Figure 2
From: Noninvasive prenatal diagnosis in a fetus at risk for methylmalonic acidemia
Noninvasive test results. (a) (Top panel) Distinguishing an affected (homozygous) fetus from mock unaffected fetuses (negative controls) by a calculated empirical Z-score (see Supplementary Equation S2 online) based on allelic count differences of each separate position. Measurement of the alleles on the mutation site directly (leftmost column) and by a multiplex amplification of 10 additional positions (right) that are linked to the mutation through a known 1.7-Mbp haplotype. (Bottom panel) Location of mutations and haplotype positions relative to the MUT gene and chromosome 6. (b) Determination of fetal fraction by tallying the allelic counts of a panel of blindly queried single-nucleotide variations that are diversely represented in the human population. By finding single-nucleotide polymorphism (SNP) positions at which the mother is homozygous and the fetus is heterozygous (i.e., AA/AG), fetal fraction can be calculated to be double the fractional count of the alternative allele in the fetus (i.e., two times the fraction count of G). To be almost guaranteed multiple useful positions that meet the criteria for fetal fraction determination, we screened the maternal cell portion against 32 SNP positions. Positions that were homozygous and had high probe quality tallied 13. These corresponding 13 probes were pooled for a multiplex polymerase chain reaction of the plasma DNA (7,200 input molecules per position). Calculation of a minor allele fraction, which is the smaller fraction of the two counted alleles and half of the fetal fraction, helped to determine which of the 13 positions were useful. Three positions, rs13218440, rs12423234, and rs1821380, had fetal fractions of 16.7, 15.4, and 17.8%, respectively.
