BACKGROUND:
Genomic chimerism, the co-occurrence of cells from different genetic
origins, provides important diagnostic information in diverse clinical
contexts, including graft injury detection and longitudinal surveillance of
hematopoietic stem cell transplantation patients, but existing assays are
limiting. Here we applied single-molecule molecular inversion probes
(smMIPs), a high throughput sequencing technology combining multiplexed
target capture with read quantitation mediated by unique molecular
identifiers, to detect chimerism based on the presence or absence of
polymorphic genomic loci.
METHODS:
We designed a 159 smMIP panel targeting 40 autosomal regions of
frequent homozygous deletion across human populations and two sex-linked
loci. We developed methods for detecting and quantitating loci absent from
one cell population but present in another, which could be used to
sensitively identify chimeric cell populations.
RESULTS:
Unrelated individuals and first-degree relatives were highly
polymorphic across the loci examined. Using synthetic DNA mixtures, limits
of detection of at least 1 in 10,000 chimeric cells was demonstrated without
prior knowledge of genotypes, and mixtures of up to four separate donors
could be deconvoluted. Quantitative linearity over four orders of magnitude
and false positive rates below 1 in 85,000 events were achieved. 11 of 11
post-transplant clinical specimens from patients with hematological
malignancies testing positive for residual cancer by conventional methods
had detectable chimeric populations by smMIP, while 11 of 11 specimens
testing negative by conventional methods were low-positive for chimerism by
smMIP.
CONCLUSIONS:
smMIPs are scalable to high sensitivity and large numbers of
informative markers, enabling ultrasensitive chimerism detection for many
clinical purposes.