Fetal fraction calculation
Three different methods to calculate fetal fractions were used in this study for different purposes, including an artificial neural network model named the FF-QuantSC [18], a Y-chromosome method [19], and the relative coverage of the trisomy chromosome. FF-QuantSC was used to calculate the overall fetal fraction of both co-twins. In pregnancies with one male co-twin, the Y-chromosome method was used to calculate the fetal fraction of the male fetus. In pregnancies with two male fetuses, the Y-chromosome method calculated the fetal fraction equal to an overall fetal fraction, and results were compared with the FF-QuantSC method. The relative coverage of the trisomy chromosome was specifically used to calculate the fetal fraction of the trisomy co-twin who was terminated by the selective reduction.
FF-QuantSC exploits an artificial neural network to calculate the fetal fraction of both male and female co-twins [18]. Briefly, a fully connected neural network model with a single hidden layer and 128 neurons was trained by the Vapnik-Chervonenkis dimension [20] and trained with over 100 thousand of male pregnancies. Sequencing reads were partitioned into continuous genomic windows of 60kb in length for feature selection. Standardization by within-sample z-score transformation was then used to generate a final feature matrix. After training, the FF-QuantSC model was testified in six testing groups of about 240 thousand pregnancies, including 36 thousand twin pregnancies and 80 thousand female pregnancies [18].
Y-chromosome method calculated fetal fractions using unique sequence reads from the Y chromosome (eq.1).
Fetal fraction = 2*\(\frac{\overset{\overline{}}{\text{UR}_{Y}}}{\overset{\overline{}}{\text{UR}}}\)(1)
where \(\overset{\overline{}}{\text{UR}_{Y}}\) represents the unique reads on chromosome Y, and \(\overset{\overline{}}{\text{UR}}\)represents the unique reads on autosome chromosomes.
In pregnancies with a trisomy co-twin, fetal fraction was calculated using the sequencing reads of the trisomic chromosome, typically chromosome 13, 18, or 21 (eq.2).
\(\varepsilon_{i}=2\times\frac{\text{UR}_{i}-\overset{\overline{}}{\text{UR}}}{\overset{\overline{}}{\text{UR}}}\)i =chromosome 13, 18, or 21 (2)
Where \(\varepsilon_{i,Y}\) represents the fetal fraction estimate by chromosome \(i\); URi represents the unique reads of chromosome \(i\); \(\overset{\overline{}}{\text{UR}}\) represents the mean of unique reads on all autosomal chromosomes.