2023 ACMG Annual Clinical Genetics Meeting Digital Edition: Poster Gallery-Long-read Sequencing Reveals a Novel Pathogenic Variant in<em> IKBKG</em> with Associated Skewed X-inactivation in Affected Females

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In this study, researchers describe a family with three generations affected by X-linked incontinentia pigmenti (IP), a disorder caused by variants in the IKBKG gene. They used whole-genome long-read sequencing (LRS) to identify a molecular diagnosis, as previous clinical genetic testing was nondiagnostic.<br /><br />The neonate in the family began displaying symptoms in her first days of life and died at 13 days of age from neurological complications related to the IP diagnosis. The mother had a clinical diagnosis of IP but previous molecular genetic evaluation did not provide a diagnostic result.<br /><br />Clinical testing results showed that targeted sequence analysis of IKBKG coding regions and long-range PCR of common exons did not detect any abnormalities in the neonate or the mother. Exome sequencing was also inconclusive.<br /><br />The researchers performed LRS on the blood-derived DNA of all four family members using the Oxford Nanopore platform. They used the sequencing data to identify a complex familial structural variant involving IKBKG. Additionally, phased methylation calls revealed skewed X-inactivation in the affected female family members, indicating selection against the X-chromosome carrying the 2,500-bp deletion during development.<br /><br />The study highlights the importance of studying X-inactivation in females with X-linked diseases and demonstrates the power of LRS as a single data source for analyzing complex genomic regions like IKBKG.<br /><br />The researchers also found that the affected individuals carried a deletion of IKBKG that removes exons 8-10. The affected adult females showed completely skewed X-inactivation at all CpG islands on the X chromosome, favoring the non-deleted IKBKG1 allele on the active X chromosome. However, the affected neonate had evidence for random X-inactivation.<br /><br />Overall, this study illustrates the utility of LRS for identifying disease-causing variants in highly repetitive and architecturally complex regions of the genome and emphasizes the importance of studying X-inactivation in X-linked diseases.

Asset Subtitle

Presenting Author - Danny E. Miller, MD, PhD; Co-Author - Camille Dash, BA in progress; Co-Author - David T. Miller, MD, PhD, FACMG; Co-Author - Miranda Galey, MS; Co-Author - Jasmine Lin, MS; Co-Author - Jill A. Madden, PhD, MSc, CGC; Co-Author - Alan H. Beggs, PhD; Co-Author - Pankaj Agrawal, MD, MSSc; Co-Author - Casie Genetti, CGC; Co-Author - Monica H. Wojcik, MD, MPH, FAAP, FACMG;

Meta Tag

Genomic Methodologies

Methylation

X-Inactivation/X-Linked Disease

Co-Author Camille Dash, BA in progress

Co-Author David T. Miller, MD, PhD, FACMG

Co-Author Miranda Galey, MS

Co-Author Jasmine Lin, MS

Co-Author Jill A. Madden, PhD, MSc, CGC

Co-Author Alan H. Beggs, PhD

Co-Author Pankaj Agrawal, MD, MSSc

Co-Author Casie Genetti, CGC

Co-Author Monica H. Wojcik, MD, MPH, FAAP, FACMG

Presenting Author Danny E. Miller, MD, PhD

Keywords

X-linked incontinentia pigmenti

IKBKG gene

whole-genome long-read sequencing

molecular diagnosis

neonate

neurological complications

targeted sequence analysis

Oxford Nanopore platform

familial structural variant

skewed X-inactivation