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
. 2017 Feb;38(2):180-192.
doi: 10.1002/humu.23146. Epub 2016 Dec 5.

Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation

Daniel Nilsson #  1   2   3   4 , Maria Pettersson #  1   2 , Peter Gustavsson  1   2   3 , Alisa Förster  1   2 , Wolfgang Hofmeister  1   2 , Josephine Wincent  1   2 , Vasilios Zachariadis  1   2 , Britt-Marie Anderlid  1   2   3 , Ann Nordgren  1   2   3 , Outi Mäkitie  1   2   3   5   6 , Valtteri Wirta  7 , Max Käller  7 , Francesco Vezzi  8 , James R Lupski  9   10 , Magnus Nordenskjöld  1   2   3 , Elisabeth Syk Lundberg  1   2   3 , Claudia M B Carvalho  9 , Anna Lindstrand  1   2   3
Affiliations

Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation

Daniel Nilsson et al. Hum Mutat. 2017 Feb.

Abstract

Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.

Keywords: balanced chromosomal aberration; microhomology; nonhomologous end joining; reciprocal translocation; replication-based repair mechanisms; whole-genome sequencing.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Molecular cytogenetic and genomic findings in subjecft 862-06Ö
A) G-banded chromosomes showing the balanced translocation between chromosome 16 and chromosome 22 present in individual 862-06Ö (the aberrant chromosome shown to the left) (B) FISH analysis with BAC clone RP11-350D02 (red) localized at chr16p11 (Ensemble, GRCh37). The signal is split between the two derivative chromosomes (der16 and der22). (C) Circos plot illustrating the WGS results in individual 862-06Ö. Fusion events between chromosome 16 and 22, as predicted by FindTranslocations, from read pair mapping data are illustrated as grey lines. On chromosome 16, COG7 is disrupted by the breakpoint. The chromosomes are karyogram painted, chr22 in gray and chr16 in blue, with the centromeres shown shaded dark red. Copy number changes according to CNVnator are shown in the central ring, with a light red bar corresponding to low coverage and light green to high. As can be seen, short read sequence mapping does not cover the centromeric region or the heterochromatic 22p-arm. All copy number changes were evaluated as benign normal variation for this patient. (D) Sanger sequencing traces showing the chromosomal junctions at the nucleotide level with der16 on top and der22 on the bottom. A two-nucleotide microhomology (TT) that may have originated from either parental chromosome is present in the der16 breakpoint junction (black box) and a clean break is present on der22 (black vertical line).
Figure 2
Figure 2. Evidence for template switching during translocation formation in individual 887-05Ö
(A) A schematic overview of chr5q14.1 and 7q34 region and the structural events in individual 887-05Ö. The derivative 5 (der5) in blue and derivative 7 (der7) in green are aligned to chromosome 5 (top) and chromosome 7 (bottom). Alu elements are shown as grey boxes. The 1579 nt upstream deletion on der 5 is shown as a dashed blue line. Both deletion breakpoints as well as the translocation breakpoints are located in Alus. (B) Sequence alignment of der5 to the corresponding regions on chromosome 5 and chromosome 7. The derivative chromosome sequences as well as the corresponding parental chromosome sequence are labeled in blue. The deletion is shown in lower case bold letters. Microhomology is highlighted in purple with the most plausible parental chromosome indicated by bold text. A 22 nt microhomology is present in the first slippage event (TSL 1) between the proximal and distal end of the der 5 upstream deletion. In the second event, chromosome 5 to chromosome 7 (TSL 2), a 3 bp microhomology is present. (C) Der7 illustrated in green otherwise as in (B). A three-nucleotide microhomology is present in the junction.
Figure 3
Figure 3. Four additional translocation carriers with evidence for templated insertions originating from nearby genomic segments
Sequence alignments of the derivative chromosome sequences to the corresponding regions on the parental chromosomes. Deletions are shown in lower case bold letters. Microhomology is highlighted in purple with the most plausible parental chromosome indicated by bold text. Insertions and SNVs are shown in pink (A) Sequence alignments from case 862-06Ö. Derivative chromosome 22 (der22) is shown on top and derivative chromosome 16 (der16) on the bottom. The derivative chromosome sequences as well as the corresponding parental chromosome (chr16 and chr22) sequences are labeled in blue for der22 and in green for der16. Short deletions are present on both parental chromosomes, 4 nt on chr16 and 5 nt on chr22. On chr16 palindromic sequences are present on each side of the breakpoint. A six nucleotide (nt) insertion is present in the junction of der22 (TTATAC), likely due to template slippage (TSL) copying from the palindrome sequence using a 3 nt (TTA) microhomology. A 2 nt microhomology is present in der16. (B) Sequence alignment from case 851-06Ö. Derivative chromosome 17 (der17) is shown on top and derivative chromosome X (derX) on the bottom. The derivative chromosome sequences as well as the corresponding parental chromosome (chr17 and chrX) sequences are labeled in blue for der17 and in green for derX. Short deletions are present on both parental chromosomes, 9 nt on chr17 and 7 nt on chrX. On der17 a 5 nt microhomology is present. A 12 nt insertion is present on der X that may originate from template switching to two different places on chr17 (- strand). In the TS1 a potential CACCT microhomology is present but for TS2 no microhomology could be observed. (C) Sequence alignment from case 337-01D. Derivative chromosome 3 (der3) is shown on top and derivative chromosome 12 (der12) on the bottom. The derivative chromosome sequences as well as the corresponding parental chromosome (chr3 and chr12) sequences are labeled in blue for der3 and in green for der12. Deletions are present on both parental chromosomes, 6594 nt on chr3 and 13 nt on chr12. On der3 a 1 nt microhomology is present A 10 nt insertion is present on der 12 that may have arisen through error prone backward slippage using a 4 nt (TTTT) microhomology. (D) Sequence alignment from case 29-03E. Derivative chromosome 9 (der9) is shown on top and derivative chromosome 16 (der16) on the bottom. The derivative chromosome sequences as well as the corresponding parental chromosome (chr9 and chr16) sequences are labeled in blue for der9 and in green for der16. On der 9, 3 nt microhomologies are present on both sides of a 27 nt resection/deletion. On der16 the junction presents with a 222 nt deletion and the 5 bp insertion (TTGGC) originates from inside the deletion.
Figure 4
Figure 4. Schematic of double stranded break (DSB) and single stranded break (SSB) prior to formation of balanced translocations
(A) The formation of two DSBs in distinct heterologous chromosomes is illustrated at the top in blue and green respectively. 1.) Left: DSB formation followed by 5′ resection. If 5' end resection occurs without 3′ end processing the translocation junctions (jcts) will be copy neutral (Right). 2.) If 5′ resection in addition to 3'end processing occurs at the breakpoints there will be formation of short deletions at the translocation jcts. (B) SSB or nick formation on top as in A. If two nearby SSBs generated on opposite strands are converted into a DSB short duplications may be present at the translocation jcts. Small letters (a, b, c, d) indicate breakpoint segments. Gap filling is indicated by dashed lines with respective breakpoint segments indicated by primed letters (a’, b’, c’, d’).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Abyzov A, Li S, Kim DR, Mohiyuddin M, Stutz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, et al. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun. 2015;6:7256. - PMC - PubMed
    1. Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21(6):974–84. - PMC - PubMed
    1. Artegiani B, de Jesus Domingues AM, Bragado Alonso S, Brandl E, Massalini S, Dahl A, Calegari F. Tox: a multifunctional transcription factor and novel regulator of mammalian corticogenesis. EMBO J. 2015;34(7):896–910. - PMC - PubMed
    1. Baptista J, Mercer C, Prigmore E, Gribble SM, Carter NP, Maloney V, Thomas NS, Jacobs PA, Crolla JA. Breakpoint mapping and array CGH in translocations: comparison of a phenotypically normal and an abnormal cohort. Am J Hum Genet. 2008;82(4):927–36. - PMC - PubMed
    1. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. - PMC - PubMed

Publication types

LinkOut - more resources