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Home > Evaluation of Breast Cancer Biomarkers Using Genexpert® on Core Biopsy-A Retrospective Laboratory Based Validation Study.

Evaluation of Breast Cancer Biomarkers Using Genexpert® on Core Biopsy-A Retrospective Laboratory Based Validation Study.

Thesis Info

Author

Chesori, Erick

Department

Pathology (East Africa)

Program

MMed

Institute

Aga Khan University

Institute Type

Private

City

Karachi

Province

Sindh

Country

Pakistan

Thesis Completing Year

2018

Thesis Completion Status

Completed

Subject

Medicine

Language

English

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676728050001

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Introduction: Breast cancer is the most common malignancy in women worldwide. It is a significant cause of cancer related morbidity and mortality among Kenyan women. Evaluation of Estrogen receptor (ER), Progesterone receptor (PR), and Human epidermal growth factor receptor 2 (HER2) in breast cancer tissue is standard of care as these biomarkers have been shown to have both prognostic and predictive utility. Immunohistochemistry (IHC) is the gold standard for evaluation of ER/PR/HER2, but its availability in Kenya is limited due to the high operational cost. There have been recent developments in alternative cheaper and readily accessible molecular based testing platforms for ER/PR/HER2. The GeneXpert®’s Breast Cancer Stratifier (BCS), is a quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR) simple cartridge based assay developed by Cepheid Inc that quantifies mRNA expression of ER, PR, HER2, and Ki-67,(a marker of proliferation). The study aimed to evaluate sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV) and accuracy of the BCS assay for ER/PR/HER2 in breast cancer tissue core biopsies compared to IHC. The association of Ki-67 expression as tested by the BCS assay and IHC with tumor grade and mitotic counts was also evaluated. Methods: Core biopsy slides and Formalin fixed paraffin embedded (FFPE) tissue blocks of pathologically confirmed breast cancer diagnosed between April 2016 and January 2018, were retrieved from the archives at Aga Khan University’s Department of Pathology. Haematoylin and Eosin (H&E) and IHC slides for ER/PR/HER2 were reviewed and the appropriate block selected for nucleic acid extraction. Tissue scrolls were cut at 10um and a single step nucleic acid extraction performed according to the BCS assay protocol. The BCS cartridges were loaded with the extracted RNA and run on the GeneXpert® instrument. Data Management and Analysis: Data from both the BCS assay and IHC was entered on a Microsoft Excel spreadsheet for each marker and transferred to SPSS version 20 (IBM corporation). Sensitivity, specificity, PPV and NPV with 95% CI was analyzed from a 2X2 table. Kappa statistics and percentage agreement between the two tests was calculated. Diagnostic odd’s ratio was calculated as a measure of association of Ki-67 to the Nottingham tumor grade and mitotic counts. Results: A total of 162 breast cancer core biopsies were analysed. The predominant histologic type and grade was grade 2 Ductal carcinoma. Sensitivity, specificity, PPV, NPV and accuracy for each marker on the BCS was as follows: 86.96%, 94.74%, 98.04%, 70.59% and 88.89%
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نوجوانوں کے تعاون سے دہشت گردی کا خاتمہ

نوجوانوں کے تعاون سے دہشت گردی کا خاتمہ
نحمدہ ونصلی علی رسولہ الکریم امّا بعد فاعوذ بااللہ من الشیطن الرجیم
بسم اللہ الرحمن الرحیم
معزز اسا تذہ کرام اور میرے ہم مکتب شاہینو!
آج مجھے جس موضوع پر اظہار خیال کرنا ہے وہ ہے:’’نو جوانوں کے تعاون سے دہشت گردی کا خاتمہ‘‘
صدرِذی وقار!
برائی جہاں بھی ہو، گھر کے اندر ہو گھر کے باہر ہو ، بازار میں ہو، تھانہ کچہری میں ہوں جہاں بھی ہو اس کو ختم کرنا، اس کو نیست و نابود کرنا، اس کو صفحہ ہستی سے مٹانا ایک مسلمان کا فرض ہے۔ اور اس کے لئے اس کا خاتمہ جزو لاینفک ہے۔
جنابِ صدر!
فرمان رسالت مآب ؐہے کہ تم میں سے جو کوئی برائی دیکھے اسے ہاتھ سے روکے، اگر ہاتھ سے نہ روک سکے تو اسے زبان سے منع کرے اور اگر زبان سے بھی منع نہ کر سکے تو اسے دل میں برا سمجھے ۔ آپ ؐنے ارشاد فر مایا کہ یہ ایمان کا آخری درجہ ہے۔
جنابِ صدر!
معاشرے کو سنوارنا، معاشرے کو نکھارنے کے لیے شب وروز ایک کرنا، انتہائی کدو کاوش کرنا، جہد مسلسل سے کام لینا تن، من، دھن کی بازی لگانے کیلئے پیہم جدوجہد کرنا ہم سب کی ذمہ داری ہے۔
درد دل کے واسطے پیدا کیا انسان کو
ورنہ طاعت کے لیے کچھ کم نہ تھے کروبیاں
صدرِذی وقار!
ہر ایک کے لیے بالعموم اور نوجوان کے لیے بالخصوص یہ ناگزیر ہے کہ ہم اس معاشرے اور قوم کے گلستان حیات میں میں اُگنے والے خودرو غیر مفید پودوں کو اپنی خداداد صلاحیت سے نکال باہر پھینکیں، گلستان ہستی میں چلنے والی بادِ نسیم کومتعفن کرنے والی غیراخلاقی بیماریوں کا قلع قمع کریں۔
جنابِ صدر!
ہمارے ملک میں دہشت گردی کا اژدہا خوف و ہراس پھیلارہا ہے، پشاور...

فقہ اسلامی اور مروجہ ملکی قوانین کے تناظر میں عذر کی جدید طبی اور نفسیاتی صورتوں کا تجزیاتی مطالعہ

Shariah is comprised of five main branches: adab (behavior, morals and manners), ibadah (ritual worship), i’tiqadat (beliefs), mu’amalat (transactions and contracts) and ‘uqubat (punishments). These branches combine to create a society based on justice, pluralism and equity for every member of that society. Furthermore, Shariah forbids to impose it on any unwilling person. Islam’s founder, Prophet Muhammad, demonstrated that Shariah may only be applied if people willingly apply it to themselves—never through forced government implementation. Muslim jurists argued that laws such as these clearly mandated by God, are stated in an unambiguous fashion in the text of the Qur'an in order to stress that the laws are in and of themselves ethical precepts that by their nature are not subject to contingency, context, or temporal variations. It is important to note that the specific rules that are considered part of the Divine shari'a are a special class of laws that are often described as Qur'anic laws, but they constitute a fairly small and narrow part of the overall system of Islamic law. In addition, although these specific laws are described as non-contingent and immutable, the application of some of these laws may be suspended in cases of dire necessity (darura). Thus, there is an explicit recognition that even as to the most specific and objective shari'a laws, human subjectivity will have to play a role, at a minimum, in the process of determining correct enforcement and implementation of the laws.

Designing and Fabrication of Microfluidic Device for Therapeutic Drug Monitoring

Cardiovascular diseases are one of the leading causes of mortality in Pakistan with prevalence rate of 19 %. Digoxin, a cardiac glycoside with positive inotropic effect is most commonly prescribed to cardiac patients; involving therapeutic monitoring of drug in serum/plasma through lengthy immunoassay procedures in practice. Also, the detection facility is restricted to private labs in major cities of Pakistan. Nanotechnology with the help of nanomaterials as compared to conventional lengthy procedures offers robust, patient centered on chip methodologies for detection of therapeutically important drugs in serum/plasma. The aim of the current study was fabrication of microfluidic device offering on chip QDs based detection of clinical range of digoxin (0.8-2.0 ng per ml) in custom-made optical setup. To achieve the said objectives, sequence of experiments were conducted. It was imperative to delineate the effect of pH of media on the fluorescence of zinc sulphide (ZnS). ZnS nanowires were conjugated with different log dilutions of mercaptoacetic acid (MAA) and digoxin antibody (Ab). To observe the effect of each dilution on fluorescence of NWs, pH of the media was monitored before conjugation. This study highlights the enhancement in PL of ZnS NWs when pH of the media is almost equal to the pKa of carboxyl group of MAA (pH ~ pKa). While, quenching in fluorescence was observed when pKa < pH> pKa. Thus, proving our hypothesis of use of ZnS as a fluorescent tag for biological applications. The effect of pH, ions in media and time of incubation on the PL of MAA coated QDs was studied by incubating dots in three different phosphate buffers. The pH of media for each buffer was adjusted as acidic (pH <7.2), neutral (7.2 - 8.0) and basic (pH> 14.0).The PL response from dots in buffer 1 was more profound as compared to other two buffers. The current study demonstrated maximum fluorescence from dots in buffer 1 within pH range of 7.0 – 10.0, which increases with increasing time of incubation.Electrochemical analysis was performed to study the mechanism of electron transfer from QDs to linker (MAA) and then to Ab using electrochemical analysis. Electrochemical analysis shows resistance in electron transfer when electrode was modified with QDs and Ab conjugated QDs (QD-MAA-Ab) as compared to when modified with MAA only. The number of electrons calculated during the oxidation or anodic cycle were: 2, 1,3 and 4 for GCE, QD, QD-MAA and QD-Ab, respectively. During the reduction or cathodic cycle, the electrons found were 2, 1,4 and 6 for GCE, QD, QD-MAA and QD-Ab. Finally, detection of different log dilutions of digoxin inclusive of the therapeutic range (0.8-2.0 ng/ml) spiked in PBS buffer (1ml) using emission (quantum dots (QD)) and plasmon based (gold nanoparticles (SERS)) methods. Limit of detection (LOD) achievable through emission-based methodology was 0.5 ng/ml while 0.4 ng/ml through plasmon resonance of gold nanoparticles. Then the emission-based detection was performed in fabricated microfluidic device using homemade optical detection setup. The fabricated device is of ((H x W x D) 2.7’’ x 0.98” x 0.005)) as compared to conventional digoxin detection machine (Architect i2000SR: (H x W x D) 48’’ x 61” x 49”). The current study envisages replacement of conventional methodologies with microfluidic device or chip using quantum dots and SERs based tags as compared to conventional enzyme-based labels. The said device would be cost effective, portable and can easily be carried to remote areas of country.