Presence of BRCA1 and BRCA2 in cell free DNA obtained from circulating blood of a pregnant woman.
In Fan et al (“Non-invasive prenatal measurement of the fetal genome”, Nature 2012), we described the sequencing of the genomes of both a mother and her fetus from cell free maternal blood1. Here, we illustrate the depth and extent coverage of the genome in the paper by looking specifically at the BRCA1 and BRCA2 genes.
Background. A figure explaining what gene coverage means can be found here.
Presence of BRCA1 and BRCA2. The BRCA1 and BRCA2 DNA sequences are well represented in the total DNA from cell free maternal blood. The data for BRCA1 can be found here and the data for BRCA can be found here. The data consist of “sequence reads” presented in the “BAM” file format (the standardized machine-readable format most commonly used).
Coverage of BRCA1 and BRCA2. While our original analyses showed that the entire genome of both fetus and mother was present, we have further examined BRCA1 and BRCA2 specifically to determine the “coverage” of the genes – that is, the number of distinct DNA molecules that we happened to sequence covering each individual position of the sequence. (This represents only a miniscule fraction of the distinct molecules present in the blood.) We have found that essentially the entirety of the BRCA1 and BRCA2 genes are present in the cell free maternal blood at high coverage. ~200- 600x coverage was achieved across the cell free exome (328X for BRCA1 and 148X for BRCA2) and 100% of the coding regions were covered as indicated in the figure links below. This level of coverage in fragments of ~170 bases corresponds to approximately 225,000 fragments from the BRCA1 and BRCA2 genomic loci in the 1 milliliter of blood analyzed, or roughly 945 million fragments in the 4.2 liters of total circulation.
Ability to distinguish maternal and fetal DNA. As described in the paper, we separately sequenced the mother’s DNA (from blood cells called lymphocytes) and the child’s DNA after birth (from umbilical cord blood cells) to demonstrate that our DNA sequencing was accurate and that we had been able to detect both maternal and fetal DNA from maternal blood. Using these independent sequences as a reference, we showed that we had been able to distinguish fetal from maternal genome in the original mixed DNA sequencing. In BRCA1, we found one sequence difference between the mother and fetus (here), while we found two differences in BRCA2 (here and here).
Summary. Examination of this DNA sequence data confirms that cell-free maternal blood contains isolated DNA fragments covering the BRCA1 and BRCA2 genes.
 H. Christina Fan et al., Non-invasive Prenatal Measurement of the Fetal Genome, 487 Nature 320 (2012);