Table 1.
Summary of whole genome, whole exome and X chromosome specific exome sequencing for two affected related individuals
| Individual III-5 | Individual IV-1 | Shared variants | |||
| Whole genome | Whole exome | X exome | X exome | ||
| Total variants | 2 647 939 | 45 182 | 1718 | 1197 | – |
| Novel variants | 251 039 | 7869 | 300 | 192 | – |
| Variants in haplotype block | 3599 | 34 | 137 | 90 | – |
| NS/MS/SS/UTR | 27 | 9 | 25 | 18 | 15 |
| Fetal nervous system expressed | – | – | – | – | 7 |
| Confirmed by sanger sequencing | – | – | – | – | 2 |
| Predicted damaging | – | – | – | – | 1 |
The number of variants for each step in the analysis pipeline for the three distinct sequencing methods is shown. There were a total of 15 variants covering 12 genes shared among the two individuals (SSX4, FOXR2, RAB40AL, GRIPAP1, CLCN5, FOXR2, SPIN3, ARHGEF9, FAM123B, KIAA2022, AR, TRPC5). Of these 12 genes, seven were expressed in the fetal nervous system (GRIPAP1, CLCN5, SPIN3, ARHGEF9, FAM123B, KIAA2022, RAB40AL) and two of these genes (ARHGEF9 and RAB40AL) contained missense mutations and segregation with the phenotype in the family.
MS, missense; NS, nonsense; SS, splice site; UTR, untranslated region.