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Original research
Comprehensive genomic filtering algorithm to expose the cause of skewed X chromosome inactivation. The proof of concept in female haemophilia expression
  1. Betiana Michelle Ziegler1,
  2. Miguel Martin Abelleyro1,
  3. Vanina Daniela Marchione1,
  4. Nicolás Lazarte2,
  5. Martín Manuel Ledesma2,
  6. Ludmila Elhelou3,
  7. Daniela Neme3,
  8. Liliana Carmen Rossetti1,
  9. Enrique Medina-Acosta4,
  10. Florencia Giliberto5,6,
  11. Carlos De Brasi1,
  12. Claudia Pamela Radic1
  1. 1Laboratorio de Genética Molecular de la Hemofilia, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
  2. 2Unidad de Bioinformática, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires, Argentina
  3. 3Hematology, Fundación de la Hemofilia, Buenos Aires, Argentina
  4. 4Center for Biosciences and Biotechnology, State University of North Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
  5. 5Laboratorio de Distrofinopatías, Facultad de Farmacia y Bioquímica, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
  6. 6Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-UBA, Buenos Aires, Argentina
  1. Correspondence to Dr Claudia Pamela Radic, Laboratorio de Genética Molecular de la Hemofilia, Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina, Buenos Aires 3081, Argentina; yocpamelita{at}yahoo.com.ar

Abstract

Background Exploring the expression of X linked disorders like haemophilia A (HA) in females involves understanding the balance achieved through X chromosome inactivation (XCI). Skewed XCI (SXCI) may be involved in symptomatic HA carriers. We aimed to develop an approach for dissecting the specific cause of SXCI and verify its value in HA.

Methods A family involving three females (two symptomatic with severe/moderate HA: I.2, the mother, and II.1, the daughter; one asymptomatic: II.2) and two related affected males (I.1, the father and I.3, the maternal uncle) was studied. The genetic analysis included F8 mutational screening, multiplex ligation-dependent probe amplification, SNP microarray, whole exome sequencing (WES) and Sanger sequencing. XCI patterns were assessed in ectoderm/endoderm and mesoderm-derived tissues using AR-based and RP2-based systems.

Results The comprehensive family analysis identifies I.2 female patient as a heterozygous carrier of F8:p.(Ser1414Ter) excluding copy number variations. A consistent XCI pattern of 99.5% across various tissues was observed. A comprehensive filtering algorithm for WES data was designed, developed and applied to I.2. A Gly58Arg missense variant in VMA21 was revealed as the cause for SXCI.

Each step of the variant filtering system takes advantage of publicly available genomic databases, non-SXCI controls and case-specific molecular data, and aligns with established concepts in the theoretical background of SXCI.

Conclusion This study acts as a proof of concept for our genomic filtering algorithm’s clinical utility in analysing X linked disorders. Our findings clarify the molecular aspects of SXCI and improve genetic diagnostics and counselling for families with X linked diseases like HA.

  • Blood Coagulation Disorders
  • Whole Exome Sequencing
  • X-Linked Genetic Diseases
  • Genetic Carrier Screening

Data availability statement

All data relevant to the study are included in the article or uploaded as supplementary information.

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Data availability statement

All data relevant to the study are included in the article or uploaded as supplementary information.

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Footnotes

  • CDB and CPR are joint senior authors.

  • X @florgili

  • Contributors BMZ, CPR and CDB performed the research, designed the study, analysed the data and wrote the paper. MMA, VDM, NL, MML, EM-A, LCR, LE and DN contributed with samples and/or analysed the genetic, clinical and bioinformatic data. FG contributed with control samples. Guarator: CPR. All authors revised and approved the final submitted version of the manuscript, and they agree to be accountable for all aspects of the work.

  • Funding This study was supported by grants from the National Research Council (CONICET) and the National Agency for Scientific and Technological Promotion (ANPCyT).

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.