Table 3.
Targeted massively parallel sequencing of maternal plasma DNA for detection of F8 int22h-related inversions
| Plasma sample | Raw reads, M | Mapped reads, M | No. of reads/ on target, M | No. of reads/ off target, M | Coverage, %* | PCR duplication rate, %† | Sequencing depth per base, -fold‡ | No. of SNPs in CEN region¶ | No. of RHDO classifications in CEN region¶ | No. of SNPs in TEL region¶ | No. of RHDO classifications in TEL region¶ | RHDO analysis | Fetal status§ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 16A | 161.8 | 153.8 | 147.1 | 16.8 | 99.96 | 70.4 | 129.2 | 15 | 4 | 1 | 0 | Affected | Affected |
| 16B | 70.6 | 67.2 | 65.0 | 7.8 | 99.67 | 39.7 | 130.6 | 13 | 5 | 1 | 0 | Affected | |
| 17A | 172.0 | 163.3 | 158.4 | 17.8 | 99.67 | 63.7 | 177.1 | 20 | 4 | 1 | 1 | Unaffected | Unaffected |
| 18A | 75.0 | 71.5 | 68.7 | 8.6 | 99.66 | 39.9 | 135.6 | 19 | 9 | 0 | 0 | Affected | Affected |
| 18B | 130.0 | 123.1 | 117.4 | 15.8 | 99.67 | 52.1 | 174.4 | 22 | 21 | 0 | 0 | Affected |
CEN, centromeric region; RHDO, relative haplotype dosage; TEL, telomeric region.
Coverage corresponds to the length of the covered nucleotides in the targeted region divided by the length of the targeted region.
PCR duplication rate corresponds to the proportion of PE reads with the same sequences and start-end coordinates.
Sequencing depth per base is defined as the sum of the bases sequenced within the targeted region divided by the length of the targeted region.
CEN corresponds to the region located up to 7 Mb downstream from the int22h-1 homolog in the direction of the F8 gene transcription start site (chrX: 147,109,089-154,109,089). TEL corresponds to a telomeric region spanning a 577-kb region downstream from the int22h-3 and covering chrX: 154,693,870-155,270,560.
Hemophilia status of the newborn was determined from the cord blood sample based on the factor VIII and factor IX assays, as appropriate.