Unraveling uniparental disomy

Chromosomes from one parent only: this is uniparental disomy (UPD)!

Normally, every human has 22 pairs of chromosomes (called homologous chromosomes or homologs or autosomes) plus one couple of sexual chromosomes (which are two X chromosomes in females and one chromosome X plus one chromosome Y in males). For normal development, we need that, for each pair of autosomes, one is inherited from the mother and another one from the father. Uniparental disomy (UPD) is an abnormal condition in which both copies of an autosome (or a part of it) are inherited from the same parent, while the contribution from the other parent is missing. There are two different types of UPD: (1) heterodisomy, in which inherited homologs are different and (2) isodisomy, in which the homologs are the same.

Uniparental disomy: how does it happen?

Here's a simple, basic scheme:

Nondisjunction in meiosis I >>> heterodisomy.

Nondisjunction in meiosis II >>> isodisomy.

UPD derives from abnormal meiotic segregation, i.e. from an error occurring in cell division during eggs and spermatozoa formation. Nondisjunction during meiosis I causes the non-division of homologous chromosomes and leads to heterodisomy; nondisjunction during meiosis II causes the non-division of sister chromatids and leads to isodisomy. Here some events that trigger UPD:

  1. Gametic complementation: a disomic gamete (an abnormal gamete with two chromosomes from the same parent) matches a nullisomic gamete (a gamete with zero chromosomes for that particular autosome pair). The result will be that of an embryo with one pair of autosomes coming from one parent only.
  2. Trisomy rescue: during fertilization, a disomic gamete (an abnormal gamete with two chromosomes from the same parent) joins a normal gamete (a gamete with one chromosome). So, the zygote (i.e. the embryo) will be trisomic for that particular chromosome, having three copies instead of two. The embryo will try to repair this situation by depleting one of the three copies: in 2 out of 3 cases we'll get a normal zygote (i.e. a zygote with a chromosome from the mother and the other one from the father), but in 1 out of 3 cases we'll get UPD (i.e. the zygote will deplete the "wrong" chromosome, retaining the chromosomes from one parent only).
  3. Monosomy rescue: during fertilization, an abnormal monosomal gamete (a gamete with just one chromosome) will meet a nullisomic gamete. Also in this case, the embryo will try to repair the situation by duplicating that single chromosome: this will lead to isodisomy.

Other less common causes of UPD include:

  1. Postzygotic errors (i.e. errors that occur after the fertilization and the formation of the embryo) due to mitotic recombination, which cause segmental UPD.
  2. Somatic replacement of a derivative chromosome or marker chromosome.
  3. Structural chromosomal abnormalities, such as Robertsonian translocations, isochromosomes and reciprocal translocations.

Uniparental dysomy: which clinical outcome?

What is the clinical outcome of UPD? Although UPD has no clinical consequence in most chromosomes, phenotypic abnormalities may occur when chromosomes 6, 7, 11, 14, 15, and 20 are involved. This is due to the fact that these chromosomes contain imprinted genes, i.e. genes which are differentially expressed based on their parental origin.

So, imprinted genes have differential parent-specific epigenetic modifications, named methylation pattern. The methylation pattern is usually completed after the first trimester of gestation and is maintained throughout adult life. The methylation pattern decides which one of the chromosome copies (maternal or paternal) will be expressed in the cell.

The most common syndromes caused by UPD are Angelman syndrome (AS) and Prader-Willi syndrome (PWS), both caused by UPD of chromosome 15; Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS), both caused by UPD of chromosome 11; Temple and Kagami-Ogata syndromes, caused by UPD of chromosome 14. However, UPD can also affect genes that are not subject to imprinting, causing mild recessive diseases.

When should we have a suspicion for UPD?

UPD should be sought in prenatal diagnosis when:

  1. Mosaicism for monosomies or trisomies involving chromosomes 6, 7, 11, 14, 15, and 20 are detected by amniocentesis or chorionic villus sampling (CVS);
  2. A genetic screening is performed in pre-implantation of embryos;
  3. Ultra-sound (US) imaging of the fetus suggest the presence of a UPD-related syndrome;
  4. Balanced Robertsonian translocations (particularly involving chromosomes 14 and 15), isochromosomes, or non-Robertsonian translocations are identified by amniocentesis or CVS.
  5. Supernumerary chromosomal markers are identified in the fetus.

UPD should be sought in postnatal diagnosis to confirm the diagnosis in:

  1. Patients with a clinical suspicion of a UPD-related syndrome  (i.e AS, BWS, SRS) or in whom a Robertsonian translocation or supernumerary chromosomal marker involving chromosomes 14 and 15 are identified;
  2. Patients with a homozygous pathogenic variant, which has been identified as heterozygous in one parent only based on familial segregation studies
  3. Patients with methylation pattern abnormalities of imprinted genes;
  4. Patients affected by a phenotype that does not follow Mendelian rules (i.e. female patients with an unusually severe phenotype for a recessive X-linked disorder and a homozygous pathogenic mutation on the X chromosome; or male patients affected by an X-linked disorder which appear to have been transmitted from father to son).

Uniparental disomy: diagnostic methods

UPD in mainly diagnosed by molecular approaches, which are based on haplotype identification in the proband and his parents. For instance:

  • Analysis of short tandem repeats (STR). This technique is the gold standard, although it may not be conclusive in the case of segmental and/or tissue-specific UPD or somatic mosaicism.
  • Chromosomal Microarray (CMA). This is excellent for the identification of isodisomy, as CMA works well in the detection of large regions of homozygosity (ROH). However, because isodisomy represents a minority of cases of UPD, CMA may fail to detect some cases of UPD.
  • Methylation analysis (MS-PCR, MS-MLPA, or exome-wide methylation profiling): this method enables the detection of abnormal methylation patterns in imprinted areas. Abnormal methylation patterns are often a consequence of UPD. However, abnormal methylation patterns may also be caused by primary methylation defects and not by UPD. Notably, nowadays, methylation pattern abnormalities may be investigated for single genes or even by exome-wide profiling.
  • Computational algorithms that identify UPD based on SNP distribution. This method is based on a specific bioinformatic pipeline to elaborate data from whole exome sequencing or whole genome sequencing. Sensibility and specificity of this method may still vary.

Breda Genetics: how do we deal with UPD?

UPD-related disorders may be often suspected by specific clinical signs, which suggest MS-MLPA for a particular chromosomal region or gene. Other disorders may show a less specific or recognizable phenotype: exome-wide methylation profiling may be indicated in these cases, especially when whole exome sequencing or whole genome sequencing are negative. If you suspect a methylation disorder in your patient, please do not hesitate to contact us for:

  • Whole exome sequencing or whole genome sequencing, plus:
  • MS-MLPA (Methylation-Specific MLPA)
  • Exome-wide methylation profiling
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References

Del Gaudio, D., Shinawi, M., Astbury, C. et al. Diagnostic testing for uniparental disomy: a points to consider statement from the American College of Medical Genetics and Genomics (ACMG). Genet Med 22, 1133–1141 (2020). https://doi.org/10.1038/s41436-020-0782-9

Benn P. Uniparental disomy: Origin, frequency, and clinical significance. Prenat Diagn. 2020 Nov 11. doi: 10.1002/pd.5837. Epub ahead of print. PMID: 33179335.

Fedoriw A, Mugford J, Magnuson T. Genomic imprinting and epigenetic control of development. Cold Spring Harb Perspect Biol. 2012 Jul 1;4(7):a008136. doi: 10.1101/cshperspect.a008136. PMID: 22687277; PMCID: PMC3385953.

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