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152. Use of copy number variation polymorphism to assess cellular and cell-free DNA chimerism following transplantation

Author

Whitlam, John Breis and Whitlam, John Breis

Abstract

A state of genetic chimerism is created by allogenic transplantation, the quality and quantity of which may have diagnostic significance. The monitoring of cellular macrochimerism following allogeneic hematopoietic cell transplantation (HCT) is standard of care. It provides an assessment of engraftment, prognostic information, and guides therapeutic interventions. Separately, the discovery of cell-free DNA (cfDNA) chimerism following solid organ transplantation has raised the possibility that increases in donor genotype graft-derived cfDNA may be biomarker for rejection. As a result of these and other developments, the clinical and research requirements for chimerism analysis in the transplantation context exceeds the capabilities offered by existing methodologies. To address this, a panel of 39 droplet digital PCR (ddPCR) assays was developed. These targeted highly polymorphic copy number variation (CNV) loci strategically selected using a population genomics approach to maximise the probability of a donor one copy, recipient zero copy genotype combination (and vice versa). These informative combinations create a negative background against which absolute quantification of the one copy genotype can be performed using ddPCR. Analytical validation of the developed chimerism analysis method for absolute quantification of cfDNA was performed. All studied assays performed linearly across the range <6-1280 copies/mL. Limit of blank was 0 copies/mL, limit of detection was 6 copies/mL, and limit of quantification was 8 copies/mL. A method for genotyping donor and recipient informative CNV loci from chimeric cfDNA was developed and conceptually validated using donor and recipient genomic DNA. The developed chimerism analysis method was used to evaluate the diagnostic validity of absolute measurements of plasma graft-derived cfDNA and total cfDNA, as well as the relative measure of graft fraction, for the diagnosis of kidney transplant (KT) rejection. 61 indication biopsy-ma

Published
2019

153. Use of a new end-stage kidney disease risk calculator in the Kidney Disease Improving Global Outcomes guideline to evaluate the impact of different living kidney donor candidate assessments

Author

Lee, Darren, primary, Manzoor, Momena, additional, Harley, Geoff, additional, Whitlam, John, additional, Cook, Natasha, additional, Choy, Suet-wan, additional, Sandiford, Megan, additional, Gibson, Charlotte, additional, McMahon, Lawrence P, additional, and Roberts, Matthew A, additional

Published
2018
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155. The Routledge Intermediate Brazilian Portuguese Reader

Author

Whitlam, John and Whitlam, John

Subjects
Readers, Portuguese language--Brazil--Readers
Abstract

The Routledge Intermediate Brazilian Reader is a comprehensive reader aimed at intermediate level students of Brazilian Portuguese. The aim is to provide a structured language teaching resource that is enjoyable and stimulating for learners, but that also provides meaningful cultural contexts.This Brazilian Reader consists of twenty readings graded on the basis of complexity of vocabulary, grammar and syntax. It presents a range of different text types which give a good representation of contemporary Brazilian writing, including fiction and non-fiction by some of Brazil's most prominent and popular authors.Key features include:vocabulary lists for quick referencereading comprehension questions exercises to learn and review important vocabulary focus on idiomatic expressionsfull answer key to vocabulary and idiom exercisesPortuguese-English glossary at the backSuitable for both class use and independent study, The Routledge Intermediate Brazilian Reader is an essential tool for facilitating vocabulary learning and increasing reading proficiency.

Published
2014

157. Modern Brazilian Portuguese Grammar Workbook

Author

Whitlam, John and Whitlam, John

Subjects
Portuguese language--Textbooks for foreign speakers--English
Abstract

Modern Brazilian Portuguese Grammar Workbook is an innovative book of exercises and language tasks for all learners of Brazilian Portuguese. The book is divided into two sections: Part A provides exercises based on essential grammatical structures Part B practises everyday functions (e.g making social contact, asking questions and expressing needs) A comprehensive answer key at the back of the book enables you to check on your progress. Modern Brazilian Grammar Workbook is ideal for all learners who have a basic knowledge of Brazilian Portuguese, including undergraduates taking Brazilian Portuguese as a major or minor part of their studies, as well as intermediate and advanced students in schools and adult education. It can be used independently or in conjunction with Modern Brazilian Portuguese Grammar: A Practical Guide.

Published
2013

158. Diagnostic application of kidney allograft‐derived absolute cell‐free DNAlevels during transplant dysfunction

Author

Whitlam, John B., Ling, Ling, Skene, Alison, Kanellis, John, Ierino, Francseco L., Slater, Howard R., Bruno, Damien L., and Power, David A.

Abstract

Graft‐derived cell‐free DNA(donor‐derived cell‐free DNA) is an emerging marker of kidney allograft injury. Studies examining the clinical validity of this biomarker have previously used the graft fraction, or proportion of total cell‐free DNAthat is graft‐derived. The present study evaluated the diagnostic validity of absolute measurements of graft‐derived cell‐free DNA, as well as calculated graft fraction, for the diagnosis of graft dysfunction. Plasma graft‐derived cell‐free DNA, total cell‐free DNA, and graft fraction were correlated with biopsy diagnosis as well as individual Banff scores. Sixty‐one samples were included in the analysis. For the diagnosis of antibody mediated rejection, the receiver‐operator characteristic area under the curves of graft‐derived cell‐free DNAand graft fraction were 0.91 (95% CI0.82‐0.98) and 0.89 (95% CI0.79‐0.98), respectively. Both measures did not diagnose borderline or type 1A cellular mediated rejection. Graft fraction was associated with a broader range of Banff lesions, including lesions associated with cellular mediated rejection, while graft‐derived cell‐free DNAappeared more specific for antibody mediated rejection. Limitations of this study include a small sample size and lack of a validation cohort. The capacity for absolute quantification, and lower barriers to implementation of this methodology recommend it for further study. The absolute measurements of plasma graft‐derived and total cell‐derived DNA, with the relative measure of calculated graft fraction, have good diagnostic performance for antibody‐mediated rejection in kidney transplant recipients undergoing for‐cause biopsy.

Published
2019
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163. Ultrafiltration in Serum Protein Binding Determinations

Author

Whitlam, John B. and Brownx, Kenneth F.

Abstract

The ultrafiltration technique was evaluated theoretically and experimentally for use in clinical serum binding determinations. It is apparent from free energy considerations that the ultrafiltrate concentration approaches the true free concentration only as the pressure gradient causing flow reduces to zero. The theory presented accounts for the previously unexplained lower ultrafiltrate concentration observed at higher filtration pressures. Mathematical simulations of the molecular separation show that the ultrafiltrate concentration remains constant during filtration, and, thus, binding equilibria are not disturbed by this procedure, suggesting that an arbitrary restriction on the volume filtered is unnecessary. This finding greatly extends the value of the ultrafiltration technique in clinical binding determinations, especially for strongly bound, potent drugs where assays may be insufficiently sensitive to detect the extremely small free fractions reliably. These theoretical findings were verified experimentally by ultrafiltration of salicylate, ibuprofen, and carprofen in buffer, purified proteins, and whole serum.

Published
1981
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165. Binding of arylpropionic acid antiinflammatory drugs to crystalline albumin and whole serum

Author

Whitlam, John B. (John Barry)

Subjects
Anti-inflammatory agents, Drugs -- Bioavailability
Abstract

The work described in this thesis was carried out in the Department of Pharmacy at the University of Sydney, under the supervision of Dr K.F. Brown. This thesis has not been submitted for a degree at any other University. Full acknowledgement has been made where the work of others has been cited or used. A number of publications are included in support of this thesis.

Published
1981

166. Studies on the binding of ibuprofen to serum albumin

Author

Whitlam, John B. (John Barry)

Subjects
Anti-inflammatory agents, Serum albumin
Abstract

Throughout the past two decades many thousands Of chemicals have been screened using an anti—oedemic assay technique, a standard procedure for the selection of potential anti-inflammatory agents (Paulus and Whitehouse, 1973). A number of these have been clinically evaluated land are now being used routinely for the symptomatic treatment of chronic inflammatory diseases.

Published
1977

171. Genomic Testing in Patients with Kidney Failure of an Unknown Cause: A National Australian Study.

Author

Mallawaarachchi AC, Fowles L, Wardrop L, Wood A, O'Shea R, Biros E, Harris T, Alexander SI, Bodek S, Boudville N, Burke J, Burnett L, Casauria S, Chadban S, Chakera A, Crafter S, Dai P, De Fazio P, Faull R, Honda A, Huntley V, Jahan S, Jayasinghe K, Jose M, Leaver A, MacShane M, Madelli EO, Nicholls K, Pawlowski R, Rangan G, Snelling P, Soraru J, Sundaram M, Tchan M, Valente G, Wallis M, Wedd L, Welland M, Whitlam J, Wilkins EJ, McCarthy H, Simons C, Quinlan C, Patel C, Stark Z, and Mallett AJ

Subjects
Humans, Australia, Male, Female, Middle Aged, Aged, Adult, Genetic Testing, Renal Insufficiency genetics, Renal Insufficiency diagnosis
Published
2024
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172. Implementation and Evaluation of a National Multidisciplinary Kidney Genetics Clinic Network Over 10 Years.

Author

Jayasinghe K, Biros E, Harris T, Wood A, O'Shea R, Hill L, Fowles L, Wardrop L, Shalhoub C, Hahn D, Rangan G, Kevin L, Tchan M, Snelling P, Sandow R, Sundaram M, Chaturvedi S, Trnka P, Faull R, Poplawski NK, Huntley V, Garza D, Wallis M, Jose M, Leaver A, Trainer AH, Wilkins EJ, White S, Elbaum Y, Prawer Y, Krzesinski E, Valente G, Winship I, Ryan J, Whitlam J, Nicholls K, West K, Donaldson L, Johnstone L, Lewit-Mendes M, Kerr PG, Bodek S, Chakera A, MacShane M, Mincham C, Stackpoole E, Willis F, Soraru J, Pachter N, Bennetts B, Forbes TA, Mallawaarachchi A, Quinlan C, Patel C, McCarthy H, Goranitis I, Best S, Alexander S, Stark Z, and Mallett AJ

Abstract

Introduction: Diagnostic genomic sequencing is the emerging standard of care in nephrology. There is a growing need to scale up the implementation of genomic diagnostics nationally to improve patient outcomes., Methods: This pragmatic study provided genomic or genetic testing to patients with suspected monogenic kidney disease through a national network of kidney genetics clinics (KGCs). We sought to evaluate the experiences of implementing genomic diagnostics across Australia and associated diagnostic outcomes between 2013 and 2022., Results: We successfully established and expanded a nationwide network of 20 clinics as of 2022; concurrently developing laboratory, research, and education programs to scale the clinical application of genomics in nephrology. We report on an Australian cohort of 1506 kidney patients, of whom 1322 received their test results. We assessed barriers to implementation in the nephrology context, and where possible, applied real-time solutions to improve clinical processes over 10 years., Conclusion: Developing a multidisciplinary kidney genetics model across multiple health services nationally was highly successful. This model supported optimal care of individuals with monogenic kidney disease in an economically responsible way. It has continued to evolve with technological and service developments and is now set to scale further as genomic testing for kidney patients transitions to health care system funding., (© 2024 International Society of Nephrology. Published by Elsevier Inc.)

Published
2024
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