgM Rapid Test result and clinical diagnosis.
1.2 Method
By testing clinical samples with known results, to evaluate the accuracy of COVID-19 IgG/IgM
Rapid Test (Whole blood/Serum/Plasma).
1.3 Material
COVID-19 IgG/IgM Rapid Test Cassette (Whole blood/Serum/Plasma)
Cassette Lot1: 2002155,Lot2:2002156,Lot3:2002157
Clinical samples
1.4 Test Procedure
1) Prepare specimens: tests were taken to clinical partner to evaluate, totally 113 specimens.
2) Perform the test according to the test procedure in the package insert
1.5 Result
1) IgM
Epidemiological Approaches for Evaluation of diagnostic tests.pptxBhoj Raj Singh
Diagnosis of a disease or a problem is the first step towards solution/ treatment. Clinical Diagnosis or Provisional Diagnosis is the first step in diagnosis and is done after a physical examination of the patient by a clinician. Clinical diagnosis may or may not be true and to reach Final diagnosis Laboratory Investigations using gross and microscopic pathological observations and determining the disease indicators are required. The diagnostic tests may be Non-dichotomous Diagnostic Tests (when continuous values are given by the test in a range starting from sub-normal to above-normal range) and Dichotomous Diagnostic Tests (when results are given either plus or minus, disease or no-disease). To make non- Dichotomous diagnostic test a Dichotomous one you need to establish the cut-off values based on reference values or Gold Standard test readings or with the use of Receiver operator characteristic (ROC) curves, Precision-Recall Curves, Likelihood Ratios, etc., and finally establishing statistical agreement (using Kappa values, Level of Agreement, χ2 Statistics) between the true diagnosis and laboratory diagnosis. Thereafter, the Accuracy, Precision, Bias, Sensitivity, Specificity, Positive Predictive value, and Negative Predictive value, of a diagnostic test are established for use in clinical practice. Diagnostic tests are also used to determine Prevalence (True prevalence, apparent prevalence) and Incidence of the disease to estimate the disease burden so that control measures can be implemented. There are several Phases in the development and use of a diagnostic assay starting from conceptualization of the diagnostic test, development and evaluation to determine flaws in diagnostic test use and Interpretation influencers. This presentation mainly deals with the epidemiological evaluation procedures for diagnostic tests.
Validation of anti niv igm capture elisa version#1krishgen
NiV is a negative-sense, non-segmented RNA virus that was first isolated from cerebrospinal fluid of human patients and classified in the family Paramyxoviridae under the new genus
Henipavirus. Its genome encodes six structural proteins: the nucleocapsid (N) protein,
phosphoprotein (P), matrix (M) protein, fusion (F) protein, glycoprotein (G), and large (L)
protein.
Nipah virus glycoprotein G has a globular head domain formed of a six-bladed beta sheet propeller, connected via a flexible stalk domain to a transmembrane anchor. The G binds to the cellular receptors ephrin B2 are ephrin B3, mediating viral attachment. Following attachment Nipah Virus glycoprotein G undergoes a conformational change that leads to triggering of glycoprotein F which leads to membrane fusion (Biering et al, 2012).
The Nipah virus glycoprotein G is a recombinant protein expressed in mammalian HEK293 cells. It is presented as a fusion protein with a mouse Fc tag linked to the C-terminus of glycoprotein G, amino acids 71-602.
We established preliminary specifications defining acceptable ranges for the parameters indicated herein below for our Anti Nipah Virus IgM Capture ELISA kit. These parameters were tracked day-to-day, run-to-run, and operator-to-operator, over a schedule defined inhouse.
Recommended assay characteristics included absorbance of a zero concentration standard; factors which describe the calibration for each standard and statistical description of the calibration curve such as coefficient of correlation, slope and/or intercept; and recovery of results on control samples. It is important to be able to relate the specifications for a parameter to expected reliability of the result. Our in-house standard defined was r=0.990.
1.A new diagnostic test has been developed to Diagnose Disease.docxmansonagnus
1.
A new diagnostic test has been developed to Diagnose Disease Y. The new test was compared to the standard diagnostic test (“the gold standard”) on the same set of patients, and the following data were obtained:
Number of patients diagnosed by the new test as having Disease Y, who actually had Disease Y = 3,252
Number of patients in the group who were diagnosed by the standard test as having Disease Y = 4,579
Number of patients diagnosed by the new test as not having Disease Y = 4, 737
Number of patients diagnosed by the new test as having Disease Y, who actually do not have Disease Y= 784
The standard diagnostic test is a tissue biopsy, and therefore, is considered to be 100% sensitive for diagnosing Disease Y.
a.
Create the 2x2 table that shows this data
b.
Calculate:
i.
The sensitivity of the new test
ii.
The specificity of the new test
iii.
The false positive rate of the new test
iv.
The false negative rate of the new test
v.
The positive predictive value of the new test
vi.
The negative predictive value of the new test
vii.
The likelihood ratio positive for the new test
viii.
The likelihood ratio negative for the new test
2.
Two new tests have been developed to diagnose Condition Z. One test (Test A) measures a metabolite “Metabolite A” in the serum. The other test (Test B) measures a different metabolite, “Metabolite B” in the urine. After appropriate preliminary testing, human trials are conducted. Following informed consent, the two tests were run on a group of patients with each patient getting both tests, as well as the “gold standard” test for diagnosing Condition Z. The following data were obtained:
Important!!!!
Since some answers depend on the results you obtained in previous sections of the problem, it is important for you that you show *all* work, since I will give partial credit if your analysis and set up are correct, even if your numerical result is incorrect.
Serum level (metabolite A)
# of patients
Disease positive
Disease negative
(mg / ml)
(by gold standard)
(by gold standard)
0 – 1.99
25
22
3
2.0 – 3.99
273
201
72
4.0 – 5.99
584
572
12
6.0 – 7.99
538
529
9
8.0 – 9.99
175
170
5
>10.0
14
14
0
Urine level (metabolite B)
(ng/ml)
0 – 2.99
30
5
25
3.0 – 5.99
245
46
199
6.0 – 8.99
423
400
23
9.0 – 11.99
628
620
8
12.0 – 14.99
175
169
6
15.0 – 17.99
99
95
4
>18.0
9
9
0
a)
For test A, a cutoff value of 4.0 mg / ml of metabolite A is chosen as the boundary between a negative and a positive test result (i.e., values below 4.0 mg / ml
are considered “negative” and values of 4.0 mg / ml or greater are considered “positive”).
For test B, a cutoff value of 6.0 ng / ml for metabolite B is chosen as the boundary between a negative and a positive test result (i.e., values below 6.0 ng / ml are considered “negative” and values of 6.0 ng / ml or greater are considered.
Ab find, an antibody test after covid 19 vaccination by meril lifeYashChopra43
Meril Life has created ABFind, India's first post-covid-19 vaccine antibody test kit. Here's where you can learn about home testing for fast neutralising antibodies.
Accuracy report of Healgen IgG/IgM Rapid Test kits AntibodyHK HuZef
1. Accuracy
1.1 Purpose
To evaluate the equivalence of COVID-19 IgG/IgM Rapid Test result and clinical diagnosis.
1.2 Method
By testing clinical samples with known results, to evaluate the accuracy of COVID-19 IgG/IgM
Rapid Test (Whole blood/Serum/Plasma).
1.3 Material
COVID-19 IgG/IgM Rapid Test Cassette (Whole blood/Serum/Plasma)
Cassette Lot1: 2002155,Lot2:2002156,Lot3:2002157
Clinical samples
1.4 Test Procedure
1) Prepare specimens: tests were taken to clinical partner to evaluate, totally 113 specimens.
2) Perform the test according to the test procedure in the package insert
1.5 Result
1) IgM
Epidemiological Approaches for Evaluation of diagnostic tests.pptxBhoj Raj Singh
Diagnosis of a disease or a problem is the first step towards solution/ treatment. Clinical Diagnosis or Provisional Diagnosis is the first step in diagnosis and is done after a physical examination of the patient by a clinician. Clinical diagnosis may or may not be true and to reach Final diagnosis Laboratory Investigations using gross and microscopic pathological observations and determining the disease indicators are required. The diagnostic tests may be Non-dichotomous Diagnostic Tests (when continuous values are given by the test in a range starting from sub-normal to above-normal range) and Dichotomous Diagnostic Tests (when results are given either plus or minus, disease or no-disease). To make non- Dichotomous diagnostic test a Dichotomous one you need to establish the cut-off values based on reference values or Gold Standard test readings or with the use of Receiver operator characteristic (ROC) curves, Precision-Recall Curves, Likelihood Ratios, etc., and finally establishing statistical agreement (using Kappa values, Level of Agreement, χ2 Statistics) between the true diagnosis and laboratory diagnosis. Thereafter, the Accuracy, Precision, Bias, Sensitivity, Specificity, Positive Predictive value, and Negative Predictive value, of a diagnostic test are established for use in clinical practice. Diagnostic tests are also used to determine Prevalence (True prevalence, apparent prevalence) and Incidence of the disease to estimate the disease burden so that control measures can be implemented. There are several Phases in the development and use of a diagnostic assay starting from conceptualization of the diagnostic test, development and evaluation to determine flaws in diagnostic test use and Interpretation influencers. This presentation mainly deals with the epidemiological evaluation procedures for diagnostic tests.
"Population Screening Tewst for difficult and Rural areas"
Very reliable methodology to obtain a map of Prevention of HIV,Sifillis, Hepatites B&C and reduce the mortality by taking effective measures...
Further details write to :
Andreefstathiou@bio-oxford.com.br
www.bio-oxford.com.br
Bio-Oxfort(Brazil)introduce the Populational Screening Test for HIV,SIfillis,Hepatites B&C for all Goverments and Lab wourlwide using Elisa filter paper(especially on difficult and rural areas).The Focus is to prevent and diagnosy those deaseas on time to be trat it and them reduce the % of mortality!
Details Available on Request..For all Goverments and Lab institutions Wourlwide..100%Approved by the Brazilian Health Authorities further write to:the_greek36@yahoo.com.br.
Validation of the Q - Preven HIV 1 2 DBS Immunoenzyme Kit REPORT FIN 11012012
1. OFFICE OF THE DEPUTY DIRECTOR
VIROLOGY
NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES
1 Modderfontein Road, Sandringham, 2031
Tel: +27 (0)11 386-6328 Fax: +27 (0)11 386-6411
Validation of the Q – Preven HIV 1 + 2 DBS Immunoenzyme Kit
Summary:
The Q-Preven HIV 1+2 DBS kit is an enzyme immunosorbent assay (ELISA) for the detection of
antibodies against HIV 1, HIV 2 and HIV 1 subtype O in Dried Blood Spot Specimens (DBS). The
kit consists of the following items: Dried Blood Spot Collection Kit which consists of the filter paper
and lancet; and the Test Kit which consists of ELISA Microplate and ELISA reagents required to
conduct an ELISA test. Supplies with the kit are negative and positive dried blood spot controls.
The following steps were completed during the validation:
Replicate testing using Kit Controls:
The negative DBS control and the positive DBS control from the Q-Preven test kit was tested 8
times in the same run and the results analyzed. All the controls passed validation and all controls
run as samples were within acceptable ranges i.e. the negative controls were negative and the
positive controls were positive.
Precision and Accuracy Testing:
Three negative and three positive controls taken from the Q-Preven test kit were tested over a
period of five consecutive days. The same operator tested the controls over the five day period and
the same plate washer, plate incubator and plate reader was used during the testing. The results of
the precision and accuracy testing are listed in Table 1 below:
2. Table 1
ID Day 1 -
Ratio
Day 2 -
Ratio
Day 3 -
Ratio
Day 4 -
Ratio
Day 5 -
Ratio
MEAN SD %CV
Negative
control
0.317 0.332 0.347 0.450 0.365 0.3622 0.0522 14.41%
Negative
control
0.328 0.328 0.325 0.399 0.355 0.347 0.0315 9.08%
Negative
control
0.257 0.328 0.332 0.383 0.329 0.3258 0.0449 13.78%
Positive
control
16.845 22.969 21.487 15.192 16.589 16.6164 3.3971 18.25%
Positive
control
18.506 22.969 17.776 19.038 19.579 19.5736 2.0116 10.28%
Positive
control
19.642 22.969 19.949 19.038 19.579 20.2354 1.563 7.72%
The %CV is detailed in the kit insert as follows for Inter Assay Reproducibility:
Negative 7.3%
Positive 3.5%
The %CV is detailed in the kit insert as follows for Inter Assay Repetitively:
Negative 17.3%
Positive 9.5%
3. The %CV obtained for all the negative samples should be between 7.3% and 17.3%. All three
negative control %CV was less than 17.3% and is acceptable. The OD value between each
negative sample over the 5 days was <30%, therefore Accuracy between each negative control
reading was good.
The %CV obtained for all the positive samples should be between 3.5% and 9.5%. Two of the three
positive control %CV was out of the acceptable range. The OD value between each positive sample
over the 5 days was <30%, therefore Accuracy between each positive control reading was good.
Sensitivity and Specificity testing:
50 known negative DBS samples and 42 known positive DBS samples were randomly selected and
tested on the Q-Preven assay. The result of the samples on the Q-Preven assay is 100% in
concordance with the initial NICD laboratory results. The sensitivity and specificity of the Q-Preven
Assay is listed below.
Sensitivity: 100%
Specificity: 100%
Negative Predictive Value: 100%
Positive Predictive Value: 100%
Replicate Testing - New Controls
Additional controls were tested.The lot numbers received were 2028200180 and 2028300180 for the
negative and the positive controls respectively. The negative and the positive controls were run 8
times in the same run and the results analyzed. All controls passed validation and all the controls
run as samples were within acceptable ranges i.e. the negative controls were negative and the
positive controls were positive.
4. The test method, calculation procedure, specifications of Validity and Interpretation of results was
taken from the Q-Preven Package insert Revision 3 – 28/12/2011
Limitations of Validation:
Specimens known to be positive or negative based on NICD test results were used.
There was no direct comparison testing between plasma/serum and dried blood spot testing to
assess performance of the kit.
Limited numbers of specimens were used for sensitivity and specificity to demonstrate that the
assay performed as expected.
General comment
The package insert although readable requires additional editing to ensure that there is no ambiguity
in terms of performing the assay.
Testing and Excel Spreadsheets done by: Ushmita Patel
Date: 28 December 2011
Report compiled by: Beverley Singh and Ushmita Patel
Date: 11 January 2012
Report Reviewed and Approved By: Prof Adrian J Puren
Date: 11 January 2012
Signature:
The report is not an endorsement or otherwise of the product.