Use of copy number deletion polymorphisms to assess DNA chimerism

Bruno, Damien L., Ganesamoorthy, Devika, Thorne, Natalie P., Ling, Ling, Bahlo, Melanie, Forrest, Sue, Veenendaal, Marieke, Katerelos, Marina, Skene, Alison, Ierino, Frank L., Power, David A. and Slater, Howard R. (2014) Use of copy number deletion polymorphisms to assess DNA chimerism. Clinical Chemistry, 60 8: 1105-1114. doi:10.1373/clinchem.2013.216077

Author Bruno, Damien L.
Ganesamoorthy, Devika
Thorne, Natalie P.
Ling, Ling
Bahlo, Melanie
Forrest, Sue
Veenendaal, Marieke
Katerelos, Marina
Skene, Alison
Ierino, Frank L.
Power, David A.
Slater, Howard R.
Title Use of copy number deletion polymorphisms to assess DNA chimerism
Journal name Clinical Chemistry   Check publisher's open access policy
ISSN 1530-8561
Publication date 2014-08
Sub-type Article (original research)
DOI 10.1373/clinchem.2013.216077
Open Access Status
Volume 60
Issue 8
Start page 1105
End page 1114
Total pages 10
Place of publication Washington DC United States
Publisher American Association for Clinical Chemistry
Collection year 2015
Subject 1308 Clinical Biochemistry
2704 Biochemistry, medical
Formatted abstract
We describe a novel approach that harnesses the ubiquity of copy number deletion polymorphisms in human genomes to definitively detect and quantify chimeric DNA in clinical samples. Unlike other molecular approaches to chimerism analysis, the copy number deletion (CND) method targets genomic loci (>50 base pairs in length) that are wholly absent from wild-type (i.e., self) background DNA sequences in a sex-independent manner.

Bespoke quantitative PCR (qPCR) CND assays were developed and validated using a series of DNA standards and chimeric plasma DNA samples collected from 2 allogeneic kidney transplant recipients and 12 pregnant women. Assay performance and informativeness were assessed using appropriate statistical methods.

The CND qPCR assays showed high sensitivity, precision, and reliability for linear quantification of DNA chimerism down to 16 genomic equivalents (i.e., 106 pg). Fetal fraction (%) in 12 singleton male pregnancies was calculated using the CNDqPCR approach, which showed closer agreement with single-nucleotide polymorphism-based massively parallel sequencing than the SRY (sex determining region Y) (Y chromosome) qPCR assay. The latter consistently underestimated the fetal fraction relative to the other methods. We also were able to measure biological changes in plasma nonself DNA concentrations in 2 renal transplant recipients.

The CND qPCR technique is suitable for measurement of chimerism for monitoring of rejection in allogeneic organ transplantation and quantification of the cell-free fetal DNA fraction in maternal plasma samples used for noninvasive prenatal genetic testing.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
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Created: Thu, 28 Aug 2014, 12:51:48 EST by Ms Kate Rowe on behalf of Institute for Molecular Bioscience