Complex 4q35 and 10q26 Rearrangements

Background and Objectives After clinical evaluation, the molecular diagnosis of type 1 facioscapulohumeral dystrophy (FSHD1) relies in most laboratories on the detection of a shortened D4Z4 array at the 4q35 locus by Southern blotting. In many instances, this molecular diagnosis remains inconclusive and requires additional experiments to determine the number of D4Z4 units or identify somatic mosaicism, 4q-10q translocations, and proximal p13E-11 deletions. These limitations highlight the need for alternative methodologies, illustrated by the recent emergence of novel technologies such as molecular combing (MC), single molecule optical mapping (SMOM), or Oxford Nanopore-based long-read sequencing providing a more comprehensive analysis of 4q and 10q loci. Over the last decade, MC revealed a further increasing complexity in the organization of the 4q and 10q distal regions in patients with FSHD with cis-duplication of D4Z4 arrays in approximately 1%–2% of cases. Methods By using MC, we investigated in our center 2,363 cases for molecular diagnosis of FSHD. We also evaluated whether previously reported cis-duplications might be identified by SMOM using the Bionano EnFocus FSHD 1.0 algorithm. Results In our cohort of 2,363 samples, we identified 147 individuals carrying an atypical organization of the 4q35 or 10q26 loci. Mosaicism is the most frequent category followed by cis-duplications of the D4Z4 array. We report here chromosomal abnormalities of the 4q35 or 10q26 loci in 54 patients clinically described as FSHD, which are not present in the healthy population. In one-third of the 54 patients, these rearrangements are the only genetic defect suggesting that they might be causative of the disease. By analyzing DNA samples from 3 patients carrying a complex rearrangement of the 4q35 region, we further showed that the SMOM direct assembly of the 4q and 10q alleles failed to reveal these abnormalities and lead to negative results for FSHD molecular diagnosis. Discussion This work further highlights the complexity of the 4q and 10q subtelomeric regions and the need of in-depth analyses in a significant number of cases. This work also highlights the complexity of the 4q35 region and interpretation issues with consequences on the molecular diagnosis of patients or genetic counseling.

[1]  R. Sompallae,et al.  Validation of Optical Genome Mapping for the Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy (FSHD). , 2021, The Journal of molecular diagnostics : JMD.

[2]  L. Popplewell,et al.  G-quadruplex ligands mediate downregulation of DUX4 expression , 2020, Nucleic acids research.

[3]  S. Boulton,et al.  SMCHD1 promotes ATM‐dependent DNA damage signaling and repair of uncapped telomeres , 2020, The EMBO journal.

[4]  F. Puppo,et al.  Methylation hotspots evidenced by deep sequencing in patients with facioscapulohumeral dystrophy and mosaicism , 2019, Neurology: Genetics.

[5]  L. Cui,et al.  Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD) , 2019, Journal of Medical Genetics.

[6]  J. Lingner,et al.  SMCHD1 Promotes ATM-dependent DNA Damage Signaling and Repair of Uncapped Telomeres , 2019, bioRxiv.

[7]  Albert David,et al.  Deciphering the complexity of the 4q and 10q subtelomeres by molecular combing in healthy individuals and patients with facioscapulohumeral dystrophy , 2019, Journal of Medical Genetics.

[8]  Shifeng Xue,et al.  SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite , 2019, Nucleic acids research.

[9]  Y. Liu,et al.  Clinical application of single‐molecule optical mapping to a multigeneration FSHD1 pedigree , 2019, Molecular genetics & genomic medicine.

[10]  F. Baas,et al.  Cis D4Z4 repeat duplications associated with facioscapulohumeral muscular dystrophy type 2 , 2018, Human molecular genetics.

[11]  M. Frith,et al.  Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy , 2017, Scientific Reports.

[12]  F. Puppo,et al.  Molecular combing reveals complex 4q35 rearrangements in Facioscapulohumeral dystrophy , 2017, Human mutation.

[13]  M. Frith,et al.  Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy , 2017, Journal of the Neurological Sciences.

[14]  A. Aguilera,et al.  Transcription–replication conflicts: how they occur and how they are resolved , 2016, Nature Reviews Molecular Cell Biology.

[15]  J. Shay,et al.  SORBS2 transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy , 2015, Genome research.

[16]  M. K. Rudd,et al.  Human Structural Variation: Mechanisms of Chromosome Rearrangements. , 2015, Trends in genetics : TIG.

[17]  Z. Songyang,et al.  Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1) Promotes Non-homologous End Joining and Inhibits Homologous Recombination Repair upon DNA Damage* , 2014, The Journal of Biological Chemistry.

[18]  A. Verbeek,et al.  Population-based incidence and prevalence of facioscapulohumeral dystrophy , 2014, Neurology.

[19]  Daniel G. Miller,et al.  Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2 , 2012, Nature Genetics.

[20]  L. Santoro,et al.  Large-scale population analysis challenges the current criteria for the molecular diagnosis of fascioscapulohumeral muscular dystrophy. , 2012, American journal of human genetics.

[21]  J. Pouget,et al.  Molecular combing reveals allelic combinations in facioscapulohumeral dystrophy , 2011, Annals of neurology.

[22]  Daniel G. Miller,et al.  A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy , 2010, Science.

[23]  E. Gilson,et al.  Replication Timing of Human Telomeres Is Chromosome Arm–Specific, Influenced by Subtelomeric Structures and Connected to Nuclear Localization , 2010, PLoS genetics.

[24]  E. Gilson,et al.  Identification of a perinuclear positioning element in human subtelomeres that requires A‐type lamins and CTCF , 2009, The EMBO journal.

[25]  C. Angelini,et al.  Facioscapulohumeral muscular dystrophy: epidemiological and molecular study in a north‐east Italian population sample , 2009, Clinical genetics.

[26]  M. Lacey,et al.  Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers , 2008, Nucleic acids research.

[27]  G. W. Padberg,et al.  Facioscapulohumeral muscular dystrophy , 2007, Current opinion in neurology.

[28]  Meena Upadhyaya.  Facioscapulohumeral Muscular Dystrophy: Genetics , 2006, eLS.

[29]  L. Sandkuijl,et al.  Mechanism and timing of mitotic rearrangements in the subtelomeric D4Z4 repeat involved in facioscapulohumeral muscular dystrophy. , 2004, American journal of human genetics.

[30]  L. Shaffer,et al.  Monosomy 1p36 breakpoint junctions suggest pre-meiotic breakage-fusion-bridge cycles are involved in generating terminal deletions. , 2003, Human molecular genetics.

[31]  G. V. Ommen,et al.  Facioscapulohumeral muscular dystrophy is uniquely associated with one of the two variants of the 4q subtelomere , 2002, Nature Genetics.

[32]  Y. Hayashi,et al.  Chromosome 4q;10q translocations; Comparison with different ethnic populations and FSHD patients , 2002, BMC neurology.

[33]  E. Bakker,et al.  Complete allele information in the diagnosis of facioscapulohumeral muscular dystrophy by triple DNA analysis , 2001, Annals of neurology.

[34]  L. Sandkuijl,et al.  Interchromosomal repeat array interactions between chromosomes 4 and 10: a model for subtelomeric plasticity. , 2000, Human molecular genetics.

[35]  H. Ding,et al.  Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element. , 1999, Gene.

[36]  E. Bakker,et al.  Inter- and intrachromosomal sub-telomeric rearrangements on 4q35: implications for facioscapulohumeral muscular dystrophy (FSHD) aetiology and diagnosis. , 1998, Human molecular genetics.

[37]  G. Deidda,et al.  Direct detection of 4q35 rearrangements implicated in facioscapulohumeral muscular dystrophy (FSHD). , 1996, Journal of medical genetics.

[38]  J. Flint,et al.  The detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation , 1995, Nature Genetics.

[39]  J E Hewitt,et al.  FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. , 1993, Human molecular genetics.

[40]  J. Lamb,et al.  De novo truncation of chromosome 16p and healing with (TTAGGG)n in the alpha-thalassemia/mental retardation syndrome (ATR-16). , 1993, American journal of human genetics.

[41]  H. Lubs,et al.  Duplication-deficiency of the short arm of chromosome 8 following artificial insemination. , 1976, Annales de genetique.

[42]  M. Foiani,et al.  Coordinating Replication with Transcription. , 2017, Advances in experimental medicine and biology.

[43]  L. Sandkuijl,et al.  De novo facioscapulohumeral muscular dystrophy: frequent somatic mosaicism, sex-dependent phenotype, and the role of mitotic transchromosomal repeat interaction between chromosomes 4 and 10. , 2000, American journal of human genetics.

[44]  L. Shaffer,et al.  Molecular mechanisms for constitutional chromosomal rearrangements in humans. , 2000, Annual review of genetics.

[45]  C. Wijmenga,et al.  Pulsed-field gel electrophoresis of the D4F104S1 locus reveals the size and the parental origin of the facioscapulohumeral muscular dystrophy (FSHD)-associated deletions. , 1994, Genomics.

[46]  M. Pericak-Vance,et al.  Regional mapping of facioscapulohumeral muscular dystrophy gene on 4q35: combined analysis of an international consortium. , 1992, American journal of human genetics.

[47]  P Halonen,et al.  [Facioscapulohumeral muscular dystrophy]. , 1990, Duodecim; laaketieteellinen aikakauskirja.