Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 May;27(5):760-771.
doi: 10.1038/s41431-019-0341-5. Epub 2019 Jan 30.

Breakpoint mapping at nucleotide resolution in X-autosome balanced translocations associated with clinical phenotypes

Mariana Moysés-Oliveira  1 , Adriana Di-Battista  1 , Malú Zamariolli  1 , Vera Ayres Meloni  1 , Silvia Bragagnolo  1 , Denise Maria Christofolini  2 , Carlos Eduardo Steiner  3 , Nadezda Kosyakova  4 , Thomas Liehr  4 , Alexandre Reymond  5 , Maria Isabel Melaragno  6
Affiliations

Breakpoint mapping at nucleotide resolution in X-autosome balanced translocations associated with clinical phenotypes

Mariana Moysés-Oliveira et al. Eur J Hum Genet. 2019 May.

Abstract

Precise breakpoint mapping of balanced chromosomal rearrangements is crucial to identify disease etiology. Ten female patients with X-autosome balanced translocations associated with phenotypic alterations were evaluated, by mapping and sequencing their breakpoints. The rearrangements' impact on the expression of disrupted genes, and inferred mechanisms of formation in each case were assessed. For four patients that presented one of the chromosomal breaks in heterochromatic and highly repetitive segments, we combined cytogenomic methods and short-read sequencing to characterize, at nucleotide resolution, breakpoints that occurred in reference genome gaps. Most of rearrangements were possibly formed by non-homologous end joining and have breakpoints at repeat elements. Seven genes were found to be disrupted in six patients. Six of the affected genes showed altered expression, and the functional impairment of three of them were considered pathogenic. One gene disruption was considered potentially pathogenic, and three had uncertain clinical significance. Four patients presented no gene disruptions, suggesting other pathogenic mechanisms. Four genes were considered potentially affected by position effect and the expression abrogation of one of them was confirmed. This study emphasizes the importance of breakpoint-junction characterization at nucleotide resolution in balanced rearrangements to reveal genetic mechanisms associated with the patients' phenotypes, mechanisms of formation that originated the rearrangements, and genomic nature of disrupted DNA sequences.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Strategy used to Sanger sequence the junction-points of translocations with breakpoints at heterochromatic regions. a IGV screenshot of whole genome sequencing pair-end reads of patient 8, visualizing split-reads (dark red) and chimeric inserts (red) in Xq13.3 breakpoint region. b Numbered reads from panel a were selected and the sequence of their mates were obtained from the FASTQ files, to assembly the sequence of the autosomal breakpoint region, which is located at chromosome 9 centromeric region. Reads in dark blue are the remaining portion of the split-reads 1 and 2 (dark red in panel a) observed in IGV. c At the top, Sanger sequencing electropherogram of the der(X) junction point. The breakpoint is indicated by an arrowhead. Below, alignment of the Sanger sequencing of the der(X) junction point, read 1, read 2, and the read 6’s mate sequences from panel a to chromosomes X and 9 references. Sequences from chromosome X and 9 are in red and blue, respectively. A deletion of 2 bp in patient 8’s chromosome X is indicated in bold in the X-chromosome reference sequence
Fig. 2
Fig. 2
Patient 3’s breakpoint characterization at the nucleotide level and rearrangement’s impact on the expression of disrupted genes. a Partial G-banding karyotype and b ideogram of the chromosomes involved in her translocation. c, d Sanger sequencing electropherograms of the der [7] (c) and der(X) (d) junction points. Black dashed box on der[7] shows microhomologies between chromosomes X and 11 breakpoint regions. Black dashed box on der(X) shows nucleotide insertions at the junction-point. Below, alignment of the junction points to chromosome X and 11 reference sequences. e RT-qPCR expression levels of APOOL in whole blood of n = 8 Brazilian female controls and patient 3. Note APOOL unmodified expression in the patient when compared to controls
Fig. 3
Fig. 3
Predicted position effect on genes neighboring the breakpoints. a HiC data visualization from ENCODE [17] of X-chromosome 37.1-41.2 Mb (hg19) region showing TAD (dashed line) that harbors patient 10’s X-chromosome breakpoint (black bar). This breakpoint is 20 kb downstream TSPAN7 gene (arrow). b RT-qPCR expression levels of TSPAN7 in whole blood of n = 8 Brazilian female controls and patient 10. Note the absence of TSPAN7 expression in the patient. c HiC data visualization from ENCODE [18] of X-chromosome 72.1-77.6 Mb (hg19) region showing TAD (dashed line) that harbors X-chromosomal breakpoint of patients 4 and 7 (black bars) and a ~850 kb duplication (gray bar) previously described [31], and the TAD (dashed line) that harbors FGF16 gene (arrow)
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Warburton D. De novo balanced chromosome rearrangements and extra marker chromosomes identified at prenatal diagnosis: clinical significance and distribution of breakpoints. Am J Hum Genet. 1991;49:995–1013. - PMC - PubMed
    1. Schluth-Bolard C, Labalme A, Cordier MP, Till M, Nadeau G, Tevissen H, et al. Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations. J Med Genet. 2013;50:144–50. doi: 10.1136/jmedgenet-2012-101351. - DOI - PubMed
    1. Bugge M, Bruun-Petersen G, Brondum-Nielsen K, Friedrich U, Hansen J, Jensen G, et al. Disease associated balanced chromosome rearrangements: a resource for large scale genotype-phenotype delineation in man. J Med Genet. 2000;37:858–65. doi: 10.1136/jmg.37.11.858. - DOI - PMC - PubMed
    1. Nilsson D, Pettersson M, Gustavsson P, Forster A, Hofmeister W, Wincent J, et al. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Hum Mutat. 2017;38:180–92. doi: 10.1002/humu.23146. - DOI - PMC - PubMed
    1. Schmidt M, Du Sart D. Functional disomies of the X chromosome influence the cell selection and hence the X inactivation pattern in females with balanced X-autosome translocations: a review of 122 cases. Am J Med Genet. 1992;42:161–9. doi: 10.1002/ajmg.1320420205. - DOI - PubMed

Publication types