A de novo complex chromosome rearrangement associated with multisystematic abnormalities, a case report
Tian et al. Molecular Cytogenetics
A de novo complex chromosome rearrangement associated with multisystematic abnormalities, a case report
Chan Tian 0 1 2
Dan Li 0 2
Ping Liu 1 2
Liping Jiao 2
Xuefeng Gao 2
Jie Qiao 1 2
0 Equal contributors
1 Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology , Beijing 100191 , China
2 Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital , Beijing 100191 , China
Background: Complex chromosomal rearrangements (CCRs) are constitutional structural rearrangements that involve three or more chromosomes or that have more than two breakpoints. Case presentation: Here, we describe a four-way CCR involving chromosomes 4, 5, 6 and 8. The patient had mild multisystematic abnormalities during his development, including defects in his eyes and teeth, exomphalos and asthenozoospermia. His wife had two spontaneous abortions during the first trimester. The translocations in 4q27, 5q22, 6q22.3, and 8p11.2 were diagnosed by conventional cytogenetic analysis and confirmed by fluorescence in situ hybridization(FISH). After analysis using a SNP array, we defined three microdeletions, including 0. 89 Mb on chromosome 4, 5.39 Mb on chromosome 5 and 0.43 Mb on chromosome 8. His mother had a chimera karyotype of 47, XXX/45, X/46, XX; the other chromosomes were normal. After one cycle of in vitro fertility (IVF) treatment followed by preimplantation genetic diagnosis (PGD), they obtained two embryos, but neither was balanced. Conclusions: The patient's phenotype resulted from the CCR and microdeletion of chromosomes 4, 5 and 8. The couple decided to use artificial insemination by donor (AID) technology.
CCR; SNP-array; FISH; Microdeletion; Rearrangement; AID
Complex chromosome rearrangements (CCRs) are
structural aberrations involving more than two
chromosome breaks with exchanges of several chromosomal
]. The phenotype of individuals with CCRs
can be normal; this largely depends on whether or not
the CCR is balanced or whether developmentally
important gene(s) are disrupted at the breakpoints.
Balanced CCRs contain unchanged amounts of genes
but unbalanced CCRs do not. According to the
literature, approximately 70% of CCRs are detected in people
without a phenotype, 20-25% are detected in patients
with congenital abnormalities and/or mental retardation
and 5-10% are detected during prenatal diagnosis [
Occasionally, cases have been detected because of
psychiatric trouble [
]. In addition, CCRs are frequently
observed in tumor cells, especially in hematological
malignancies . Among phenotypically normal CCR
carriers, most suffer reproductive failures, including
spontaneous abortions, stillbirths, the delivery of
children with congenital malformations, and male
There are various classifications of CCRs due to their
complex nature. CCRs can be considered familial or de
novo, according to the mode of transmission [
on the number of chromosome breaks, CCRs are divided
into two groups: those with four or fewer breaks and
those with more than four breaks [
]. CCRs are also divided
into three classes according to their structure [
three-way rearrangement, which refers to three
chromosome breaks and exchanges of chromosomal segments;
2) exceptional CCRs, involving rearrangements in which
there is more than one breakpoint per chromosome; and
3) double two-way translocations, which indicates two
or three independent, simple reciprocal or Robertsonian
translocations that co-exist in the same carrier.
Here, we describe a de novo CCR case that involves
four chromosomes and four breakpoints. The patient
displayed mild multisystematic abnormalities, which
were identified by conventional cytogenetics and
molecular genetic technologies. After a failure to obtain
normal embryos with PGD, they chose to accept AID
with donor spermatozoa.
A 25-year-old man and his 26-year-old wife were
referred to our reproductive medical center due to two
spontaneous abortions in the past 3 years after their
marriage. The abortions occurred at the sixth and
seventh week of gestation for the first and second time,
The physical examination of the husband showed that
his eyes had refractive errors; his left eye displayed
congenital amblyopia and his vision was 0.2 (Fig. 1a). He
also had bilateral primary open angle glaucoma (POAG)
and the intraocular pressure of his eyes was more than
40 mmHg. His eyes were subjected to a trabeculotomy
and the intraocular pressure was well-controlled. He also
had exomphalos (Fig. 1b). His two central incisors were
congenitally lost as implant, his lower right primary
canine was retained (Fig. 1c) and his lower left permanent
canine was congenitally missing (Fig. 1d). He had
graduated from high school and is now employed. He can
communicate normally. His routine semen analysis
demonstrated a sperm deformity rate of 99%, sperm
viability rate of 9.56%, DNA fragmentation index (DFI) of
13.58%, and high DNA stainability (HDS) of 15.36%.
He is the second child of non-consanguineous parents
and has two sisters. His parents and both sisters are
healthy. After discovering his chromosome
abnormalities, his family members underwent genetic testing
(except his older sister, who was abroad).
After genetic counseling, the couple insisted on
preimplantation genetic diagnosis (PGD). Initially, they
obtained two embryos to undergo PGD; both were
unbalanced. After counseling, they decided to accept
artificial insemination with donor spermatozoa.
Methods and results
Metaphase chromosomes obtained from
colchicinestimulated cultures of peripheral blood lymphocytes and
fibroblast cultures were used for GTL-banding and
fluorescence in situ hybridization(FISH) analysis. FISH
was performed according to the method described by
Wieczorek et al. [
]. A SNP-array was performed using
Cyto12 genechip (Illumina, USA) according to the
The patient, his parents and his younger sister were
examined. A classical cytogenetic examination revealed that the
patient’s karyotype was 46, XY, t(4; 8; 6; 5) (q27; p11.2;
q22.3; q22) (Fig. 2a). The father and younger sister’s
Gbanded karyotypes were normal. Unexpectedly, his mother’s
karyotype was 47, XXX[
]/46, XX (data not
shown). As the patient and his wife had described, his
mother was normal during her pregnancy with the patient.
To confirm the presence of a complex translocation
involving four chromosomes, FISH was performed with
the whole chromosome painting (wcp) probes wcp5,
wcp6, wcp8, the chromosome terminal probes 4pter,
4qter, 5pter and 5qter, as well as the specific probes
EGR1, D5S23, DMYB and RP11-244 M13. The
combined karyotype of the patient was 46, XY,? t(4;8;6;5)
(q27;p11.2;q22.3;q22).ish der(4) t(4;8) (q27;p11.2) (4pter
+,4qter-,EGR1+,5qter+), der(8) t(8;6) (p11.2;q22.3) (8pter-,
4qter+, WCP8+), der(6) t(6;5) (q22.3;q22) (WCP8+, WCP6+),
der(5) del(5) (q21.1q21.3) t(5;4) (q22;q27) (RP11-244 M13-,
5pter+, D5S23+, EGR1-, 5qter-, WCP6+, MYB+) (Fig. 2).
After using wcp, we observed material from der(5)
present on der(4), material from der(6) present on
der(5), and material from der(8) present on der(6)
(Fig. 2b-d). The rearrangement of these chromosomes
was confirmed by the terminal and specific probes
(Fig. 2e-i). When the probes were hybridized with 4pter
and 4qter, we observed that 4qter was present on der(8),
whereas 5qter was present on der(4) (Fig. 2e-f ). When we
used the probes EGR and D5S23, which are specific for
5q31.2 and 5p15.2, respectively, one EGR signal was
observed on der(4) (Fig. 2g). When we used the probe
RP11-244 M13, which is specific for 5q21.1q21.2, only
one copy was observed, indicating a deletion on
chromosome 5 (Fig. 2h). A signal from the MYB probe, which is
specific for 6q23.2, was observed on der(5) (Fig. 2i). The
FISH results were in accordance with the karyotype.
To confirm the FISH results and to determine the
presence of microdeletions during chromosome
rearrangement, we examined DNA from the patient’s
peripheral blood using a SNP-array assay according to
the manufacturer’s instructions (Illumina). The results
were as follows: arr[hg19] 4q25(110499958-111,393,691)×1,
arr[hg19] 5q21.1(100718992-106,104,465)×1 and arr[hg19]
8p22(14547284-14,972,402)×1, which revealed three
microdeletions on three different chromosomes (Fig. 3). The
genes involved in these regions are shown in Table 1. These
genes included five OMIM genes (which belong to the
phospholipase A2 group XIIA (PLA2G12A)), ELOVL fatty
acid elongase 6 (ELOVL6), solute carrier organic anion
transporter family member 4C1 (SLCO4C1),
diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2, also known as
HISPPD1) and nudix hydrolase 12 (Nudt12). These genes
are not associated with known disorders. Among them,
SLCO4C1 is an organic anion transporter, HISPPD1 is a
kinase (which acts as a cell signaling molecule), and the
remaining genes are enzyme-encoding genes that are
involved in several metabolic processes, including
phospholipid, fatty acid and nucleotide metabolism. Interestingly,
two genes, RRH and LRIT3, were related to his ocular
disorder. RRH (retinal pigment epithelium-derived rhodopsin
homolog) belongs to the seven-exon subfamily of
mammalian opsin genes [
]; mutation of this gene has been linked
to retinitis pigmentosa and allied diseases [
The LRIT3 (leucine rich repeat, Ig-like and
transmembrane domains 3) encoded protein may regulate
fibroblast growth factor receptors and affect the modification
of these receptors, which are glycosylated differently in
the Golgi and endoplasmic reticulum. Mutations in this
gene are associated with congenital stationary night
blindness, type 1F [
]. Our results demonstrate that
although these genes are not associated with known
disorders, they show haploinsufficiency.
To determine whether the patient’s microdeletions
were inherited from his parents or whether they
appeared de novo, the parents were subjected to a
SNP-array analysis. The results demonstrated that the
parents do not have microdeletions in the three
chromosomes mentioned above (Fig. 4), indicating that
the loss of chromosome fragments was derived from
Discussion and conclusion
Here, we describe a four-way CCR involving several
microdeletions on chromosomes 4, 5, 6 and 8. The
patient had mild multisystematic abnormalities during
development, including defects in his eyes and teeth,
exomphalos and asthenozoospermia. After completing a
cycle of PGD, he did not obtain normal embryos and
decided to use AID.
CCRs are rare events with an estimated frequency of
]. Most CCR cases are unknown to the carriers
or their families. Some chromosomes, including 2, 3, 4,
7, and 11, are more frequently implicated in CCR than
would be expected. This is the first CCR case to involve
chromosomes 4, 5, 6, and 8 [
CCRs can involve up to 15 breakpoints. According to
a 2011 summary, cases that included four breakpoints
accounted for 29.1% of all 251 CCR cases [
However, this CCR occurred de novo; the patient’s
mother’s karyotype was 47, XXX[
and she had a low level of mosaic 47, XXX and 45, X,
which was less than 10%. She had three children at 19,
21 and 35 years of age and had no fertility issues during
her childbearing age. Her mosaic karyotype is possibly
due to a gain or a loss of X chromosomes as she aged
] or chromosomal nondisjunction during the
culture of peripheral blood lymphocytes.
Breakpoint analysis of a growing number of complex
rearrangements has revealed that translocations
involving three or more chromosomes are likely formed via
]. Most constitutional
chromothripsis events occur de novo and those investigated
thus far have been verified as paternal in origin [
Alternatively, mitotic errors in the early embryo [
the pulverization of micronuclei [
] could be
responsible for numerous DNA breaks. We speculate that this
de novo CCR is due to chromothripsis.
According to the literature, a three-way CCR would
theoretically form 64 different gametes: one normal, one
balanced, and the rest unbalanced [
]. A four-way CCR,
as in this case study, has a probability of producing
normal and balanced gametes of less than 1/32. We
disclosed this possible risk and as a result of genetic
counseling, the couple opted for PGD. After a failure to
obtain normal embryos with PGD, they chose to accept
AID with donor spermatozoa.
In conclusion, we systematically investigated this CCR
and the accompanying microdeletions and were able to
characterize the genetic defects that resulted in the
patient’s multisystematic abnormalities, which had
bothered him for many years. After receiving genetic
counseling, the couple understood that they could not
conceive a chromosomally balanced child because the
husband had microdeletions in three chromosomes.
They chose to undergo AID.
AID: Artificial insemination by donor; CCR: Complex chromosome rearrangements;
FISH: Fluorescence in situ hybridization; PGD: Preimplantation diagnosis
This work was supported by the Chinese National Natural Science Foundation
Grant (81472004), the National Key Research and Development Program,
Ministry of Science and Technology, P.R. China (Grant No. 2016YFC1000500,
2016YFC1000501). The funders had no role in the study design, data collection
and analysis, decision to publish, or preparation of the manuscript.
Availability of data and materials
Data sharing is not applicable for this article as no datasets were generated
or analyzed during the current study.
CT and DL performed the genetic analysis, collected data from the patient,
and wrote the manuscript. PL is the patient’s doctor. LJ and XG performed
the genetic analysis. JQ designed the study and revised the manuscript. All
authors read and approved the final manuscript.
Ethics approval and consent to participate
This study was approved by the Ethics Committee of Peking University Third
Hospital. The committee’s reference number is 2016S2-021. The patient gave
his consent for participation in this study.
Consent for publication
Informed written consent for publication of the clinical details was obtained
from the patient. A copy of the consent form is available for inspection by
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
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