Noninvasive Fetal Genotyping by Droplet Digital PCR to Identify Maternally Inherited Monogenic Diabetes Variants
BACKGROUND: Babies of women with heterozygous pathogenic glucokinase (GCK) variants causing mild fasting hyperglycemia are at risk of macrosomia if they do not inherit the variant. Conversely, babies who inherit a pathogenic hepatocyte nuclear factor 4α (HNF4A) diabetes variant are at increased risk of high birth weight. Noninvasive fetal genotyping for maternal pathogenic variants would inform pregnancy management. METHODS: Droplet digital PCR was used to quantify reference and variant alleles in cell-free DNA extracted from blood from 38 pregnant women heterozygous for a GCK or HNF4A variant and to determine fetal fraction by measurement of informative maternal and paternal variants. Droplet numbers positive for the reference/alternate allele together with the fetal fraction were used in a Bayesian analysis to derive probability for the fetal genotype. The babies’ genotypes were ascertained postnatally by Sanger sequencing. RESULTS: Droplet digital PCR assays for GCK or HNF4A variants were validated for testing in all 38 pregnancies. Fetal fraction of ≥2% was demonstrated in at least 1 cell-free DNA sample from 33 pregnancies. A threshold of ≥0.95 for calling homozygous reference genotypes and ≤0.05 for heterozygous fetal genotypes allowed correct genotype calls for all 33 pregnancies with no false-positive results. In 30 of 33 pregnancies, a result was obtained from a single blood sample. CONCLUSIONS: This assay can be used to identify pregnancies at risk of macrosomia due to maternal monogenic diabetes variants.
Citation
@article{r.c.2020,
author = {Caswell, R. C. and Snowsill, T. and Houghton, J. A. L. and
Chakera, A. J. and Shepherd, M. H. and Laver, T. W. and Knight, B.
A. and Wright, D. and Hattersley, A. T. and Ellard, S.},
title = {Noninvasive {Fetal} {Genotyping} by {Droplet} {Digital} {PCR}
to {Identify} {Maternally} {Inherited} {Monogenic} {Diabetes}
{Variants}},
journal = {Clinical Chemistry},
volume = {66},
number = {7},
pages = {958-965},
date = {2020-07-01},
url = {https://tristansnowsill.co.uk/noninvasive-fetal-genotyping-by-droplet-digital-pcr.html},
doi = {10.1093/clinchem/hvaa104},
langid = {en},
abstract = {BACKGROUND: Babies of women with heterozygous pathogenic
glucokinase (GCK) variants causing mild fasting hyperglycemia are at
risk of macrosomia if they do not inherit the variant. Conversely,
babies who inherit a pathogenic hepatocyte nuclear factor 4α (HNF4A)
diabetes variant are at increased risk of high birth weight.
Noninvasive fetal genotyping for maternal pathogenic variants would
inform pregnancy management. METHODS: Droplet digital PCR was used
to quantify reference and variant alleles in cell-free DNA extracted
from blood from 38 pregnant women heterozygous for a GCK or HNF4A
variant and to determine fetal fraction by measurement of
informative maternal and paternal variants. Droplet numbers positive
for the reference/alternate allele together with the fetal fraction
were used in a Bayesian analysis to derive probability for the fetal
genotype. The babies’ genotypes were ascertained postnatally by
Sanger sequencing. RESULTS: Droplet digital PCR assays for GCK or
HNF4A variants were validated for testing in all 38 pregnancies.
Fetal fraction of ≥2\% was demonstrated in at least 1 cell-free DNA
sample from 33 pregnancies. A threshold of ≥0.95 for calling
homozygous reference genotypes and ≤0.05 for heterozygous fetal
genotypes allowed correct genotype calls for all 33 pregnancies with
no false-positive results. In 30 of 33 pregnancies, a result was
obtained from a single blood sample. CONCLUSIONS: This assay can be
used to identify pregnancies at risk of macrosomia due to maternal
monogenic diabetes variants.}
}