
Demonstration of a novel Xp22.2 microdeletion as the cause of familial extreme skewing of X‐inactivation utilizing case‐parent trio SNP microarray analysis
Author(s) -
Mason Jane A.,
Aung Hnin T.,
Nandini Adayapalam,
Woods Rickie G.,
Fairbairn David J.,
Rowell John A.,
Young David,
Susman Rachel D.,
Brown Simon A.,
Hyland Valentine J.,
Robertson Jeremy D.
Publication year - 2018
Publication title -
molecular genetics and genomic medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.765
H-Index - 29
ISSN - 2324-9269
DOI - 10.1002/mgg3.378
Subject(s) - proband , genetics , x inactivation , sanger sequencing , x chromosome , biology , snp array , skewed x inactivation , dosage compensation , gene , exon , mutation , single nucleotide polymorphism , genotype
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 SNP s. 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 , AP 1S2, 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 SNP s, 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.