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DOI: 10.1002/pd.4132 
ORIGINAL ARTICLE 
Noninvasive twin zygosity assessment and aneuploidy detection by 
maternal plasma DNA sequencing 
Tak Y. Leung1†, James Z. Z. Qu2,3†, Gary J. W. Liao2,3, Peiyong Jiang2,3, Yvonne K. Y. Cheng1, K. C. Allen Chan2,3, Rossa W. K. Chiu2,3 
and Y. M. Dennis Lo2,3* 
1Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China 
2Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China 
3Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China 
*Correspondence to: Y. M. Dennis Lo. E-mail: loym@cuhk.edu.hk 
†These authors contributed equally. 
ABSTRACT 
Objective This study aimed to provide an individualized assessment of fetal trisomy 21 and trisomy 18 status for twin 
pregnancies by maternal plasma DNA sequencing. 
Method Massively parallel sequencing was performed on the plasma/serum DNA libraries of eight twin pregnancies 
and 11 singleton pregnancies. The apparent fractional fetal DNA concentrations between genomic regions were 
assessed to determine the zygosities of the twin pregnancies and to calculate the fetal DNA concentrations of 
each individual member of dizygotic twin pairs. Z-scores were determined for the detection of trisomy 18 and 
trisomy 21. 
Results Circulating DNA sequencing showed elevated chromosome 21 representation in one set of twins and elevated 
chromosome 18 representation in another pair of twins. Apparent fractional fetal DNA concentration analysis 
revealed both sets of twins to be dizygotic. The fractional fetal DNA concentrations for each individual fetus of the 
dizygotic twin pregnancies were determined. Incorporating the information about the fetal DNA fraction, we 
ascertained that each fetus contributed adequate amounts of DNA into the maternal circulation for the aneuploidy 
test result to be interpreted with confidence. 
Conclusion Noninvasive prenatal assessment of fetal chromosomal aneuploidy for twin pregnancies can be 
achieved with the use of massively parallel sequencing of cell-free DNA in maternal blood. © 2013 John Wiley 
& Sons, Ltd. 
Funding sources: The study is supported by the University Grants Committee of the Government of the Hong Kong Special Administrative Region, China, under the 
Areas of Excellence Scheme (AoE/M-04/06), a Sponsored Research Agreement from Sequenom, Inc. and by funding from the S. K. Yee Foundation. Y. M. D. Lo is 
supported by an endowed chair from the Li Ka Shing Foundation. 
Conflicts of interest: T. Y. L., P. J., K. C. A. C., R.W.K. C. and Y. M. D. Lo hold patents or have filed patent applications on noninvasive prenatal diagnosis using fetal 
nucleic acids in maternal plasma. Part of this intellectual property portfolio has been licensed to Sequenom, Inc. R.W.K. C. and Y. M. D. Lo have received research 
support from, are consultants to, and hold equities in Sequenom, Inc. 
INTRODUCTION 
Noninvasive prenatal testing of fetal chromosomal aneuploidies 
has been achieved with the use of massively parallel maternal 
plasma DNA sequencing.1 The test is based on detecting a 
change in representation among DNA molecules (from 
mother and fetus) present in maternal plasma as a result of 
the abnormal chromosome dosages contributed by the 
aneuploid fetus. For example, the genome of a trisomy 21 
fetus has a third copy of chromosome 21 that results in 
increased proportions of chromosome 21 DNA content in 
maternal plasma. Massively parallel sequencing-based 
noninvasive prenatal testing (MPS-NIPT) has been shown by 
several studies to provide highly sensitive and specific 
detection of trisomies 21, 18 and 13 among high risk singleton 
pregnancies.2–6 
Canick et al.7 applied MPS-NIPT for fetal aneuploidy 
detection in multi-fetus pregnancies. It was shown that Down 
syndrome was correctly classified in seven sets of twin 
pregnancies (two sets of twins where both twin fetuses had 
Down syndrome and five sets of twins where only one of the 
two twin fetuses had Down syndrome). Trisomy 13 was also 
correctly classified in one set of twin pregnancy. For the 17 sets 
of euploid twins and two sets of euploid triplets, Down 
syndrome was correctly excluded. However, the sensitivity of 
MPS-NIPT for aneuploidy detection is governed by the 
fractional fetal DNA concentration of the affected fetus.2,4 
Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley & Sons, Ltd.
676 T. Y. Leung et al. 
Maternal plasma samples with higher fetal DNA fractions are 
associated with a greater degree of overrepresentation of 
DNA amounts from the trisomic chromosome. For example, 
with the sequencing depth used for a number of the currently 
used MPS-NIPT laboratory protocols, the lower limit of fetal 
fraction for aneuploidy detection is 4%.2,4 A fetal DNA fraction 
lower than this limit may lead to false-negative detection. 
For aneuploidy diagnosis by MPS-NIPT, monozygotic twins 
can be interpreted like a singleton pregnancy. This method 
can be applied as long as the combined fetal DNA fraction 
contributed by the pair of monozygotic twins reached the 
minimum requirement, that is, the aforementioned 4%. On 
the contrary, for dizygotic twins, the fetal DNA fraction 
contributed by each individual twin member would need to 
reach the minimum requirement in order for the chromosomal 
representation of each twin to be adequately assessed by MPS-NIPT. 
However, currently adopted methods for quantifying the 
fetal DNA fractions do not determine the contributions from 
individual dizygotic twin fetuses. In the study performed by 
Canick et al., each twin fetus was assumed to have contributed 
adequate amounts of fetal DNA into maternal plasma. 
Recently, our group developed a noninvasive approach for 
determining the zygosity of twins by looking for evidence of 
genetic differences between the twins as inferred by 
differences in the apparent fractional fetal DNA concentrations 
across multiple genomic regions.8 With this approach, we can 
also estimate the fractional fetal DNA concentrations of 
individual members of dizygotic twins. Here, we incorporate 
this approach for achieving MPS-NIPT trisomy 21 and trisomy 
18 detection for twin pregnancies. 
MATERIALS AND METHODS 
Sample collection and processing 
This study was approved by the Joint Chinese University of 
Hong Kong – Hospital Authority New Territories East Cluster 
Clinical Research Ethics Committee. With informed consent, 
we recruited eight twin pregnancies and 11 singleton 
pregnancies (Table 1). The 11 singleton pregnancies involved 
euploid fetuses as confirmed by full karyotyping. Six of the twin 
pregnancies were part of the cohort previously studied,8 and 
healthy fetuses were observed at birth. Two of the twin 
pregnancies in the previous study did not have adequate 
amounts of sample available to be included in this study. 
Two other twin pregnancies in the present study, cases 01 
and 02, each involving one aneuploid fetus and one euploid 
fetus, were recruited after the completion of the earlier study 
on twin zygosity assessment. Maternal peripheral blood 
samples were taken on one occasion before any invasive 
obstetrics procedures between 11 and 36 weeks of gestation 
for all cases. 
For case 01, chorionic villus sampling was performed, and 
full karyotyping revealed one euploid fetus and one trisomy 
21 fetus. For case 02, trisomy 18 was suspected after observing 
multiple structural abnormalities during ultrasound scanning 
in the second trimester. Prenatal diagnosis was declined, and 
trisomy 18 in one child was confirmed postnatally. The other 
child was healthy. No fetal tissues were available for this study, 
but a maternal serum sample taken just before delivery was 
retrieved for analysis. For all the other cases in this study, 
maternal plasma was used. DNA from chorionic villus biopsy 
Table 1 Clinical cases and the sequencing output 
Case 
Gestational age 
(weeks + days) Twins/singleton Karyotype Utility Sequencing counts Chr21 Z-scores Chr18 Z-scores 
01 14 + 6 Twins T21 + Euploid Test 16 919 203 14.25 0.05 
02 36 + 3 Twins T18 + Euploid Test 21 797 758 0.05 38.65 
03 21 + 5 Twins Euploid2 Test 23 937 979 2.83 2.16 
04 19 + 0 Twins Euploid2 Test 18 817 253 0.42 1.69 
05 21 + 5 Twins Euploid2 Test 8 708 537 1.99 1.53 
06 19 + 0 Twins Euploid2 Test 8 055 232 1.26 0.89 
07 27 + 3 Twins Euploid2 Test 3 486 194 1.96 1.39 
08 30 + 1 Twins Euploid2 Test 15 620 487 1.00 1.33 
09 16 + 4 Singleton Euploid Reference 21 248 214 NA NA 
10 16 + 1 Singleton Euploid Reference 24 563 124 NA NA 
11 13 + 0 Singleton Euploid Reference 22 001 984 NA NA 
12 16 + 1 Singleton Euploid Reference 15 198 875 NA NA 
13 12 + 5 Singleton Euploid Reference 16 913 971 NA NA 
14 16 + 2 Singleton Euploid Reference 14 581 277 NA NA 
15 12 + 4 Singleton Euploid Reference 11 551 742 NA NA 
16 17 + 3 Singleton Euploid Reference 16 476 854 NA NA 
17 11 + 2 Singleton Euploid Reference 17 752 722 NA NA 
18 14 + 0 Singleton Euploid Reference 16 002 683 NA NA 
19 12 + 4 Singleton Euploid Reference 13 924 820 NA NA 
Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley  Sons, Ltd.
Noninvasive twin zygosity and aneuploidy detection 677 
or cord blood from each twin fetus, except case 02, was 
genotyped. The degree of concordance in the genotypes 
between each twin pair was used to confirm if the twins were 
monozygotic or dizygotic. For case 02, the different postnatal 
phenotypes of the two neonates served as the evidence 
indicating that they were dizygotic. 
Maternal blood samples were centrifuged twice9 to separate 
the plasma/serum portion from the blood cell portion. Plasma 
or serum DNA was extracted. For each twin pregnancy, two 
analyses were performed. One analysis was based on target 
capture sequencing for the purpose of determining the 
zygosity of the twins.8 The other analysis was performed for 
the purpose of noninvasive aneuploidy detection.1–5 
Noninvasive zygosity assessment 
The noninvasive zygosity assessment for the six euploid twin 
pregnancies was performed in our recent study,8 and the same 
protocol was applied to cases 01 and 02. Briefly, the plasma or 
serum DNA libraries were constructed with the Paired-End 
Sample Preparation Kit (Illumina), and target capturing of 
selective genomic regions was performed using the SureSelect 
Target Enrichment System (Agilent).8,10,11 The capture library 
covered 5.5Mb of genomic regions distributed over 14 
chromosomes, which were designed to target single nucleotide 
polymorphisms (SNPs) on the Affymetrix Genome-Wide 
Human SNP Array 6.0 system. As previously reported, to 
achieve accurate genotype deduction for the mother and fetus 
using the plasma DNA sequenced reads from samples 
containing at least 5% fetal DNA, each informative SNP 
would need to be sequenced to an average depth of 100 
times.8 Therefore, the plasma DNA library of case 01 was 
sequenced using four lanes in a flowcell on the Genome 
Analyzer IIx sequencer (Illumina), and case 02 was 
sequenced using two lanes in a flowcell on the HiSeq 2000 
sequencer (Illumina). The choice of the model of sequencer 
used was based on which instrument was available at the 
time of the experiments. 
After sequencing, the FetalQuant algorithm12 was used to 
analyze the ratio of alleles of SNPs that were located within 
the captured genomic regions to identify loci where the mother 
was homozygous and at least one of the twin fetuses was 
heterozygous, termed informative SNPs. The ratio of the 
fetal-specific allele to the major allele was calculated for each 
locus. Allelic ratios of adjacent SNP loci were combined to 
obtain an apparent fractional fetal DNA concentration for a 
chromosomal region. Apparent fractional fetal DNA 
concentrations were calculated for multiple chromosomal 
regions. For monozygotic twins, because the fetuses are 
genetically identical, the apparent fractional fetal DNA 
concentrations should be similar across different genomic 
regions. On the contrary, for dizygotic twins, because they are 
not genetically identical and each fetus is heterozygous at 
different sets of loci, the apparent fractional fetal DNA 
concentrations would vary across different genomic regions. 
Noninvasive aneuploidy detection 
For aneuploidy testing, plasma or serum DNA libraries 
were constructed with the TruSeq DNA Sample Preparation 
Kit (Illumina). Each DNA sample was ligated with a unique 
adaptor and then pooled to form two multiplex libraries. 
Each multiplexed pool was composed of nine or ten 
samples. For MPS-NIPT aneuploidy testing by the random 
sequencing protocol,1–5 only a low sequencing depth is 
needed. Therefore, each multiplexed pool of samples was 
sequenced using three lanes of a flowcell using the HiSeq 
2000 sequencer. 
For aneuploidy testing, sequence reads from chromosomes 
X and Y were excluded for calculating the genomic 
representation of each autosome. Z-scores were calculated 
for chromosome 21 and chromosome 18 as previously 
described.1,4 A Z-score3 is considered to indicate an 
abnormally increased chromosomal representation and hence, 
the presence of trisomy. 
Plasma DNA sequencing and alignment 
DNA libraries were sequenced by the standard paired-end 
protocol (Illumina) with a read length of 75 bp for each 
end on the HiSeq 2000 sequencer (Illumina) and a read 
length of 50 bp for each end on the Genome Analyzer IIx 
sequencer (Illumina). All sequenced reads were aligned to 
the nonrepeat-masked human reference genome (Hg18) 
using SOAP2.13 
RESULTS 
Determination of twin zygosity by maternal plasma DNA analysis 
Microarray-based genotype analysis of the chorionic villus 
biopsy or cord blood DNA provided the gold standard for 
determining the zygosities of the twins in case 01 (Table 2). 
The noninvasive determination of twin zygosity by maternal 
plasma DNA sequencing for the six pairs of euploid twins was 
carried out in our previous study.8 Four of these previously 
studied twin pregnancies were monozygotic (Table 2). The 
noninvasive twin zygosity test for cases 01 and 02 had not been 
performed previously. For case 01, 187106 raw paired-end 
reads were sequenced, and 157106 reads were mappable. 
Each SNP locus in the target captured regions was covered an 
average of 210 times. For case 02, 462106 raw paired-end 
reads were sequenced, and 387106 reads were mappable. 
Each SNP locus in target captured regions was covered an 
average of 493 times. We calculated the average apparent 
fractional fetal DNA concentration for every 1000 informative 
SNPs on contiguous genomic blocks within the targeted 
regions. We compared if these average values varied from 
block to block. Large fluctuations of average apparent 
fractional fetal DNA concentrations were observed for both 
cases 01 and 02 (Figure 1). The proportions of data points 
lying outside the extent of stochastic variations expected for 
monozygotic twins were 73% for case 01 and 55% for case 
02. As a reference, the proportions of data points lying 
outside these boundaries ranged from 0% to 1.93% for 
the monozygotic twin cases as previously reported. These 
data suggested that both cases 01 and 02 were dizygotic 
twin pregnancies. 
Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley  Sons, Ltd.
678 T. Y. Leung et al. 
Table 2 Zygosity status and the fractional fetal DNA concentrations of the twin fetuses 
Fractional fetal DNA concentrations of individual members 
of twins 
The range of apparent fetal DNA concentrations as shown by 
every 1000 SNPs was noted. The overall distribution of the 
observed apparent fractional fetal DNA concentrations of both 
fetuses and the combined total concentration was assumed to 
be governed by a mixture of three binomial distributions.8 By 
adopting the binomial mixture model, we resolved two of the 
distributions and their associated peaks of fetal DNA 
concentrations that had the highest likelihood of producing 
the combined total amounts of circulating fetal DNA observed 
in cases 01 and 02. For case 01, the data suggested that one 
fetus contributed 10.7% of the DNA in maternal plasma, the 
other fetus contributed 16.9% and the combined fractional 
concentration of circulating fetal DNA from both fetuses was 
27.6%. For case 02, one fetus contributed 8.80% of the DNA 
in maternal plasma, the other fetus contributed 16.3% and 
the combined fractional concentration of circulating fetal 
DNA from both fetuses was 25.1%. For case 01, to validate the 
estimated fetal DNA fraction, we retrieved the microarray-based 
genotype information of each individual twin. The 
massively parallel sequencing data covering confirmed 
informative SNPs were retrieved to calculate the fractional fetal 
DNA concentration of each individual twin member. The 
concentrations estimated using the binomial mixture statistics 
were consistent with those calculated using the known fetal 
genotype information (Table 2). The data also suggested that 
each fetus among the twin pregnancies had fractional fetal 
DNA concentrations that reached the lowest requirement, 
namely at least 4%, for aneuploidy detection by one of the 
currently used MPS-NIPT protocols.4 
Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy 
For the diagnosis of fetal chromosomal aneuploidy, the 11 
euploid singleton cases served as the reference controls. The 
eight twin pregnancies were the test cases. A median of 
16106 (range: 3106 to 24106) aligned (i.e. mapped) 
paired-end reads were sequenced from the plasma or serum 
Case 
Zygosity assessment 
Predicted fetal 
DNA % 
Measured fetal DNA % using 
microarray-based genotypes 
% Concordance in genotypes by microarray Monozygotic or dizygotic Twin 1 Twin 2 Twin 1 Twin 2 
01 78.8 Dizygotic 10.7 16.9 13.8 15.3 
02 — Dizygotic 8.8 16.3 — — 
03(6774)a 78.0 Dizygotic 7.0 11.4 7.9 10.9 
04(6870)a 99.6 Monozygotic — — — — 
05(6905)a 79.6 Dizygotic 13.9 7.0 11.2 7.8 
06(7585)a 99.7 Monozygotic — — — — 
07(8114)a 99.8 Monozygotic — — — — 
08(8207)a 99.6 Monozygotic — — — — 
aThese cases were part of a cohort investigated in a previous study.8 The case numbers adopted in the previous study8 are shown in parentheses. Two other dizygotic twin 
cases included in the previous study did not have sufficient plasma DNA available for the present study. 
Figure 1 Regional variation in apparent fractional fetal DNA concentrations. Solid line shows the average apparent fractional fetal DNA 
concentrations across blocks of 1000 consecutive informative single nucleotide polymorphisms (SNPs) for the twin pregnancy. Grey shadow 
shows the results of the computer simulation analysis of the background level of stochastic variation. Dashed lines show the maximum and 
minimum values of the predicted stochastic variation. The proportion of data points outside the boundaries is given at the top of each plot. Case 
numbers are given in the upper right corner. Large fluctuations are expected for dizygotic twin pregnancies 
Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley  Sons, Ltd.
Noninvasive twin zygosity and aneuploidy detection 679 
DNA libraries. Paired-end reads with identical start and end 
coordinates in the genome were removed. The number of 
reads originating from each autosome was counted and 
then expressed as a percentage of the total reads sequenced 
from all autosomes for the sample. This percentage value is 
the genome representation of that chromosome in the 
maternal plasma sample. Guanine–cytosine correction was 
performed for the calculation of genome representation 
of each chromosome. For the reference group, the mean 
genomic representation of chromosome 21 (%chr21) was 
1.311 (standard deviation (SD) was 0.007), and the mean 
genomic representation of chromosome 18 (%chr18) was 
2.808 (SD was 0.004). The %chr21 values for the six euploid 
twin cases ranged from 1.297 to 1.331, and the z-scores were 
all 3 (Table 1 and Figure 2). The %chr18 values for the 
six euploid twin cases ranged from 2.812 to 2.818, and the 
z-scores were all 3 (Table 1 and Figure 2). For case 01, 
the %chr21 was 1.412, which resulted in a z-score of 14.25 
(Figure 2). Because the z-score for chromosome 21 was 3, 
the result suggested that case 01 involved at least one fetus 
with trisomy 21. For case 02, the %chr18 value was 2.975, 
which gave a z-score of 38.65 (Figure 2). Because the z-score for 
chromosome 18 was 3, the result suggested that case 02 
involved at least one fetus with trisomy 18. Case 01 had normal 
representation for chromosome 18, whereas case 02 had normal 
representation for chromosome 21. 
Aneuploidy assessment of dizygotic twin fetuses 
Theoretically, the genomic representation of the aneuploid or 
trisomic chromosome (%chrT) should have a linear relationship 
with the fractional fetal DNA concentration for all trisomy cases2 
but not the euploid cases. The reason is the elevated genomic 
representation of a chromosome is contributed by the aneuploid 
fetus. One should be able to predict the %chrT of an aneuploid 
fetus when the mean value of %chrT of the reference group 
and the fetal DNA fraction of the trisomy fetus is known. We 
established the relationship between the %chr21 or %chr18 
values and the fetal DNA fraction using the following: 
%chrTsample ¼ mean%chrTreference 
þ 0:5f  mean%chrTreference 
where %chrTsample is the %chrT value of the test sample, % 
chrTreference is the %chrT value of the reference group and f 
is the fetal DNA fraction. The correlation plots are shown 
in Figure 3. 
For case 01, the correlation line for %chr21 intersected with 
the observed genomic representation of the affected twin 
pregnancy when the fractional fetal DNA concentration was 
15.4%. For case 02, the correlation line for %chr18 intersected 
with the observed genomic representation of the affected twin 
pregnancy when the fractional fetal DNA concentration was 
11.9%. For both cases, the correlation lines intercepted at fetal 
DNA concentrations that were much lower than the combined 
fetal DNA concentrations contributed by both twins. The 
results therefore suggested that only one fetus had aneuploidy 
in each twin pair. Our results also confirmed that each twin 
fetus contributed adequate amounts of DNA into maternal 
plasma to render the MPS-NIPT aneuploidy test valid for 
interpretation, that is, not a false-negative result due to 
inadequate fetal DNA percentage. 
There were seven male fetuses among the 11 euploid 
singleton cases. We determined the fetal DNA concentration 
of these cases using a real-time polymerase chain reaction 
assay targeting a gene on chromosome Y, the sex-determining 
region Y (SRY) gene. All values deviated from the correlation 
lines for %chr21 and %chr18. This was as expected because 
there was no elevation in %chr21 and %chr18 values in the 
euploid cases; hence, there should be no relationship with 
the fractional fetal DNA concentration. 
DISCUSSION 
Previously, Canick et al. investigated the use of MPS-NIPT 
for chromosomal aneuploidy detection among multi-fetus 
pregnancies.7 However, on the basis of the MPS-NIPT 
aneuploidy assessment alone, it is not known if one or both 
fetuses were affected. More important, for dizygotic twins, it is 
not known if each fetus contributed adequate amounts of DNA 
to pass the minimum quality control requirement for valid 
assessment. Here, we have demonstrated that our recently 
developed noninvasive twin zygosity test provides useful 
information for the MPS-NIPT assessment of chromosomal 
aneuploidy among twin pregnancies.8 When the twins are 
determined to be monozygotic, the MPS-NIPT aneuploidy test 
can be interpreted in the same manner as for singleton 
pregnancies. When the twins are determined to be dizygotic, 
the fractional fetal DNA concentration of each fetus can be 
calculated. This has allowed us to confirm if the fetus 
contributing the lesser amount of fetal DNA also has a value that 
reaches the minimum requirement. In this study, we have 
further shown that by exploiting the relationship between the 
genomic representation of the aneuploid chromosome and the 
Figure 2 Genomic representations (GR) of chromosome 21 and 
chromosome 18 for the reference and test cases. Broken lines 
indicate the cut-off value of genomic representation corresponding 
to a z-score that is equal to 3. The chromosome 21 genomic 
representation of case 01 is elevated, and the data point lies 
above the cut-off. The chromosome 18 genomic representation of 
case 02 is elevated, and the data point lies above the cut-off. All 
singleton control pregnancies and all other twin pregnancies show 
genomic representations for chromosomes 21 and 18 that are 
below the cut-off 
Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley  Sons, Ltd.
680 T. Y. Leung et al. 
fetal DNA fraction,2 we could further determine if one or both 
fetuses were affected. Although the method cannot pinpoint 
which one of the twins had aneuploidy, the aneuploidy 
assessment of the twin fetuses could be made with greater 
certainty to justify the need for invasive confirmatory testing. 
Because of the proof-of-principle nature of this study, 
further studies with larger sample size are needed. For case 
02, trisomy 18 was diagnosed postnatally; hence, fetal tissues 
were not available for analysis in this study. However, our 
results were consistent with the postnatal diagnosis. 
Although the noninvasive twin zygosity test provides useful 
information for interpreting the MPS-NIPT for fetal 
chromosomal aneuploidy testing, it is an added procedure 
and additional costs are involved. With the rapid reduction in 
sequencing costs, the zygosity test could be considered as an 
optional quality control step for additional reassurance in 
A 
B 
Figure 3 Determination of the number of twin fetus(es) with chromosomal aneuploidy. The red line shows the expected relationship between 
the maternal plasma genomic representation of the aneuploid chromosome and the fetal DNA fraction. The dashed line marks the genomic 
representation of the affected twin pregnancy. The black solid lines mark the fetal DNA percentage estimated for each fetus of the dizygotic 
twin pair and the combined fetal DNA percentage from both fetuses. The genomic representation and fetal DNA percentage values for the 
seven male singleton control pregnancies are depicted by squares. (A) Plot of %chr21 and fetal DNA percentage values for case 01. The 
correlation line for %chr21 intercepts with the observed genomic representation of the affected twin pregnancy when the fractional fetal DNA 
concentration is 15.4%. (B) Plot of %chr18 and fetal DNA percentage values for case 02. The correlation line for %chr18 intercepts with the 
observed genomic representation of the affected twin pregnancy when the fractional fetal DNA concentration is 11.9%. Each plot suggests that 
there is only one fetus affected by aneuploidy in each twin pair 
Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley  Sons, Ltd.
Noninvasive twin zygosity and aneuploidy detection 681 
interpretation of the aneuploidy test results. In our opinion, as 
twin pregnancies represent only a minority of pregnancies, the 
increased costs of adding this quality control step to the overall 
prenatal healthcare costs in the population as a whole should 
be affordable. On the other hand, we believe that the 
noninvasive twin zygosity test may provide additional clinical 
utility. For example, it is known that a number of pregnancy-related 
complications are associated with abnormal levels of 
circulating fetal DNA.14,15 With our approach, we could 
monitor the dynamic changes of the fetal DNA concentration 
of each dizygotic twin member for monitoring the well-being 
of each twin. 
CONCLUSION 
With the use of massively parallel sequencing of maternal 
plasma DNA, we have successfully determined the zygosity of 
twins with chromosomal aneuploidies and estimated the fetal 
DNA fraction of each dizygotic twin member. Our approach 
has made it possible to confidently interpret the MPS-NIPT 
results for trisomy 21 and trisomy 18 diagnoses among 
twin pregnancies. 
ACKNOWLEDGMENTS 
We thank Yongjie Jin for performing the sequencing and Coral 
Lee for bioinformatics support. 
WHAT’S ALREADY KNOWN ABOUT THIS TOPIC? 
• By using massively parallel maternal plasma DNA sequencing, 
noninvasive prenatal detection of fetal chromosomal aneuploidies 
has been achieved. The sensitivity of the maternal plasma DNA 
sequencing test for aneuploidy detection is governed by the 
fractional fetal DNA concentration. 
WHAT DOES THIS STUDY ADD? 
• We have recently developed a maternal plasma DNA sequencing-based 
method for the noninvasive assessment of twin zygosity. The 
method also allows the determination of the fetal DNA fraction 
contributed by each member of a pair of dizygotic twin in maternal 
plasma. In this study, we applied the new method to two dizygotic 
twin pregnancies involving one aneuploid fetus each. We 
confirmed that each fetus contributed adequate amounts of DNA 
into maternal plasma so that the aneuploidy test result could be 
interpreted with confidence. 
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Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley  Sons, Ltd.

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Twin zygosity nipt

  • 1. DOI: 10.1002/pd.4132 ORIGINAL ARTICLE Noninvasive twin zygosity assessment and aneuploidy detection by maternal plasma DNA sequencing Tak Y. Leung1†, James Z. Z. Qu2,3†, Gary J. W. Liao2,3, Peiyong Jiang2,3, Yvonne K. Y. Cheng1, K. C. Allen Chan2,3, Rossa W. K. Chiu2,3 and Y. M. Dennis Lo2,3* 1Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China 2Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China 3Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China *Correspondence to: Y. M. Dennis Lo. E-mail: loym@cuhk.edu.hk †These authors contributed equally. ABSTRACT Objective This study aimed to provide an individualized assessment of fetal trisomy 21 and trisomy 18 status for twin pregnancies by maternal plasma DNA sequencing. Method Massively parallel sequencing was performed on the plasma/serum DNA libraries of eight twin pregnancies and 11 singleton pregnancies. The apparent fractional fetal DNA concentrations between genomic regions were assessed to determine the zygosities of the twin pregnancies and to calculate the fetal DNA concentrations of each individual member of dizygotic twin pairs. Z-scores were determined for the detection of trisomy 18 and trisomy 21. Results Circulating DNA sequencing showed elevated chromosome 21 representation in one set of twins and elevated chromosome 18 representation in another pair of twins. Apparent fractional fetal DNA concentration analysis revealed both sets of twins to be dizygotic. The fractional fetal DNA concentrations for each individual fetus of the dizygotic twin pregnancies were determined. Incorporating the information about the fetal DNA fraction, we ascertained that each fetus contributed adequate amounts of DNA into the maternal circulation for the aneuploidy test result to be interpreted with confidence. Conclusion Noninvasive prenatal assessment of fetal chromosomal aneuploidy for twin pregnancies can be achieved with the use of massively parallel sequencing of cell-free DNA in maternal blood. © 2013 John Wiley & Sons, Ltd. Funding sources: The study is supported by the University Grants Committee of the Government of the Hong Kong Special Administrative Region, China, under the Areas of Excellence Scheme (AoE/M-04/06), a Sponsored Research Agreement from Sequenom, Inc. and by funding from the S. K. Yee Foundation. Y. M. D. Lo is supported by an endowed chair from the Li Ka Shing Foundation. Conflicts of interest: T. Y. L., P. J., K. C. A. C., R.W.K. C. and Y. M. D. Lo hold patents or have filed patent applications on noninvasive prenatal diagnosis using fetal nucleic acids in maternal plasma. Part of this intellectual property portfolio has been licensed to Sequenom, Inc. R.W.K. C. and Y. M. D. Lo have received research support from, are consultants to, and hold equities in Sequenom, Inc. INTRODUCTION Noninvasive prenatal testing of fetal chromosomal aneuploidies has been achieved with the use of massively parallel maternal plasma DNA sequencing.1 The test is based on detecting a change in representation among DNA molecules (from mother and fetus) present in maternal plasma as a result of the abnormal chromosome dosages contributed by the aneuploid fetus. For example, the genome of a trisomy 21 fetus has a third copy of chromosome 21 that results in increased proportions of chromosome 21 DNA content in maternal plasma. Massively parallel sequencing-based noninvasive prenatal testing (MPS-NIPT) has been shown by several studies to provide highly sensitive and specific detection of trisomies 21, 18 and 13 among high risk singleton pregnancies.2–6 Canick et al.7 applied MPS-NIPT for fetal aneuploidy detection in multi-fetus pregnancies. It was shown that Down syndrome was correctly classified in seven sets of twin pregnancies (two sets of twins where both twin fetuses had Down syndrome and five sets of twins where only one of the two twin fetuses had Down syndrome). Trisomy 13 was also correctly classified in one set of twin pregnancy. For the 17 sets of euploid twins and two sets of euploid triplets, Down syndrome was correctly excluded. However, the sensitivity of MPS-NIPT for aneuploidy detection is governed by the fractional fetal DNA concentration of the affected fetus.2,4 Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley & Sons, Ltd.
  • 2. 676 T. Y. Leung et al. Maternal plasma samples with higher fetal DNA fractions are associated with a greater degree of overrepresentation of DNA amounts from the trisomic chromosome. For example, with the sequencing depth used for a number of the currently used MPS-NIPT laboratory protocols, the lower limit of fetal fraction for aneuploidy detection is 4%.2,4 A fetal DNA fraction lower than this limit may lead to false-negative detection. For aneuploidy diagnosis by MPS-NIPT, monozygotic twins can be interpreted like a singleton pregnancy. This method can be applied as long as the combined fetal DNA fraction contributed by the pair of monozygotic twins reached the minimum requirement, that is, the aforementioned 4%. On the contrary, for dizygotic twins, the fetal DNA fraction contributed by each individual twin member would need to reach the minimum requirement in order for the chromosomal representation of each twin to be adequately assessed by MPS-NIPT. However, currently adopted methods for quantifying the fetal DNA fractions do not determine the contributions from individual dizygotic twin fetuses. In the study performed by Canick et al., each twin fetus was assumed to have contributed adequate amounts of fetal DNA into maternal plasma. Recently, our group developed a noninvasive approach for determining the zygosity of twins by looking for evidence of genetic differences between the twins as inferred by differences in the apparent fractional fetal DNA concentrations across multiple genomic regions.8 With this approach, we can also estimate the fractional fetal DNA concentrations of individual members of dizygotic twins. Here, we incorporate this approach for achieving MPS-NIPT trisomy 21 and trisomy 18 detection for twin pregnancies. MATERIALS AND METHODS Sample collection and processing This study was approved by the Joint Chinese University of Hong Kong – Hospital Authority New Territories East Cluster Clinical Research Ethics Committee. With informed consent, we recruited eight twin pregnancies and 11 singleton pregnancies (Table 1). The 11 singleton pregnancies involved euploid fetuses as confirmed by full karyotyping. Six of the twin pregnancies were part of the cohort previously studied,8 and healthy fetuses were observed at birth. Two of the twin pregnancies in the previous study did not have adequate amounts of sample available to be included in this study. Two other twin pregnancies in the present study, cases 01 and 02, each involving one aneuploid fetus and one euploid fetus, were recruited after the completion of the earlier study on twin zygosity assessment. Maternal peripheral blood samples were taken on one occasion before any invasive obstetrics procedures between 11 and 36 weeks of gestation for all cases. For case 01, chorionic villus sampling was performed, and full karyotyping revealed one euploid fetus and one trisomy 21 fetus. For case 02, trisomy 18 was suspected after observing multiple structural abnormalities during ultrasound scanning in the second trimester. Prenatal diagnosis was declined, and trisomy 18 in one child was confirmed postnatally. The other child was healthy. No fetal tissues were available for this study, but a maternal serum sample taken just before delivery was retrieved for analysis. For all the other cases in this study, maternal plasma was used. DNA from chorionic villus biopsy Table 1 Clinical cases and the sequencing output Case Gestational age (weeks + days) Twins/singleton Karyotype Utility Sequencing counts Chr21 Z-scores Chr18 Z-scores 01 14 + 6 Twins T21 + Euploid Test 16 919 203 14.25 0.05 02 36 + 3 Twins T18 + Euploid Test 21 797 758 0.05 38.65 03 21 + 5 Twins Euploid2 Test 23 937 979 2.83 2.16 04 19 + 0 Twins Euploid2 Test 18 817 253 0.42 1.69 05 21 + 5 Twins Euploid2 Test 8 708 537 1.99 1.53 06 19 + 0 Twins Euploid2 Test 8 055 232 1.26 0.89 07 27 + 3 Twins Euploid2 Test 3 486 194 1.96 1.39 08 30 + 1 Twins Euploid2 Test 15 620 487 1.00 1.33 09 16 + 4 Singleton Euploid Reference 21 248 214 NA NA 10 16 + 1 Singleton Euploid Reference 24 563 124 NA NA 11 13 + 0 Singleton Euploid Reference 22 001 984 NA NA 12 16 + 1 Singleton Euploid Reference 15 198 875 NA NA 13 12 + 5 Singleton Euploid Reference 16 913 971 NA NA 14 16 + 2 Singleton Euploid Reference 14 581 277 NA NA 15 12 + 4 Singleton Euploid Reference 11 551 742 NA NA 16 17 + 3 Singleton Euploid Reference 16 476 854 NA NA 17 11 + 2 Singleton Euploid Reference 17 752 722 NA NA 18 14 + 0 Singleton Euploid Reference 16 002 683 NA NA 19 12 + 4 Singleton Euploid Reference 13 924 820 NA NA Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley Sons, Ltd.
  • 3. Noninvasive twin zygosity and aneuploidy detection 677 or cord blood from each twin fetus, except case 02, was genotyped. The degree of concordance in the genotypes between each twin pair was used to confirm if the twins were monozygotic or dizygotic. For case 02, the different postnatal phenotypes of the two neonates served as the evidence indicating that they were dizygotic. Maternal blood samples were centrifuged twice9 to separate the plasma/serum portion from the blood cell portion. Plasma or serum DNA was extracted. For each twin pregnancy, two analyses were performed. One analysis was based on target capture sequencing for the purpose of determining the zygosity of the twins.8 The other analysis was performed for the purpose of noninvasive aneuploidy detection.1–5 Noninvasive zygosity assessment The noninvasive zygosity assessment for the six euploid twin pregnancies was performed in our recent study,8 and the same protocol was applied to cases 01 and 02. Briefly, the plasma or serum DNA libraries were constructed with the Paired-End Sample Preparation Kit (Illumina), and target capturing of selective genomic regions was performed using the SureSelect Target Enrichment System (Agilent).8,10,11 The capture library covered 5.5Mb of genomic regions distributed over 14 chromosomes, which were designed to target single nucleotide polymorphisms (SNPs) on the Affymetrix Genome-Wide Human SNP Array 6.0 system. As previously reported, to achieve accurate genotype deduction for the mother and fetus using the plasma DNA sequenced reads from samples containing at least 5% fetal DNA, each informative SNP would need to be sequenced to an average depth of 100 times.8 Therefore, the plasma DNA library of case 01 was sequenced using four lanes in a flowcell on the Genome Analyzer IIx sequencer (Illumina), and case 02 was sequenced using two lanes in a flowcell on the HiSeq 2000 sequencer (Illumina). The choice of the model of sequencer used was based on which instrument was available at the time of the experiments. After sequencing, the FetalQuant algorithm12 was used to analyze the ratio of alleles of SNPs that were located within the captured genomic regions to identify loci where the mother was homozygous and at least one of the twin fetuses was heterozygous, termed informative SNPs. The ratio of the fetal-specific allele to the major allele was calculated for each locus. Allelic ratios of adjacent SNP loci were combined to obtain an apparent fractional fetal DNA concentration for a chromosomal region. Apparent fractional fetal DNA concentrations were calculated for multiple chromosomal regions. For monozygotic twins, because the fetuses are genetically identical, the apparent fractional fetal DNA concentrations should be similar across different genomic regions. On the contrary, for dizygotic twins, because they are not genetically identical and each fetus is heterozygous at different sets of loci, the apparent fractional fetal DNA concentrations would vary across different genomic regions. Noninvasive aneuploidy detection For aneuploidy testing, plasma or serum DNA libraries were constructed with the TruSeq DNA Sample Preparation Kit (Illumina). Each DNA sample was ligated with a unique adaptor and then pooled to form two multiplex libraries. Each multiplexed pool was composed of nine or ten samples. For MPS-NIPT aneuploidy testing by the random sequencing protocol,1–5 only a low sequencing depth is needed. Therefore, each multiplexed pool of samples was sequenced using three lanes of a flowcell using the HiSeq 2000 sequencer. For aneuploidy testing, sequence reads from chromosomes X and Y were excluded for calculating the genomic representation of each autosome. Z-scores were calculated for chromosome 21 and chromosome 18 as previously described.1,4 A Z-score3 is considered to indicate an abnormally increased chromosomal representation and hence, the presence of trisomy. Plasma DNA sequencing and alignment DNA libraries were sequenced by the standard paired-end protocol (Illumina) with a read length of 75 bp for each end on the HiSeq 2000 sequencer (Illumina) and a read length of 50 bp for each end on the Genome Analyzer IIx sequencer (Illumina). All sequenced reads were aligned to the nonrepeat-masked human reference genome (Hg18) using SOAP2.13 RESULTS Determination of twin zygosity by maternal plasma DNA analysis Microarray-based genotype analysis of the chorionic villus biopsy or cord blood DNA provided the gold standard for determining the zygosities of the twins in case 01 (Table 2). The noninvasive determination of twin zygosity by maternal plasma DNA sequencing for the six pairs of euploid twins was carried out in our previous study.8 Four of these previously studied twin pregnancies were monozygotic (Table 2). The noninvasive twin zygosity test for cases 01 and 02 had not been performed previously. For case 01, 187106 raw paired-end reads were sequenced, and 157106 reads were mappable. Each SNP locus in the target captured regions was covered an average of 210 times. For case 02, 462106 raw paired-end reads were sequenced, and 387106 reads were mappable. Each SNP locus in target captured regions was covered an average of 493 times. We calculated the average apparent fractional fetal DNA concentration for every 1000 informative SNPs on contiguous genomic blocks within the targeted regions. We compared if these average values varied from block to block. Large fluctuations of average apparent fractional fetal DNA concentrations were observed for both cases 01 and 02 (Figure 1). The proportions of data points lying outside the extent of stochastic variations expected for monozygotic twins were 73% for case 01 and 55% for case 02. As a reference, the proportions of data points lying outside these boundaries ranged from 0% to 1.93% for the monozygotic twin cases as previously reported. These data suggested that both cases 01 and 02 were dizygotic twin pregnancies. Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley Sons, Ltd.
  • 4. 678 T. Y. Leung et al. Table 2 Zygosity status and the fractional fetal DNA concentrations of the twin fetuses Fractional fetal DNA concentrations of individual members of twins The range of apparent fetal DNA concentrations as shown by every 1000 SNPs was noted. The overall distribution of the observed apparent fractional fetal DNA concentrations of both fetuses and the combined total concentration was assumed to be governed by a mixture of three binomial distributions.8 By adopting the binomial mixture model, we resolved two of the distributions and their associated peaks of fetal DNA concentrations that had the highest likelihood of producing the combined total amounts of circulating fetal DNA observed in cases 01 and 02. For case 01, the data suggested that one fetus contributed 10.7% of the DNA in maternal plasma, the other fetus contributed 16.9% and the combined fractional concentration of circulating fetal DNA from both fetuses was 27.6%. For case 02, one fetus contributed 8.80% of the DNA in maternal plasma, the other fetus contributed 16.3% and the combined fractional concentration of circulating fetal DNA from both fetuses was 25.1%. For case 01, to validate the estimated fetal DNA fraction, we retrieved the microarray-based genotype information of each individual twin. The massively parallel sequencing data covering confirmed informative SNPs were retrieved to calculate the fractional fetal DNA concentration of each individual twin member. The concentrations estimated using the binomial mixture statistics were consistent with those calculated using the known fetal genotype information (Table 2). The data also suggested that each fetus among the twin pregnancies had fractional fetal DNA concentrations that reached the lowest requirement, namely at least 4%, for aneuploidy detection by one of the currently used MPS-NIPT protocols.4 Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy For the diagnosis of fetal chromosomal aneuploidy, the 11 euploid singleton cases served as the reference controls. The eight twin pregnancies were the test cases. A median of 16106 (range: 3106 to 24106) aligned (i.e. mapped) paired-end reads were sequenced from the plasma or serum Case Zygosity assessment Predicted fetal DNA % Measured fetal DNA % using microarray-based genotypes % Concordance in genotypes by microarray Monozygotic or dizygotic Twin 1 Twin 2 Twin 1 Twin 2 01 78.8 Dizygotic 10.7 16.9 13.8 15.3 02 — Dizygotic 8.8 16.3 — — 03(6774)a 78.0 Dizygotic 7.0 11.4 7.9 10.9 04(6870)a 99.6 Monozygotic — — — — 05(6905)a 79.6 Dizygotic 13.9 7.0 11.2 7.8 06(7585)a 99.7 Monozygotic — — — — 07(8114)a 99.8 Monozygotic — — — — 08(8207)a 99.6 Monozygotic — — — — aThese cases were part of a cohort investigated in a previous study.8 The case numbers adopted in the previous study8 are shown in parentheses. Two other dizygotic twin cases included in the previous study did not have sufficient plasma DNA available for the present study. Figure 1 Regional variation in apparent fractional fetal DNA concentrations. Solid line shows the average apparent fractional fetal DNA concentrations across blocks of 1000 consecutive informative single nucleotide polymorphisms (SNPs) for the twin pregnancy. Grey shadow shows the results of the computer simulation analysis of the background level of stochastic variation. Dashed lines show the maximum and minimum values of the predicted stochastic variation. The proportion of data points outside the boundaries is given at the top of each plot. Case numbers are given in the upper right corner. Large fluctuations are expected for dizygotic twin pregnancies Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley Sons, Ltd.
  • 5. Noninvasive twin zygosity and aneuploidy detection 679 DNA libraries. Paired-end reads with identical start and end coordinates in the genome were removed. The number of reads originating from each autosome was counted and then expressed as a percentage of the total reads sequenced from all autosomes for the sample. This percentage value is the genome representation of that chromosome in the maternal plasma sample. Guanine–cytosine correction was performed for the calculation of genome representation of each chromosome. For the reference group, the mean genomic representation of chromosome 21 (%chr21) was 1.311 (standard deviation (SD) was 0.007), and the mean genomic representation of chromosome 18 (%chr18) was 2.808 (SD was 0.004). The %chr21 values for the six euploid twin cases ranged from 1.297 to 1.331, and the z-scores were all 3 (Table 1 and Figure 2). The %chr18 values for the six euploid twin cases ranged from 2.812 to 2.818, and the z-scores were all 3 (Table 1 and Figure 2). For case 01, the %chr21 was 1.412, which resulted in a z-score of 14.25 (Figure 2). Because the z-score for chromosome 21 was 3, the result suggested that case 01 involved at least one fetus with trisomy 21. For case 02, the %chr18 value was 2.975, which gave a z-score of 38.65 (Figure 2). Because the z-score for chromosome 18 was 3, the result suggested that case 02 involved at least one fetus with trisomy 18. Case 01 had normal representation for chromosome 18, whereas case 02 had normal representation for chromosome 21. Aneuploidy assessment of dizygotic twin fetuses Theoretically, the genomic representation of the aneuploid or trisomic chromosome (%chrT) should have a linear relationship with the fractional fetal DNA concentration for all trisomy cases2 but not the euploid cases. The reason is the elevated genomic representation of a chromosome is contributed by the aneuploid fetus. One should be able to predict the %chrT of an aneuploid fetus when the mean value of %chrT of the reference group and the fetal DNA fraction of the trisomy fetus is known. We established the relationship between the %chr21 or %chr18 values and the fetal DNA fraction using the following: %chrTsample ¼ mean%chrTreference þ 0:5f mean%chrTreference where %chrTsample is the %chrT value of the test sample, % chrTreference is the %chrT value of the reference group and f is the fetal DNA fraction. The correlation plots are shown in Figure 3. For case 01, the correlation line for %chr21 intersected with the observed genomic representation of the affected twin pregnancy when the fractional fetal DNA concentration was 15.4%. For case 02, the correlation line for %chr18 intersected with the observed genomic representation of the affected twin pregnancy when the fractional fetal DNA concentration was 11.9%. For both cases, the correlation lines intercepted at fetal DNA concentrations that were much lower than the combined fetal DNA concentrations contributed by both twins. The results therefore suggested that only one fetus had aneuploidy in each twin pair. Our results also confirmed that each twin fetus contributed adequate amounts of DNA into maternal plasma to render the MPS-NIPT aneuploidy test valid for interpretation, that is, not a false-negative result due to inadequate fetal DNA percentage. There were seven male fetuses among the 11 euploid singleton cases. We determined the fetal DNA concentration of these cases using a real-time polymerase chain reaction assay targeting a gene on chromosome Y, the sex-determining region Y (SRY) gene. All values deviated from the correlation lines for %chr21 and %chr18. This was as expected because there was no elevation in %chr21 and %chr18 values in the euploid cases; hence, there should be no relationship with the fractional fetal DNA concentration. DISCUSSION Previously, Canick et al. investigated the use of MPS-NIPT for chromosomal aneuploidy detection among multi-fetus pregnancies.7 However, on the basis of the MPS-NIPT aneuploidy assessment alone, it is not known if one or both fetuses were affected. More important, for dizygotic twins, it is not known if each fetus contributed adequate amounts of DNA to pass the minimum quality control requirement for valid assessment. Here, we have demonstrated that our recently developed noninvasive twin zygosity test provides useful information for the MPS-NIPT assessment of chromosomal aneuploidy among twin pregnancies.8 When the twins are determined to be monozygotic, the MPS-NIPT aneuploidy test can be interpreted in the same manner as for singleton pregnancies. When the twins are determined to be dizygotic, the fractional fetal DNA concentration of each fetus can be calculated. This has allowed us to confirm if the fetus contributing the lesser amount of fetal DNA also has a value that reaches the minimum requirement. In this study, we have further shown that by exploiting the relationship between the genomic representation of the aneuploid chromosome and the Figure 2 Genomic representations (GR) of chromosome 21 and chromosome 18 for the reference and test cases. Broken lines indicate the cut-off value of genomic representation corresponding to a z-score that is equal to 3. The chromosome 21 genomic representation of case 01 is elevated, and the data point lies above the cut-off. The chromosome 18 genomic representation of case 02 is elevated, and the data point lies above the cut-off. All singleton control pregnancies and all other twin pregnancies show genomic representations for chromosomes 21 and 18 that are below the cut-off Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley Sons, Ltd.
  • 6. 680 T. Y. Leung et al. fetal DNA fraction,2 we could further determine if one or both fetuses were affected. Although the method cannot pinpoint which one of the twins had aneuploidy, the aneuploidy assessment of the twin fetuses could be made with greater certainty to justify the need for invasive confirmatory testing. Because of the proof-of-principle nature of this study, further studies with larger sample size are needed. For case 02, trisomy 18 was diagnosed postnatally; hence, fetal tissues were not available for analysis in this study. However, our results were consistent with the postnatal diagnosis. Although the noninvasive twin zygosity test provides useful information for interpreting the MPS-NIPT for fetal chromosomal aneuploidy testing, it is an added procedure and additional costs are involved. With the rapid reduction in sequencing costs, the zygosity test could be considered as an optional quality control step for additional reassurance in A B Figure 3 Determination of the number of twin fetus(es) with chromosomal aneuploidy. The red line shows the expected relationship between the maternal plasma genomic representation of the aneuploid chromosome and the fetal DNA fraction. The dashed line marks the genomic representation of the affected twin pregnancy. The black solid lines mark the fetal DNA percentage estimated for each fetus of the dizygotic twin pair and the combined fetal DNA percentage from both fetuses. The genomic representation and fetal DNA percentage values for the seven male singleton control pregnancies are depicted by squares. (A) Plot of %chr21 and fetal DNA percentage values for case 01. The correlation line for %chr21 intercepts with the observed genomic representation of the affected twin pregnancy when the fractional fetal DNA concentration is 15.4%. (B) Plot of %chr18 and fetal DNA percentage values for case 02. The correlation line for %chr18 intercepts with the observed genomic representation of the affected twin pregnancy when the fractional fetal DNA concentration is 11.9%. Each plot suggests that there is only one fetus affected by aneuploidy in each twin pair Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley Sons, Ltd.
  • 7. Noninvasive twin zygosity and aneuploidy detection 681 interpretation of the aneuploidy test results. In our opinion, as twin pregnancies represent only a minority of pregnancies, the increased costs of adding this quality control step to the overall prenatal healthcare costs in the population as a whole should be affordable. On the other hand, we believe that the noninvasive twin zygosity test may provide additional clinical utility. For example, it is known that a number of pregnancy-related complications are associated with abnormal levels of circulating fetal DNA.14,15 With our approach, we could monitor the dynamic changes of the fetal DNA concentration of each dizygotic twin member for monitoring the well-being of each twin. CONCLUSION With the use of massively parallel sequencing of maternal plasma DNA, we have successfully determined the zygosity of twins with chromosomal aneuploidies and estimated the fetal DNA fraction of each dizygotic twin member. Our approach has made it possible to confidently interpret the MPS-NIPT results for trisomy 21 and trisomy 18 diagnoses among twin pregnancies. ACKNOWLEDGMENTS We thank Yongjie Jin for performing the sequencing and Coral Lee for bioinformatics support. WHAT’S ALREADY KNOWN ABOUT THIS TOPIC? • By using massively parallel maternal plasma DNA sequencing, noninvasive prenatal detection of fetal chromosomal aneuploidies has been achieved. The sensitivity of the maternal plasma DNA sequencing test for aneuploidy detection is governed by the fractional fetal DNA concentration. WHAT DOES THIS STUDY ADD? • We have recently developed a maternal plasma DNA sequencing-based method for the noninvasive assessment of twin zygosity. The method also allows the determination of the fetal DNA fraction contributed by each member of a pair of dizygotic twin in maternal plasma. In this study, we applied the new method to two dizygotic twin pregnancies involving one aneuploid fetus each. We confirmed that each fetus contributed adequate amounts of DNA into maternal plasma so that the aneuploidy test result could be interpreted with confidence. REFERENCES 1. Chiu RWK, Chan KCA, Gao Y, et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA 2008;105:20458–63. 2. Chiu RWK, Akolekar R, Zheng YWL, et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ 2011;342:c7401. 3. Palomaki GE, Kloza EM, Lambert-Messerlian GM, et al. DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med 2011;13:913–20. 4. Palomaki GE, Deciu C, Kloza EM, et al. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13, as well as Down syndrome: an international collaborative study. Genet Med 2012;14:296–305. 5. Bianchi DW, Platt LD, Goldberg JD, et al. Genome-wide fetal aneuploidy detection by maternal plasma DNA sequencing. Obstet Gynecol 2012;119:890–901. 6. Norton ME, Brar H, Weiss J, et al. Non-Invasive Chromosomal Evaluation (NICE) Study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. Am J Obstet Gynecol 2012;207:137.e1–8. 7. Canick JA, Kloza EM, Lambert-Messerlian GM, et al. DNA sequencing of maternal plasma to identify Down syndrome and other trisomies in multiple gestations. Prenat Diagn 2012;32:1–5. 8. Qu JZZ, Leung TY, Jiang P, et al. Noninvasive prenatal determination of twin zygosity by maternal plasma DNA analysis. Clin Chem 2013;59:427–35. 9. Chiu RWK, Poon LL, Lau TK, et al. Effects of blood-processing protocols on fetal and total DNA quantification in maternal plasma. Clin Chem 2001;47:1607–13. 10. Liao GJW, Lun FMF, Zheng YWL, et al. Targeted massively parallel sequencing of maternal plasma DNA permits efficient and unbiased detection of fetal alleles. Clin Chem 2011;57:92–101. 11. Liao GJW, Chan KCA, Jiang P, et al. Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA. PLoS One 2012;7: e38154. 12. Jiang P, Chan KCA, Liao GJW, et al. FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. Bioinformatics 2012;28:2883–90. 13. Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009;25:1966–7. 14. Lo YMD, Leung TN, Tein MSC, et al. Quantitative abnormalities of fetal DNA in maternal serum in preeclampsia. Clin Chem 1999;45:184–8. 15. Hahn S, Rusterholz C, Hösli I, Lapaire O. Cell-free nucleic acids as potential markers for preeclampsia. Placenta 2011;32(Suppl): S17–20. Prenatal Diagnosis 2013, 33, 675–681 © 2013 John Wiley Sons, Ltd.