Background
We report a kindred referred for molecular investigation of severe hemophilia A in a young female in which extremely skewed X‐inactivation was observed in both the proband and her ...clinically normal mother.
Methods
Bidirectional Sanger sequencing of all F8 gene coding regions and exon/intron boundaries was undertaken. Methylation‐sensitive restriction enzymes were utilized to investigate skewed X‐inactivation using both a classical human androgen receptor (HUMARA) assay, and a novel method targeting differential methylation patterns in multiple informative X‐chromosome SNPs. Illumina Whole‐Genome Infinium microarray analysis was performed in the case‐parent trio (proband and both parents), and the proband's maternal grandmother.
Results
The proband was a cytogenetically normal female with severe hemophilia A resulting from a heterozygous F8 pathogenic variant inherited from her similarly affected father. No F8 mutation was identified in the proband's mother, however, both the proband and her mother both demonstrated completely skewed X‐chromosome inactivation (100%) in association with a previously unreported 2.3 Mb deletion at Xp22.2. At least three disease‐associated genes (FANCB, AP1S2, and PIGA) were contained within the deleted region.
Conclusions
We hypothesize that true “extreme” skewing of X‐inactivation (≥95%) is a rare occurrence, but when defined correctly there is a high probability of finding an X‐chromosome disease‐causing variant or larger deletion resulting in X‐inactivation through a survival disadvantage or cell lethal mechanism. We postulate that the 2.3 Mb Xp22.2 deletion identified in our kindred arose de novo in the proband's mother (on the grandfather's homolog), and produced extreme skewing of X‐inactivation via a “cell lethal” mechanism. We introduce a novel multitarget approach for X‐inactivation analysis using multiple informative differentially methylated SNPs, as an alternative to the classical single locus (HUMARA) method. We propose that for females with unexplained severe phenotypic expression of an X‐linked recessive disorder trio‐SNP microarray should be undertaken in combination with X‐inactivation analysis.
We report a kindred referred for molecular investigation of severe hemophilia A in a young female in which extremely skewed X‐inactivation was observed in both the proband and her clinically normal mother. No F8 mutation was identified in the proband's mother, however both the proband and her mother demonstrated completely skewed X‐chromosome inactivation in association with a previously unreported 2.3 Mb deletion at Xp22.2
Gene expression profiling is a widely used technique with data from the majority of published microarray studies being publicly available. These data are being used for meta-analyses and in silico ...discovery; however, the comparability of toxicogenomic data generated in multiple laboratories has not been critically evaluated. Using the power of prospective multilaboratory investigations, seven centers individually conducted a common toxicogenomics experiment designed to advance understanding of molecular pathways perturbed in liver by an acute toxic dose of N-acetyl-p-aminophenol (APAP) and to uncover reproducible genomic signatures of APAP-induced toxicity. The nonhepatotoxic APAP isomer N-acetyl-m-aminophenol was used to identify gene expression changes unique to APAP. Our data show that c-Myc is induced by APAP and that c-Myc–centered interactomes are the most significant networks of proteins associated with liver injury. Furthermore, sources of error and data variability among Centers and methods to accommodate this variability were identified by coupling gene expression with extensive toxicological evaluation of the toxic responses. We show that phenotypic anchoring of gene expression data is required for biologically meaningful analysis of toxicogenomic experiments.
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