Copy number gain at Xp22.31 includes
complex duplication rearrangements
and recurrent triplications
Pengfei Liu1, Ayelet Erez1, Sandesh C. Sreenath Nagamani1, Weimin Bi1,
Claudia M. B. Carvalho1, Alexandra D. Simmons1, Joanna Wiszniewska1, Ping Fang1,
Patricia A. Eng1, M. Lance Cooper1, V. Reid Sutton1, Elizabeth R. Roeder4,
John B. Bodensteiner5, Mauricio R. Delgado6, Siddharth K. Prakash1, John W. Belmont1,
Pawel Stankiewicz1,7, Jonathan S. Berg8, Marwan Shinawi9, Ankita Patel1, Sau Wai Cheung1
and James R. Lupski1,2,3,∗
1Department of Molecular and Human Genetics and2Department of Pediatrics, Baylor College of Medicine, One
Baylor Plaza, Room 604B, Houston, TX 77030, USA,3Texas Children’s Hospital, Houston, TX 77030, USA,
4Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78207, USA,
5Division of Child Neurology, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA,6Department of
Neurology, University of Texas Southwestern Medical School, Dallas, TX 75390, USA,7Department of Medical
Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland,8Department of Genetics, University of
North Carolina, Chapel Hill, NC 27599, USA and9Division of Genetics and Genomic Medicine, Department of
Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
Received October 26, 2010; Revised January 27, 2011; Accepted February 21, 2011
Genomic instability is a feature of the human Xp22.31 region wherein deletions are associated with X-linked
ichthyosis, mental retardation and attention deficit hyperactivity disorder. A putative homologous recombina-
tion hotspot motif is enriched in low copy repeats that mediate recurrent deletion at this locus. To date, few
efforts have focused on copy number gain at Xp22.31. However, clinical testing revealed a high incidence of
duplication of Xp22.31 in subjects ascertained and referred with neurobehavioral phenotypes. We systemati-
lar assays. We detected not only the anticipated recurrent and simple nonrecurrent duplications, but also
unexpectedly identified recurrent triplications and other complex rearrangements. Breakpoint analyses
rent duplications and triplications were assessed using different approaches. We cannot find any evidence to
support pathogenicity of the Xp22.31 duplication. However, our data suggest that the Xp22.31 duplication may
serve as a risk factor for abnormal phenotypes. Our findings highlight the need for more robust Xp22.31 tripli-
cation detection in that such further gain may be more penetrant than the duplications. Our findings reveal the
distribution of different mechanisms for genomic duplication rearrangements at a given locus, and provide
insights into aspects of strand exchange events between paralogous sequences in the human genome.
The distal portion of the short arm of the human X chromo-
some (Xp22.3) is a region that undergoes frequent genomic
rearrangements. In the pseudoautosomal region PAR1, at the
tip of the X chromosome, an obligatory recombination
occurs in every male meiosis to maintain the homology
∗To whom correspondence should be addressed. Tel: +1 7137986530; Fax: +1 7137985073; Email: email@example.com
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Human Molecular Genetics, 2011, Vol. 20, No. 10
Advance Access published on February 25, 2011
between chromosomes X and Y PAR1 regions. Proximal to
the PAR1 boundary of the X chromosome, a series of histori-
cal duplication and inversion events occurred. Several gene
families, such as the sulfatase gene family, VCX/Y gene
family and the CD99 gene family, may have arisen from evol-
utionary genomic segmental duplications. These rearrange-
ments occurring both within this region and between the
homologous regions on the X–Y chromosomes, shaped the
intricate genomic structure therein during primate genome
rearrangements causing disease in Xp22.3 have been fre-
quently observed. Deletions in males (females in a few
cases) are associated with contiguous gene syndromes (4).
Unbalanced translocations between X and Y homologous
regions were also reported in different patients (5,6).
Xp22.31 is one of the most extensively studied genomic
intervals on the short arm of the X chromosome; deletion of
the steroid sulfatase gene [STS (MIM 300747)] accounts for
90% of X-linked ichthyosis [XLI (MIM 30870)] (4,7,8).
Complex traits, including X-linked nonspecific mental retar-
dation [MRX (MIM 309530)] and attention deficit hyperactiv-
ity disorder [ADHD (MIM 143465)], have also been observed
in addition to XLI (9–11). Interspersed around these deletions
are S232 low copy repeats (LCRs). In the reference human
haploid genome, there are six paralogous copies of S232
LCRs, four at Xp22.31 and two at Yq11.22 (Table 1). Each
of them contains two variable number of tandem repeat
(VNTR) elements, termed repeating unit 1 and 2 (RU1 and
RU2) (12). The RU2 element consists of a variable-sized
monomeric unit of ?26–37 bp, with an embedded poly-
morphic tetranucleotide repeat. It consists of purine-rich
highly asymmetric sequences without cytosines on one
strand (12). Yen et al. (13) showed that unequal recombination
involving two of the S232 elements flanking the STS region
frequently produces the 1.6 Mb recurrent deletion. Fine
mapping of recombination sites in four patients carrying the
common deletion narrowed the breakpoint region into the
RU2 element, implicating nonallelic homologous recombina-
tion (NAHR) (14) as the mechanism for these deletions (10).
Recently, a 13-mer, cis-acting, homologous recombination
(HR) stimulating motif (5′-CCNCCNTNNCCNC-3′) has
been identified from population-based studies of historical
recombinants and shown to be associated with 40% of the
allelic homologous recombination (AHR) hotspots identified
from the HapMap Phase II data (15). In addition, the same
motif was found to bind a protein, PR-domain containing 9
(PRDM9), thought to be involved in hotspot specification.
This protein possesses histone H3K4 trimethylase activity
and contains multiple zinc finger motifs (16–18). Empirical
studies suggest that HR crossovers, or Holliday structure res-
olution, occur within a 400 bp range either upstream or down-
stream from this motif (19). Interestingly, almost every repeat
unit within the RU2 element contains one copy of this motif.
Based on the sequence of the haploid reference genome, the
RU2 elements in the six paralogous S232 LCRs contain 12–
28 copies of this motif. If calculated on a genome-wide mega-
base scale, the concentration of the 13-mer motifs is highest in
the Xp22.31 region (15). However, the exact position at which
crossover occurs with respect to the associated hotspot motif
remains to be elucidated.
To date, efforts to understand rearrangements in the
Xp22.31 region have focused on deletions and translocations,
but rarely duplications. This may partly be due to the fact that
the duplication is present in some ‘phenotypically normal’
individuals; therefore, it has been considered as a benign
copy number variant (CNV). Recently, Li et al. (20) summar-
ized clinical phenotypes in 23 patients with Xp22.31 dupli-
duplications reported in the literature. However, the clinical
significance of Xp22.31 duplications is still debated and
further investigation is necessary.
We have identified frequent duplication events at Xp22.31
(0.46%) in clinical samples referred for chromosome microar-
ray analysis (CMA) in the Medical Genetics Laboratories
(MGL) at Baylor College of Medicine (BCM). We systemati-
cally investigated 61 unrelated subjects with CMA-detected
copy gains involving the Xp22.31 region to determine the
size, extent and genomic content of these duplications. We
confirm NAHR as a major mechanism in the presence of
large highly homologous directly oriented LCRs and extend
our mechanistic observations to the strand exchange level.
Among these NAHR-mediated events, breakpoint-sequencing
data reveal enrichment of breakpoints in proximity to the HR
hotspot motif, and suggest that multiple hotspot motifs in
tandem may have an additive effect on stimulating HR. Sur-
prisingly, both recurrent triplications and complex rearrange-
ments were observed in different subjects. To investigate the
potential clinical significance of the Xp22.31 duplication and
triplication, we studied the phenotypes and prevalence of
these two types of rearrangements. In addition, we compared
the phenotypes of duplications and triplications to investigate
whether dosage increments correlate with either penetrance or
severity of the phenotype.
other patients withsimilar
Fine mapping of Xp22.31 duplications
Samples from 69 subjects (61 unrelated) who were ascertained
in the MGL clinical diagnostic laboratory as having Xp22.31
gains were anonymized and analyzed by array comparative
genomic hybridization (aCGH) using region-specific custom
arrays (Fig. 1 and Supplementary Material, Fig. S1). Forty-
four (72%) unrelated cases were found to have a 1.6 Mb
common recurrent duplication flanked by two S232 LCRs,
which is the apparent reciprocal rearrangement to the pre-
viously reported recurrent deletion (13). Nine cases carry
apparently simple nonrecurrent duplications ranging in size
from ?350 kb to ?1.9 Mb. Three (BAB2861, BAB3084
and BAB3089) of them have one breakpoint located within
the S232 LCR. Surprisingly, we found that the region is appar-
ently triplicated in three unrelated cases as evidenced by the
log2 ratio of the aCGH result (?1.58 for male; 1 for
female). These triplications have a similar size and extent
and thus genomic content as the common recurrent dupli-
cations. The recurrent duplications occur ?14-fold more fre-
quently than the recurrent triplications (Fig. 1B). In addition,
apparently complex rearrangements were also detected by
aCGH in five cases. In BAB 2833, a 45 kb segment is tripli-
cated at the distal portion of the recurrent duplication and a
1976 Human Molecular Genetics, 2011, Vol. 20, No. 10
92 kb segment is duplicated proximal to the recurrent dupli-
cation. In the other four cases, complex rearrangements with
a duplication–normal–duplication pattern were observed. Of
note, in these cases with apparent complex rearrangements,
almost half (10 of 21) of all breakpoints are located within
one of the S232 LCRs.
Recurrent triplication can occur at Xp22.31
Our aCGH data suggested that three cases might carry recur-
rent triplications in Xp22.31. The triplications were inherited
from mothersintwo male
BAB2822, but de novo in a female patient, BAB2828. Three
independent experimental molecular approaches, fluorescent
in situ hybridization (FISH), multiplex ligation-dependent
amplification (MLPA) and quantitative PCR (qPCR), were
used to verify the copy number gains. In each case, all three
additional approaches provided CNV information, showing
triplication consistent with the findings initially revealed by
aCGH (Fig. 2, Supplementary Material, Figs S2 and S3).
Breakpoints located within the LCRs
Previously, Van Esch et al. (10) showed that the breakpoint of
Xp22.31 deletion is located within the RU2 element in the
S232 LCRs in four male subjects. In our cohort, aCGH
results suggest that S232 LCRs are involved in breakpoints
of the anticipated reciprocal recurrent duplications and tripli-
cations, as well as other rearrangement types including
complex rearrangements and nonrecurrent simple dupli-
cations. We hypothesized that the RU2 element, where the
AHR hotspot motif is enriched (15), also acts as a ‘hotspot’
for NAHR-mediated duplications and rearrangements occur-
ring by other mechanisms.
To test our hypothesis, we designed PCR assays to amplify
the breakpoint junctions for fine mapping of the crossover
region. Because of the high copy number (8/10 copies in a
male/female duplication versus four copies in an XLI-affected
male with deletion) and the unusual structure of the S232
LCR, breakpoint junctions have been challenging to map
and sequence. We sequenced the breakpoints of 41 subjects,
including 34 subjects with recurrent duplications (BAB
2814, BAB2815, BAB2827, BAB2829, BAB2830, BAB
2835, BAB2831, BAB2837, BAB2840, BAB2841, BAB2842,
BAB2850, BAB2851, BAB2853, BAB2854, BAB2856, BAB
2858, BAB2859, BAB2862, BAB2863, BAB2864, BAB2938,
BAB3078, BAB3081, BAB3082,
BAB3086 and BAB3092), all three subjects with recurrent trip-
lications (BAB2817, BAB2822 and BAB2828), one subject
with a complex rearrangement (BAB3088) and three subjects
with nonrecurrent duplications (BAB2861, BAB3084 and
BAB3089). Consistent with our hypothesis, all of these
cases have either one or two breakpoints located within the
RU2 element (Fig. 3). There is one exception in the
BAB2822 triplication subject. In this subject, one crossover
resides within the RU2 element, whereas the other occurs
withina 98 bp interval (chrX:8 095 471–8 095 568
chrX:6 459 040–6 459 137) that is ?1.7 kb distal to the
RU2 elements, but still within an S232 paralogue (Fig. 3).
Of note, PCR amplification of all recombinant RU2 elements
resulted in fragments of 600–700 bp based on agarose gel
electrophoresis migration and comparison with size standards,
suggesting one to four copies of the repeat unit, which is sig-
nificantly shorter than the length of repeat unit arrays in RU2
elements as listed in the reference sequence (12–28 copies).
Sanger sequencing could not resolve the RU2 element copy
number as the sequence read terminated upon entry into the
repeats, potentially due to its unusual structure and high GC
content. When we used a bacterial artificial chromosome
(BAC) clone, RP11–527B14 that contains the S232–VCX2
repeat, as the PCR template, the size estimate of the amplified
product suggested ?4 copies of the repeat unit in its RU2
element, whereas the sequence of this BAC (GeneBank acces-
sion no. AC097626) suggested 25 copies.
To gain more insight into the role of the hotspot motifs in
potentially stimulating the rearrangements, it is important to
know the precise region of crossover or strand exchange
within the hotspot motifs in RU2. Unique specification of
breakpoints has been a challenge for the recurrent dupli-
cation/deletion cases, wherein both sides of the breakpoint
map within the RU2 elements, whose sequence exhibits
Table 1. Sizes and percent identities of S232 LCRs
Each pair of S232 LCRs are aligned with each other and the numbers in the table represent: size of the LCR in the row(bp)\size of LCR in the column (bp), fraction
matching. Data are obtained from the Segmental Duplications track in UCSC genome browser (http://genome.ucsc.edu/).
Human Molecular Genetics, 2011, Vol. 20, No. 101977
considerable interindividual variation. However, our aCGH
analysis detected a special configuration of rearrangement
that solves this problem. In this configuration, only one
side of the breakpoint maps to the hypervariable RU2
element, whereas the other side of the breakpoint maps to a
nonvariable sequence. The exact intervals of crossovers
were defined in three such cases (Fig. 3C). In BAB3084,
the crossover occurred in a 2 bp region within the hotspot
motif. In BAB2861 and BAB3089, the breakpoint mapped
to the same 4 bp interval adjacent to the hotspot motif.
Microhomologies were observed at the breakpoints in all
Unexpectedly, bioinformatic analysis of sequences from
subject BAB2828 indicates that the breakpoints do not map
to the directly oriented LCR pairs that usually mediate recur-
rent rearrangements. Instead, they map to inverted LCRs
S232-VCX and S232-VCX2, potentially suggesting that this
subject carries an inversion haplotype (Fig. 4), which will be
further elaborated upon in the Discussion section.
Breakpoints that do not involve S232 LCRs
To investigate the underlying molecular mechanisms, we
sequenced the breakpoints of six subjects with simple
Figure 1. Summary of aCGH results. (A) A schematic representation (top) of Xp22.31 genomic region based on the reference genome (hg18). Individual genes
are shown as black rectangles. The vertical yellow shadow areas represent S232 LCRs, with the relative orientations of each of the LCR indicated. Below, hori-
zontal bars depict the involved genomic intervals for each subject from the interpretations of aCGH results. Red bars represent duplications and blue bars rep-
resent triplications; white normal copy. Colors of subject numbers indicate genders, with black depicting male and red female individuals; 44 subjects (27 males,
17 females) carry recurrent duplications as shown in the top row. (B) Distribution of different rearrangement types. Note that BAB2861 is classified as carrying a
complex rearrangement here because breakpoint analysis described later revealed complex rearrangements in this subject.
1978 Human Molecular Genetics, 2011, Vol. 20, No. 10
nonrecurrent duplications. The exact coordinates of the
tandem duplications and microhomologies found at the break-
points are summarized in Table 2. Two- or three-base pair
microhomologies were detected in five of six subjects, impli-
cating either a fork stalling and template switching (FoSTeS)/
microhomology-mediated break induced replication (MMBIR)
(21,22) with a single template switch or a non-homologous
end joining (NHEJ) mechanism. Long or short interspersed
nuclear elements (LINEs or SINEs) are found at the break-
pointsof three nonrecurrent
BAB2824, BAB3090 and BAB3093, the proximal breakpoint
is located within an AluJ element in the first patient, and
within an L1-LINE element in the other patients.
In the subjects in which aCGH results suggested complex
rearrangements, the sequences of all breakpoints located
outside of LCRs were characterized. Results are summarized
in Figure 5. Microhomologies of 1–4 bp were observed at
eight of nine breakpoints, supporting a replication-based
rearrangement mechanism for formation. Subject BAB3088
lacks microhomology at the breakpoints, favoring NHEJ as
the underlying mechanism. In subjects BAB2833 and
BAB3095, we detected short tandem duplications at one
breakpoint. These locally duplicated short sequence segments
are consistent with fingerprints of serial replication slippage
(SRS) (23). Within two subjects, BAB2833 and BAB3094,
the proximal and the distal sequences of one breakpoint map
to opposite strands. These findings are consistent with the sub-
ject’s rearrangements having occurred on a chromosomal
inversion haplotype (Fig. 4).
Breakpoint analyses also uncovered complexity that was not
initially revealed by aCGH. The breakpoint of subject
BAB2861 contains a 40 bp microduplication that was not
detected by aCGH (Fig. 5). Complex rearrangements at this
locus were probably mediated by FoSTeS/MMBIR with mul-
tiple template switches, reflecting a low processivity DNA
polymerase, utilizing the microhomologies at both ends of
this 40 bp segment.
Clinical consequences of the recurrent Xp22.31 duplication
The Xp22.31 gains are among the most frequent findings in
the clinical cytogenetic laboratories (20,24). Nevertheless, it
has been debated whether CNV gain of this genomic interval
is benign or disease causing. In order to address this conun-
drum, we focused on the two types of recurrent gains, the
recurrent duplication and triplication, and studied their clinical
features, patterns of inheritance, X-chromosome inactivation
(XCI) status and population frequencies.
Figure 2. Ascertainment of triplications in patients and carrier parents. Shown above is the genome structure (horizontal black line) and below the genomic
location of the probes for qPCR (green), MLPA (blue) and FISH (black), with the positions shown as vertical tics. Copy number calls of the three different
approaches are compared in representative male (left) and female (right) subjects. The x-axis represents the relative genomic locations of each probe.
Results in subject BAB2817 and mother BAB2818 are shown in this figure. Additional subjects/parents carrying triplication can be found in Supplementary
Material, Figures S2 and S3.
Human Molecular Genetics, 2011, Vol. 20, No. 101979
Following informed consent, we obtained detailed clinical
information for 14 subjects with recurrent duplications and
all three subjects with recurrent triplications (ages from
14 months to 10 years) (Tables 3 and Supplementary Material,
Table S1). Patients with Xp22.31 recurrent duplications gener-
ally presented with a neurocognitive and behavioral pheno-
type, including developmental delay, which was the primary
reason for referral to neurology or genetics. Seven of
11 males (64%) and 2 of 3 females (67%) presented with mod-
erate to severe delay involving motor and/or language areas.
Our findings are consistent with recent observations of devel-
opmental problems in 69% of the patients with Xp22.31 dupli-
cations (20). Additionally, 7 of the 11 males (64%) with
duplications had social interaction deficits or behavioral
abnormalities, including stereotypic features such as hand flap-
ping and avoidance of eye contact, that are consistent with fea-
tures seen in autistic spectrum disorder.
For the Xp22.31 triplications, all three subjects (100%) pre-
sented with developmental delay and both males (100%) pre-
sented with aggressive behavior with features of ADHD.
for analysis, the triplication seems to be potentially more pene-
trant than the duplication with respect to a possible association
with abnormal phenotypes. In the family of the male subject
BAB2817, the triplication carrier mother had short stature and
learning difficulties. The mother had two girls (carrier status
unknown due to unavailability of blood samples) with another
partner. Both girls had short stature and learning difficulties;
one girl had developmental delay. The carrier mother of the
other subject BAB2822 had microcephaly.
Among all the anonymized subjects with recurrent dupli-
cations, 17 subjects had parental studies performed, and the
duplication was inherited in all cases. Eleven male subjects
apparently inherited the duplication maternally; in six female
subjects, the duplications were paternal in two and maternal
in four. We performed XCI studies in all the affected
females and healthy mothers to test whether skewed XCI is
associated with manifestation of abnormal phenotypes.
However, the majority of the subjects showed random or non-
informative patterns of XCI in their blood DNA, implicating
no direct association of XCI with disease manifestation
(Supplementary Material, Table S2).
Given the presence of both affected and healthy carriers, we
sought to compare the frequencies of this rearrangement in the
clinically ascertained population and that in the general popu-
lation. In our MGL sample cohort, the prevalence of the recur-
rent duplication is 0.289% (58 of 20 095). When the data are
parsed by gender, the male or female prevalence is 0.226 or
0.382%, respectively. Our control cohort consists of 5088 indi-
viduals from five different dbGaP cohorts. We identified a
total of 21 control individuals with the recurrent duplication,
for a prevalence of 0.41% (male or female prevalence equals
0.182 or 0.523%, respectively). Therefore, the overall preva-
lence of the common recurrent duplication is not significantly
different between cases and controls (Pearson’s x2test, P ¼
0.1573). When comparing the male or female prevalence sep-
arately, the male prevalence is higher in the affected cohort
than in the healthy cohort whereas the reverse is true for the
female prevalence. However, neither of these differences is
significant (Fisher’s exact test, P ¼ 1 for male, P ¼ 0.28 for
Figure 3. Breakpoints within S232 LCR. (A) Schematic representation of the structure of S232 LCR and location of breakpoints. One member of the S232 LCR
family,S232-VCX2,ischosenarbitrarilytoshow thecontentof theS232LCR.TheorangebardepictstheRU2element,whichhasvariablelengthamongdifferent
individuals. The black bar depicts the VCX2 gene. The red arrow on the left indicates a 98 bp crossover region (chrX:8 095 471–8 095 568) of one recombination
eventinBAB2822.Itislocated ?1.7 kbdistaltotheRU2element.ThethreedashedredverticalarrowspointingtoRU2indicatetheapproximateregionofcrossover
in41rearrangements.Theexactcrossoverregioninthehypervariable RU2element couldnotbe furtherrefined.(B)TherepeatunitinRU2.Thefirstlineshowsthe
representative sequence of a repeat unit from an RU2 element summarized from the sequence from the reference genome. Each unit contains two to five copies of
TCCC. The underlined sequence is variable among different repeat units and the sequence shown here (CCTCTTCC) is the most commonly seen one. The RU2
element is composed of a tandem array of such repeat units. The second line shows the same repeat unit sequence but with the homologous recombination
in green. These green sequences have the potential to adopt the H-DNA conformation. (C) The 2 bp breakpoint interval for the rearrangement in BAB3084 maps
within the hotspot motif. The 4 bp breakpoint interval for BAB2861 and BAB3089 maps adjacent to the hotspot motif.
1980 Human Molecular Genetics, 2011, Vol. 20, No. 10
female). Haplotype analysis in duplication carriers in the
control cohort indicates that duplications occurred on different
haplotype backgrounds, consistent with these duplications
being recurrent as opposed to being inherited from a
common ancestor. The recurrent triplication is not found in
the control cohort (data not shown). Of note, 10 of the 58
(17.2%) subjects with the recurrent duplication and 1 of the
3 subjects with the recurrent triplication carry additional chro-
mosomal CNV that potentially contribute to their clinical phe-
notypes (Supplementary Material, Table S3).
Using NAHR events to study features at the HR hotspots
Previously, investigations into the molecular signature at HR
hotspots have relied on sites of AHR surmised from popu-
lation genetic variation among single nucleotide polymorph-
isms (SNPs) including multisite variants (25) or SNP data
from the HapMap project (15). The latter approach led to
the identification of the 13-mer HR hotspot-associated motif.
In our work, we studied recombination products that occurred
by the NAHR mechanism, instead of AHR, to further examine
the features at the HR hotspots and capitalize on paralogous
sequence variants (PSVs), which is much more frequent than
the previously used SNPs, as markers to refine crossovers.
Because of our clinical testing screen, we have assembled a
large collection of subjects to increase the potential diversity
of rearrangement types identified. Our findings have demon-
strated the power of this approach.
Recombination hotspots for all rearrangement types are
enriched in S232 LCRs
Our results suggest that the recombination breakpoints for all
rearrangement types cluster within the RU2 elements. There
are three dynamic features of the RU2 repeat that may poten-
tially cause genomic instability and predispose to rearrange-
ments: (i) it includes a tandem array of a 26–37 bp repeating
unit and thus represents a minisatellite (26) or VNTR (27);
Figure 4. Alternative interpretations of the inversions in subjects BAB2833, BAB3094 and BAB2828. (A) aCGH interpretation based on the reference haplotype.
The small blue bars below array interpretation of BAB2828 indicate the mapping position of the sequence from one breakpoint junction in this subject. (B) aCGH
interpretation based on a hypothesized inversion haplotype. Inversion haplotype 1 is predicted to be mediated by the LCRs S232-VCX3A and S232-VCX3B.
Inversion haplotype 2 could be mediated by the LCRs S232-VCX3A and S232-VCX. Compared with (A), interpretations in (B) simplify the mechanistic pro-
cesses needed to produce the rearrangements. Note that BAB3094 may not represent a complex rearrangement (Fig. 1) given this interpretation. Similar inter-
pretive challenges posed by a haploid reference human genome that does not incorporate structural variation information have been reported recently (33,41).
Table 2. Summary of nonrecurrent duplications
Subject no. Coordinate of tandem duplicationMicrohomology at breakpointPossible mechanism
chrX:6 558 299–7 371 465
chrX:6 764 860–7 131 598
chrX:7 480 688–8 077 529
chrX:7 049 533–7 400 035
chrX:6 558 299–7 371 465
chrX:5 865 411–6 592 588
FoSTeS/MMBIR×1 or NHEJ
FoSTeS/MMBIR×1 or NHEJ
FoSTeS/MMBIR×1 or NHEJ
FoSTeS/MMBIR×1 or NHEJ
FoSTeS/MMBIR×1 or NHEJ
Human Molecular Genetics, 2011, Vol. 20, No. 101981
furthermore, each repeat monomer harbors a tetranucleotide
microsatellite-likestructure; (ii) embedded within the repeating
unitis the recombination
(5′-CCNCCNTNNCCNC-3′); and (iii) the RU2 element con-
tains a homopurine–homopyrimidine mirror repeat (H palin-
drome), which has been proposed to facilitate formation of the
H-form DNA conformation (Fig. 3B) (28,29). Any single or
combination of these features may account for the frequent
involvement of S232 LCRs in recombinations.
The number of the HR hotspot motifs in the RU2 element
may reflect their recombinogenic potential. In Xp22.31,
there are two pairs of directly oriented LCRs, S232-VCX3A/
S232-VCX2 and S232-VCX/S232-VCX3B.
NAHR causing recurrent deletion/duplication occurs only
between the former pairs. We propose that this phenomenon
may be explained by the increased number of tandem motifs
in the reference genome in the former (24 and 25, respect-
ively) than in the latter (12 and 28, respectively) LCR pairs.
Additionally, the LCRs of the former pair share greater
sequence identity than the latter pair (95.2 versus 91.93%).
Nevertheless, it must be recognized that the absence of any
phenotype associated with duplications involving the latter
Figure 5. Breakpoint sequences of complex rearrangements. (A) The mapping of distal and proximal breakpoint sequences. For each subject, the structure at the
breakpoint suggested by the breakpoint sequence is shown above the copy number interpretation from aCGH results. The ends of each breakpoint are mapped to
the reference genome, represented by green, pink or orange bars connected by dashed lines. (B) Sequence of breakpoints aligned to distal and proximal reference
sequences. The color code is in accordance with colors in (A). The strand of reference sequences are indicated by ‘+’ or ‘2’. The red boxes outline micro-
homologies identified at the breakpoint junctions. The underlined sequences are the segments proposed to be involved with rearrangements by the SRS mech-
1982 Human Molecular Genetics, 2011, Vol. 20, No. 10
LCRs may have biased our ascertainment. Furthermore, both
structure (e.g. minisatellite) and conformation (potential
H-form) of DNA, rather than primary DNA sequence motifs,
could potentially contribute to regional genomic instability.
The vast majority (?72%) of our cases carry recurrent dupli-
cations, indicating that NAHR is the major rearrangement
mechanism at this locus, probably due to the enrichment of
both directly oriented LCRs and the HR hotspot motifs within
the LCRs. Approximately 90% (55 of 61) of the patients
studied herein have breakpoints, ranging from one to four,
located in S232 LCRs. S232 LCRs were overrepresented in
rearrangements mediated by NAHR as well as other mechan-
isms, indicating that the HR hotspot motif may potentially act
by diverse recombinational mechanisms. This motif might (i)
stimulate DNA lesions in the nearby region, perhaps by
PRDM9-facilitated entry of factors inducing a DNA break or
(ii) facilitate template switching or strand invasions given the
reiterative microhomology found in the breakpoint sequences.
trophoresis suggest ?1–4 copies of the repeat unit in RU2 after
recombination. One interpretation for this observation is that
the RU2 element is shortened by the recombination, perhaps by
replication slippage during recombination, which may reduce
genome stability in this region. This interpretation potentially
suggests that the recurrent duplication may arise by some
replication-based mechanism in addition to, or instead of, the
widely accepted NAHR mechanism. However, it should also be
noted that the apparent shortening of the RU2 element repeat
copy number relative to the human reference genome may
reflect that our PCR assay is more efficient in amplifying short
RU2 repeats or the inability of the polymerase utilized in PCR
to extend through this complex repeat. Further investigations of
to understand the features and underlying mechanisms of
rearrangements stimulated by either tandem arrays of the
hotspot motif or potential unusual DNA conformations.
Recurrent triplication at Xp22.31
Here, we report for the first time that recurrent triplications can
occur at Xp22.31. Due to the limitations of the dynamic range
of aCGH with increasing copy number, it has been challenging
to differentiate triplications from duplications, particularly on
autosomal chromosomes. The identification of triplication was
facilitated by using high-density aCGH. Previously, tripli-
cations have been reported in other genomic loci (30–35).
In these cases, the triplications are usually embedded in
complex rearrangements and their mechanism for formation
is proposed to be FoSTeS/MMBIR. From the four cases
with triplications in our study, FoSTeS/MMBIR could be the
underlying mechanism for one case: BAB2833, particularly
with inversion. With two breakpoints obtained in LCRs, the
triplication in BAB2822 seems to be generated by two
NAHR events. It is unclear whether these two events are con-
comitant with each other or not. With our knowledge about
genomic disorders growing, the need to have diagnostic
arrays that are robust enough to differentiate triplications
from duplications is becoming more evident.
Nonrecurrent, including complex, duplications at Xp22.31
are generated by different mechanisms
The breakpoint sequences enabled us to surmise potential sub-
strates and attempt to understand the molecular mechanisms
that produced such rearrangements. Microhomology is the
most prevailing feature observed at the breakpoints. It is found
in 13 of 15 (87%) nonrecurrent breakpoints. Interestingly, two
recent studies identified microhomology as a prevalent feature
at the breakpoints of either pathogenic (30 of 38; 79%) (36) or
apparently benign (219 of 315; 70%) (37) CNVs. Although
NHEJ can possibly account for the mechanism for these
rearrangements, more and more evidence that links formation
mulated (21,32,33,38). Notably, in subjects BAB2833 and
BAB3095, both carrying complex rearrangements, the break-
point sequences show concurrent rearrangements between
Table 3. Summary of clinical phenotypes for the subjects with the recurrent Xp22.31 duplication or triplication and the comparison with the summarized data
from the literature
Recurrent duplications (n ¼ 12)
Male (n ¼ 11)
Recurrent Triplications (n ¼ 3)
Male (n ¼ 2)
All duplications from the literature (n ¼ 35)20
Female (n ¼ 3) Female (n ¼ 1)
MRI/CT brain abnormalities
3 (27%)– 1 (50%)– 3 (9%)
‘–’ indicatesthe featureis not presentinthe corresponding categoryor thisinformationisnot available. In thesubjectswith duplications, thereare two siblingsand
one set of twins. Note that the data from the last column are phenotypes collected from different types of Xp22.31 gains (not restricted to recurrent duplications).
Human Molecular Genetics, 2011, Vol. 20, No. 10 1983
distantly located and closely (within the same replication fork)
located segments, strongly suggesting a replicative mechanism
(both FoSTeS/MMBIR and SRS). In addition, the breakpoint
sequence of BAB3095 suggests replication template switching
between positive and negative DNA strands, further supporting
replicative rearrangement mechanism.
Two subjects with complex rearrangements, BAB3088 and
ment (duplication in BAB3088 and deletion in BAB3091,
respectively) and a nonrecurrent rearrangement (deletion in
BAB3088 and duplication in BAB3091, respectively). These
proposed structures are strongly supported by the breakpoint
sequences of nonrecurrent rearrangements in both subjects
(Fig. 5) and of a recurrent duplication in subject BAB3088.
The two rearrangements in each subject are likely to be caused
by different mechanisms, with recurrent rearrangements appar-
ently by the NAHR mechanism and nonrecurrent rearrange-
mentsby NHEJor FoSTeS/MMBIR×1
depending on whether microhomology is present. We cannot
conclude whether the two rearrangements occurred in the same
meiosis without tracing the de novo event that produced them.
Structural variation may exist at Xp22.31
NAHR between LCRs arranged in an inverted orientation can
cause inversion (39). Such inversions may convey a phenotype
by disrupting genes or regulatory regions, or altering chroma-
tin structures and potentially causing position effects. We have
not directly experimentally demonstrated the presence of an
inversion chromosome in the parent of origin; nevertheless,
the pattern of complex rearrangements seen in subjects
BAB2833, BAB3094 and BAB2828 suggests that these indi-
viduals may carry an inversion polymorphism in their personal
genome with respect to the haploid reference human genome
sequence (Fig. 4). Such an inversion haplotype can simplify
mechanistic processes that produced this rearrangement, and
more parsimoniously explains the aCGH observed complexity
in these three subjects. In support of our prediction, the
segment between S232-VCX and S232-VCX2 in the chimpan-
zee genome is inverted with respect to the human genome
(40). If inversion polymorphism exists in our patient cohort,
this may explain why we cannot readily determine the break-
point junctions in some of our cases.
Inversions may also occur in a nonrecurrent fashion, i.e. by
rearrangements not involving LCR. These inversions may be
misinterpreted as being overly complex by aCGH in compari-
son to the haploid reference genome (33,41). However, unlike
the LCR-mediated inversions proposed above, such inversions
are unpredictable based on our current knowledge of genomic
structure and the aCGH technique. Therefore, the LCR-rich
Xp22.31 region presents a terrific opportunity to further inves-
tigate the impact of structural variations on our haploid–refer-
ence–genome-based interpretation of aCGH data.
The Xp22.31 duplication: a benign CNV or disease-causing
It has been controversial whether the Xp22.31 duplication is
disease causing or merely a benign CNV. Although the clini-
cal features for subjects with Xp22.31 duplications are
variable, our detailed clinical analyses showed that these
patients generally presented with neurocognitive and behav-
ioral phenotypes, which argues for the pathogenic potential
of the duplication. In support of a causal relationship
between CNV gain and observed clinical phenotypes, one of
the genes duplicated, VCX3A, was recently found to be
expressed in human brain, and modulates the stability and
translation of mRNAs involved in neuronal differentiation
and arborization (42). Either deficiency or SNPs of the STS
gene has been associated with cognitive impairment, ADHD,
autism (AUTSX2 [MIM 300495]) and disorders of social com-
With the duplication almost always inherited, most of the
ationofpotential phenotypicassociation isparticularly challen-
ging to discern (44). We proposed that incomplete penetrance
may account for the absence of abnormal phenotypes in some
carriers and performed a case–control study to test this hypoth-
esis. However, we detected an unexpectedly high prevalence of
the Xp22.31 recurrent duplication in the control cohort, which
argues against potential pathogenicity. Nevertheless, it should
be noted that the subtle clinical features and behavioral pheno-
types may obfuscate the definition of ‘normal’ phenotype and
result in misdiagnosis in the control cohort; prevalence differ-
ence between ethnic groups may also potentially add to the dif-
understand the issue. However, since most of our subjects are
anonymized, we do not have parental clinical information for
A genomic dosage model has been proposed to explain
manifestation of some disease traits, in which a combination
of two or more genetic alterations is needed to present a clini-
cal phenotype that is otherwise not as severe or not as pene-
trant(45). Examplesof two
additively or synergistically include a patient with Potocki-
Lupski syndrome (PTLS [MIM 610883]) duplication as well
as hereditary neuropathy with liability to pressure palsy
(HNPP [MIM 162500]) deletion (46), microdeletions in
Thrombocytopenia-Absent Radius syndrome (47) and dupli-
cation/deletion of the 15q24 region (48). Recently, the
two-hit model was statistically tested for the 16p12.1 deletion
syndrome in which a 520 kb CNV within 16p12.1 occurs in
combination with another genomic CNV (49). In line with
these findings, we have shown at least 17.2% (this estimation
is conservative since a number of our patients were tested on a
relatively lower-coverage BAC array) of the patients with
recurrent Xp22.31 duplication carry additional large genomic
changes. We assessed whether the additional CNVs by them-
selves are sufficient to cause the abnormal phenotypes by lit-
erature review. In 81.8% (9 of 11) of the cases, the
secondary CNVs alone are not unambiguously pathogenic
(Supplementary Material, Table S3), further supporting the
second-hit model. Consistent with the idea that the Xp22.31
duplication does not cause a strong enough genomic burden
to convey a disease phenotype, our data suggest that the recur-
rent triplications may be more penetrant than the duplications.
Therefore, we suggest that the recurrent Xp22.31 duplication
may predispose an individual to disease; but manifestation of
the disease phenotype requires additional genetic changes,
including modifiers in the genomic background, additional
1984 Human Molecular Genetics, 2011, Vol. 20, No. 10
changes elsewhere in the genome and additional changes at
the Xp22.31 locus (e.g. triplications and other complex
With these considerations, it remains uncertain whether the
recurrent Xp22.31 duplications alone are associated with
abnormal phenotypes. Further clinical study is warranted for
more individuals with the Xp22.31 recurrent or simple nonre-
rearrangements in order to reach conclusions whether these
changes are pathogenic or benign CNVs.
MATERIALS AND METHODS
The MGL has performed CMA testing with aCGH assay on
20 095 samples that were referred for clinical diagnosis from
20 February 2004 to 1 July 2009. A total of 92 (0.46%) unre-
lated subjects (49 females and 43 males) were found to have
Xp22.31 duplications by the clinical CMA array. Among the
92 subjects, 69 anonymized subjects (59 unrelated individuals,
1 set of twins, 2 siblings and 6 parents) were selected ran-
domly for further rearrangement analyses. All studies were
approved by the Institutional Review Board (IRB) of BCM.
Targeted clinical aCGH and custom high-density aCGH
The samples were initially analyzed in the MGL on consecu-
tive versions of CMA arrays (50–55). The criteria for Xp22.31
duplication case identification by aCGH was based on copy
number gain of all or either one or two of the BAC clones
RP11-483M24, GS1-227L7 and RP11-143E20 or by oligonu-
cleotides emulating the genomic interval chrX:6 455 604–
8 109 387 (hg18).
To fine map the duplications identified by the clinical
arrays, we designed two versions of Agilent customized
HD-CGH microarrays interrogating specifically the Xp22.31
region. The two array designs were in either the Agilent 8 ×
15K (#G4427A) or the 8 × 60K (#G4126A) format. Probes
(14 261 in the 8 × 15K format and 24 358 in the 8 × 60K
format) were selected from the Agilent eArray system (https
://earray.chem.agilent.com/earray/), with an average spacing
of 400/250 bp, spanning 4 Mb at Xp22.31 (chrX:5 000 000–
9 000 000) and 1.6 Mb at Yq11.22
16 000 000). The 8 × 60K array contains probes that represent
LCR sequences whereas the 8 × 15K array utilized only
unique sequence oligonucleotides of interrogating probes.
Labeling, hybridization and microarray analyses were per-
formed as previously described (56).
(chrY:14 310 000–
FISH was used to assess the copy numbers in subjects/parents
who have Xp22.31 triplication suggested by aCGH data. Con-
firmatory FISH analyses were performed with BAC clones
using standard procedures. The BAC clones RP11-483M24
at Xp22.31 and RP11-46A23 at Xp21.2 were used as test
and control probes, respectively. Terrific broth media with
20 mg/ml chloramphenicol was used to grow the BAC
clones of interest. DNA was extracted from BAC clones
(Eppendorf Plasmid Mini Prep kit, Hamburg, Germany) and
directly labeled with SpectrumOrangeTM/SpectrumGreenTM
(test/control) dUTP by nick-translation (Vysis, Downer
Grove, IL). A Power Macintosh G3 System using MacProbe
software version 4.4 (Applied Imaging, San Jose, CA, USA)
was used to capture the FISH images.
MLPA was used to assess the copy numbers in subjects/parents
edu/mlpa/cgi-bin/mlpa.cgi). SALSA MLPA reagents were
commercially available from MRC-Holland (Amsterdam, The
Netherlands). The analysis was carried out following the manu-
facturer’s instructions. Ligation products were PCR amplified
and resolved on a 3730xl DNA analyzer (Applied Biosystems,
Foster City, CA, USA). For quantitative analysis, peak heights
using GeneMarker v1.5 software (Softgenetics, State College,
TaqManwcopy number assays (Applied Biosystems) were
used to assess the copy numbers in subjects/parents who
have Xp22.31 triplication suggested by the aCGH data.
Three predesigned primer–probe
TaqMan copy numberreference
Applied Biosystems was used as reference. Experiments
were carried out according to the manufacturer’s protocol.
Four technical replicates were used for each genomic DNA
sample. Reactions were run on the ABI 7900HT fast system.
Results were analyzed by the CopyCallerTMsoftware v1.0
PCR analyses for breakpoint sequences
Breakpoint junctions of nonrecurrent rearrangements were
obtained by long-range PCR with the TAKARA LA TaqTM
kit (RR002M for regular buffer or RR02AG for GC buffer I)
(TAKARA Bio Inc.) as previously described (33). For break-
points of recurrent duplications, we used LCR-specific primers
to amplify the hypothesized crossover interval. A two-step
mismatch PCR strategy was employed to ensure the specificity
and efficiencyof amplification
sequences and particular PCR strategies are available in Sup-
plementary Material, Table S5.
XCI studies were performed based on the protocol described
by Allen et al. (58) with modification as described previously
Human Molecular Genetics, 2011, Vol. 20, No. 101985
Algorithms for identifying the recurrent Xp22.31
duplications in the control population
The primary controls for the study were Illumina genotypes of
6809 subjects obtained from the Database of Genotypes and
Phenotypes (dbGaP, http://www.ncbi.nlm.nih.gov/gap). Our
analysis was confined to unrelated adult individuals of Euro-
phs000001.v2.p1 and phs000142.v1.p1). After allele detection
and genotype calling were performed with Genome Studio
software (Illumina, Inc., San Diego, CA, USA), B allele fre-
quencies (BAFs) and log R ratios were exported as text files
for PennCNV analysis. CNVPartition was run as a plug-in
within the Genome Studio browser with settings: confidence
threshold 50, minimum number of probes 5. Sample-level
quality control analysis was performed using PennCNV soft-
ware. Samples were excluded from further analysis if any of
the following criteria were met: standard deviation of log R
ratios .0.35, BAF drift .0.1, waviness factor .0.05 or
number of CNVs identified .2 standard deviations above
the mean of each dataset. CNVs in pericentromeric and immu-
noglobulin regions were also excluded. A total of 5088 indi-
viduals met these criteria and were included in our analysis.
CNV regions called by both PennCNV and CNVPartition
were identified using the overlap function for rare CNVs in
Supplementary Material is available at HMG online.
her outstanding technical support. The control datasets used for
the analyses described in the manuscript were used with per-
mission and derived from dbGaP through accession numbers
phs000001.v2.p1 and phs000142.v1.p1. The BAC clone
RP11-527B14 was kindly provided by Dr Steven Scherer
from the Human Genome Sequencing Center at Baylor
College of Medicine.
Conflict of Interest statement. J.R.L. is a consultant for Athena
Diagnostics and Ion Torrent Systems, and is a coinventor on
multiple United States and European patents for DNA diag-
nostics. Furthermore, the Department of Molecular and
Human Genetics at BCM derives revenue from molecular
diagnostic testing (MGL).
This work was supported in part by the National Institute of
Neurological Disorders and Stroke (National Institutes of
Health, grant R01NS058529) to J.R.L., Texas Children’s Hos-
pital General Clinical Research Center (grant M01RR00188)
and Intellectual and Developmental Disabilities Research
Centers (grant P30HD024064). A.E. is supported by NIH
5K08DK081735. P.S. is supported in part by grant R13-
0005-04/2008 from the Polish Ministry of Science and
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