Chromosome Rearrangements in Cornelia de Lange Syndrome (CdLS): Report of a der(3)t(3;12)(p25.3;p13.3) in Two Half Sibs With Features of CdLS and Review of Reported CdLS Cases With Chromosome Rearrangements

Abstract

Cornelia de Lange syndrome (CdLS; OMIM 122470) is a dominantly inherited disorder characterized by multisystem involvement, cognitive delay, limb defects, and characteristic facial features. Recently, mutations in NIPBL have been found in ~50% of individuals with CdLS. Numerous chromosomal rearrangements have been reported in individuals with CdLS. These rearrangements may be causative of a CdLS phenotype, result in a phenocopy, or be unrelated to the observed phenotype. We describe two half siblings with a der(3)t(3;12)(p25.3;p13.3) chromosomal rearrangement, clinical features resembling CdLS, and phenotypic overlap with the del(3)(p25) phenotype. Region-specific BAC probes were used to fine-map the breakpoint region by fluorescence in situ hybridization (FISH). FISH analysis places the chromosome 3 breakpoint distal to RP11-115G3 on 3p25.3; the chromosome 12 breakpoint is distal to BAC RP11-88D16 on 12p13.3. A review of published cases of terminal 3p deletions and terminal 12p duplications indicates that the findings in these siblings are consistent with the del(3)(p25) phenotype. Given the phenotypic overlap with CdLS, we have reviewed the reported cases of chromosomal rearrangements involved in CdLS to better elucidate other potential loci that could harbor additional CdLS genes. Additionally, to identify chromosome rearrangements, genome-wide array comparative genomic hybridization (CGH) was performed on eight individuals with typical CdLS and without identifiable deletion or mutation of NIPBL. No pathologic rearrangements were identified.

INTRODUCTION

Cornelia de Lange syndrome (CdLS), a dominantly inherited disorder, is characterized by facial dysmorphism, limb abnormalities, somatic and cognitive retardation, and growth abnormalities. Recently, mutations in the NIPBL gene, on chromosome 5p13, were shown to cause CdLS [Krantz et al., 2004; Tonkin et al., 2004]. Mutations in NIPBL are currently detected in ~50% of CdLS cases [Gillis et al., 2004]. The remaining cases may be explained by as yet undetected mutations in NIPBL or there may be other genes involved. There have been more than 30 reports describing chromosomal abnormalities, involving chromosomes 1–5, 7–14, 17, 18, 21, and X, associated with the CdLS phenotype (Table I). We report two half siblings with clinical features suggestive of CdLS and an unbalanced chromosomal rearrangement (der(3)t(3;12)(p25.3;p13.3)) inherited from a balanced translocation (t(3;12)(p25.3;p13.3)) in an unaffected mother. While these children have many features consistent with CdLS (microcephaly, growth retardation, mental retardation, hirsutism, synophrys, anteverted nares, single palmar creases, 2–3 syndactyly of the toes), they also have features seen in other children with terminal 3p deletions. A review of all reported cases of CdLS with chromosomal rearrangements has been undertaken to determine genomic regions, other than 5p, which may harbor potential candidates for additional CdLS genes.

TABLE I.

Chromosome Rearrangements in Individuals With CdLS

Chromosome	Karyotype	Reference
1	46,XX,del(1)(q44)	Borck et al. [2004]
	See chromosome 5
2	46,XY,t(2;12)de novo	Craig and Luzzatti [1965]*
3	46,XY,der(3)(3;12)(p25.3;p13.3)mat	This report
	46,XY,r(3)de novo	Lakshminarayana and Nallasivam [1990]*
	46,XX,t(3;17)(q26.3;q23.1)de novo	Ireland et al. [1991]
	46,XX,ins(10;3)(q21.2;q25.1q26.2)	Holder et al. [1994]
	46,XY,?del(3q)	Szemere et al. [1972]
	46,XX,dup(3q)mat	Centerwall et al. [1977]
	46,XX,dup(3)(q23q27)	Sciorra et al. [1979]
	inv dup(3)(q29q25)a	Wilson et al. [1978]
	dup(3)(q25q29)b	Wilson et al. [1978]
4	46,XX,der(9)t(4;9)mat	Hersh et al. [1985]*
	46,XY,t(4;11)[6]/46,XY[3]de novoc	Payne and Maeda [1965]*
5	46,XY,t(5;12)/46,Xyde novod	Geudeke et al. [1963]*
	46,XX,der(5)t(5;9;13)(q23;p24;q22)mat	Eeg-Olofsson and Liedgren [1981]*
	46,XX,der(5)t(1;5)(q41;q35)	Telvi et al. [1999]
	46,XX,del(5)(p13)de novo	Taylor and Josifek [1981]
	46,XX,t(5;13)(p13.2;q12.1)de novo	Krantz et al. [2004]; Tonkin et al. [2004]
	46,XY,del(5)(p13.1p14.2)de novo	Hulinsky et al. [2003]
7	46,XY,der(7)t(7;10)(q32:q24)pat	Randall-Pinto et al. [2000]
8	46,XX,t(8;?)de novo	D’Oelsnitz et al. [1971]*
9	46,XX,r(9)de novo	Motl and Opitz [1971]*
	46,XY,9qh + pat	Berg et al. [1967]*
	46,XY,9qh + qh + patmate	Babu et al. [1985]*
	See chromosomes 4 and 5
10	See chromosome 7
11	46,XY,del(11q)[3]/46,XY[14]de novoc	Payne and Maeda [1965]*
	See chromosome 4
12	See chromosomes 2,3, and 5
13	46,XY,t(13q;14q)matf	Beck and Mikkelsen [1981]*
	See chromosome 5
14	46,XX,t(14;21)(q32;q11.2)de novog	Wilson et al. [1983]*
17	46,XY,?del(17q)de novo	Gans and Thurston [1965]*
	See chromosome 3
18	47,XX, + i(18)(p10)	Borck et al. [2004]
21	See chromosome 14
X	45,X/46,XYde novo	Calo et al. [1968]*; Beck and Mikkelsen [1981]*
	45,X/46,XXde novo	Klosowski et al. [1968]*
D group	45,XY,t(Dq;Dq)mat	Ott et al. [1968]*
	46,XX,del(Dq)/46,XXde novo	Westermann et al. [1977]*
G group	46,XY,Gp + de novo	Hooft et al. [1965]
Unknown marker	Nine different reports	Reviewed by Kousseff et al. [1994]

^*Reviewed by Kousseff et al. [1994].

^aTwo separate cases reported.

^bThree separate cases reported.

^cLeukocytes.

^dAbnormality in 2/3 leukocytes and 4/5 fibroblasts.

^eThis child is homozygous for a recurring inversion considered to be a normal variant, inv(9).

^fPhenotypically normal mother and maternal grandmother both carried the same translocation.

^gNIPBL S1459X [Gillis et al., 2004].

CLINICAL REPORT

Patient 1

Patient 1 (Fig. 1) is an 8-year, 8-month-old male born at 36 weeks gestation by Cesarean section due to breech presentation. His birth weight was 2.63 kg (50–75th centile). Apgar scores were 9 at both 1 and 5 min. Pregnancy was complicated by premature labor at ~33 weeks. There was no exposure to medications, cigarettes, alcohol, or illicit drugs.

Fig. 1.

Photographs of Patient 1 (proband) and Patient 2 (half sister of the proband). [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Clinical findings included gastroesophageal reflux, poor weight gain, multiple anomalies, mild to moderate bilateral sensorineural hearing loss, and developmental delay (noted at 6 months). He sat at 2 years, stood alone and cruised at 33 months, and walked by 4 years. He had one word at 34 months; however, at the time of the exam, there were no words. There is a history of self-injurious behavior.

Physical Examination

At 8 years 8 months of age, his height was 118 cm (<5th centile; 50th for 6 years 6 months) and head circumference was 50 cm (<3rd centile; 50th for 2 years 5 months). Dysmorphic features included arched eyebrows with synophrys, long eyelashes, broad nasal bridge, high arched palate with widely spaced teeth, bilateral preauricular ear pits, shawl scrotum, proximally placed thumbs, and clinodactyly of the fifth fingers (Table II). Palm length was 8.25 cm (25–50th centile). Middle finger length was 5.25 cm (<3rd centile, 50th for 5 years). Foot length was 18 cm (<3rd centile; 50th for 6 years); no syndactyly was present.

TABLE II.

Clinical Findings in Individuals With Deletions of 3p25

	del(3)(p25pter) and smaller	del(3) (3p25pter)	del(3)(p25.3pter)	del(3)(p25.3p26.2)	del(3)(p25.3pter)
	Kariya et al. [2000]	Benini et al. [1999]	Angeloni et al. [1999]	Cargile et al. [2002]	This report	This report
Sex (male/female)	17/18	Male	Male	Male	Male	Female
Low birth weight	20 (57%)	Yes	No	No	Yes	Yes
Growth retardation	26 (74%)	Yes	Yes	Yes	Yes	Yes
Psychomotor retardation	25/26 (96%)a	Yes	Yes	Yes	Yes	Yes
Short neck	7 (20%)	No	NR	NR	No	No
Epilepsy	9 (25%)	Yes	NR	NR	No	No
Hands/feet
Syndactyly	2 (0.05%)	NR	No	NR	No	Yes
Clinodactyly	9 (25%)	Yes	No	NR	Yes	Yes
Polydactyly	12 (34%)	No	No	NR	No	No
Abnormal dermatoglyphics	9 (25%)	NR	No	NR	No	No
Rocker bottom feet	3 (0.08%)	No	NR	NR	No	No
Prominent heels	3 (0.08%)	NR	NR	NR	No	No
Sacral skin dimple	10 (28%)	Yes	NR	Yes	No	Yes
Hypotonia	13 (37%)	Yes	Yes	Yes	No	No
Hypertonia	5 (14%)	NR	NR	NR	No	No
Hernia	7 (20%)	Yes	No	NR	No	No
Abnormal internipple distance	5 (14%)	No	NR	NR	No	No
Congenital heart disease	11 (31%)	No	NR	No	No	murmur
Urinary tract anomalies	10 (28%)	Yes	NR	NR	No	No
GI tract anomalies	6 (17%)	NR	No	Yes	Yes	No
Cryptorchism	6/17 (35%)	No	NR	NR	No	No
Anomalies of external genitalis	6 (17%)	Yes	Yes	NR	Yes	No
Hearing loss	8 (22%)	No	Yes	NR	Yes	No
Brain anomalies	5 (14%)	Yes	NR	NR	No	No
Craniofacial
Asymmetric skull	2 (0.05%)	No	NR	NR	No	No
Triangular face	9 (25%)	No	NR	NR	No	No
Microcephaly	15 (43%)	Yes	No	Yes	Yes	Yes
Dolichocephaly	3 (0.08%)	No	NR	NR	No	No
Flat occiput	9 (25%)	Yes	NR	NR	No	No
Epicanthal fold	15 (43%)	Yes	NR	Yes	No	No
Hypertelorism/telecanthus	18 (51%)	No	Yes	Yes	No	No
Short palpebral fissure	9 (25%)	NR	NR	NR	No	No
Blepharoptosis	28 (80%)	Yes	NR	Yes	No	No
Synophrys	11 (31%)	No	NR	NR	Yes	Yes
Abnormal nose	25 (71%)	Yes	No	Yes	Yes	Yes
Long philtrum	25 (71%)	Yes	No	Yes	Yes	Yes
Thin lip	10 (28%)	Yes	NR	Yes	No	Yes
Downturned mouth	11 (31%)	No	NR	NR	No	Yes
High arched palate	13 (37%)	Yes	Yes	NR	Yes	Yes
Cleft palate	1 (0.03%)	NR	No	NR	No	No
Micrognathia	21 (60%)	Yes	NR	Yes	No	No
Retrognathia	6 (17%)	NR	NR	NR	No	No
Preauricular pit(s)	9 (25%)	No	NR	NR	Yes	No
Low set ear	21 (60%)	Yes	NR	Yes	No	No
Other ear malformation	21 (60%)	No	Yes	Yes	No	Yes
Low hair line	11 (31%)	No	No	NR	No	No

NR, not reported.

^aThis assessment was possible in 26/35 individuals: in five cases, the child died in the first few months of life; one case was a newborn; in three cases, information was not available.

Patient 2

Patient 2 (Fig. 1), the half sibling (through the mother) of Patient 1, is a 7-year-old female born at term to a 21-year-old mother and a 24-year-old father. She was delivered by Cesarean section due to breech presentation. Her birth weight was 2.09 kg (<10th centile for 40 weeks gestational age; 50th for 34 weeks).

She has had a history of chronic ear infections requiring bilateral myringotomy tubes, strabismus, reflux with nasal regurgitation, urinary tract infection, and a heart murmur. She sat at 1 year, walked at 2.5 years, and had approximately 10 words at 7 years.

Physical Examination

At 7 years of age, height was 100 cm (<5th centile; 50th for 4 years). Head circumference was 44.5 cm (<3rd centile, 50th for 9 months). Dysmorphic features included synophrys, arched eyebrows, long eyelashes, depressed nasal bridge with anteverted nares, thin upper lip with down-turned corners of the mouth, high arched palate, low set ears with left perauricular skin tag, small hands with proximally-placed thumbs, and short fifth fingers (Table II). Palm length was 6.5 cm (<3rd centile; 50th for 3 years). Middle finger length was 4.5 cm (<3rd centile; 50th for 2.5 years). She had a single palmer crease on the right, 2–3 syndactyly of the toes (foot length, 15.5 cm <3rd centile; 50th for 3.5 years), and a deep sacral dimple.

Family History

Patients 1 and 2 are half siblings through their mother. Their mother has asthma and slight arthritis of the hands. She has two sisters, one of whom has a healthy son. The father of Patient 1 was healthy; he is adopted. There is no other family history of birth defects, repeated miscarriages, or mental retardation. The father of Patient 2 was treated with Ritalin for 2 years (in 5th and 6th grades) for attention deficit-hyperactivity disorder (ADHD). During this time, he was in special education classes; he subsequently returned to regular classes and completed school without difficulty.

MATERIALS AND METHODS

Human Subjects

All individuals studied were enrolled under an IRB-approved protocol of informed consent.

Cytogenetic Analysis

Chromosomal analysis was performed on peripheral blood lymphocytes. Metaphase spreads were prepared from peripheral blood culture and G-banded for karyotyping (550 band level resolution) (Fig. 2A,B), or probed with selected BACs (Fig. 2C–H) and commercial fluorescence in situ hybridization (FISH) probes (Vysis, Inc., Downers Grove, IL) using standard protocols.

Fig. 2.

G-banded partial karyotypes (A, B) and FISH analysis (C–H) of Patients 1 and 2 and their mother. BAC probes (Green) and commercial probes (Red) show that in Patients 1 and 2, the chromosome 3p breakpoint is between RP11-115G3 (C), proximally and RP11-128A5 (D), distally; the chromosome 12p breakpoint is between RP11-88D16 (F), proximally and RP11-79K20 (G), distally. Patients 1 and 2 are monosomic for RP11-128A5 (D) on 3p25.3 and trisomic for RP11-79K20 (G) on 12p13.33. Their mother carries a t(3;12)(p25.3;p13.33) balanced translocation; RP11-128A5 has been translocated to 12p (E) and RP11-79K20 has been translocated to 3p (H).

Five BAC clones (RP11-128A5, RP11-115G3, RP11-625C9, RP11-271E2, RP11-90I9, distal to proximal) were chosen to span ~10 Mb of 3p24.3-p25.3. Six BAC clones (RP11-88D16, RP11-91B13, RP11-451M6, RP11-277E18, RP11-434C1, and RP11-79K20, distal to proximal) were chosen to span ~10 Mb of 12p13.2-p13.33. The map position of each BAC clone was determined according to the UCSC Human Genome Project (July 2003 assembly) (http://genome.cse.ucsc.edu). All BAC clones were obtained through CHORI BACPAC Resources (Oakland, CA). BAC DNA was isolated (Perfect Prep Plasmid XL, Eppendorf, Hamburg, Germany) and labeled by nick translation (Nick Translation Reagent Kit, Vysis, Inc.) in the presence of Spectrum Green dUTP (Vysis, Inc.). Commercial FISH probes (Vysis, Inc.) for 12q telomere (TelVysion12q) and centromeres 3 (CEP3/D3Z1) and 12 (CEP12/D12Z3) were used. FISH probes were hybridized to metaphase preparations overnight; slides were then washed and counterstained with DAPI using standard protocols.

Array Comparative Genomic Hybridization

DNA was extracted from lymphocytes (Puregene^™ DNA Isolation Kit, Gentra Systems, Minneapolis, MN), labeled by nick translation (BioPrime DNA Labeling System, Invitrogen, Carlsbad, CA) with Cy3-dCTP or Cy5-dCTP (Amersham Biosciences), and purified through a Sephadex G-50 column. Purified probe and Human Cot-1 DNA (Invitrogen) were dissolved in hybridization mixture (dextran sulfate, formamide, and SSC, as described, http://cc.ucsf.edu/microarray/), denatured (99C), and allowed to reanneal (37C, 2 hr) to block repetitive probe sequence. The microarray contains 2,464 BAC and P1 clones, printed in triplicate, which span the genome with an average resolution of ~1.4 Mb [Snijders et al., 2001]. Microarray slides were UV-crosslinked, prehybridized with hybridization mixture, hybridized (37C, ~68 hr), and subjected to post-hybridization washes as described (http://cc.ucsf.edu/microarray/). Slides were stained with DAPI and imaged with a CCD Imager. Analysis was performed with UCSF SPOT software [Jain et al., 2002].

RESULTS

Cytogenetic Testing

Both children presented here (Patients 1 and 2) were found to have the same chromosomal abnormality. These individuals are partially monosomic for 3p and partially trisomic for 12p. The karyotype of Patient 1 is 46,XY,der(3)(3;12)(p25.3;p13.33); the karyotype of Patient 2 is 46,XX,der(3)(3;12)(p25.3;p13.33) (partial karyotype, Fig. 2A). Analysis of G-banded chromosomes from the mother of Patients 1 and 2 showed a balanced translocation involving chromosomes 3 and 12; her karyotype was 46,XX,t(3:12)(p25.3;p13.3) (partial karyotype, Fig. 2B) with no apparent phenotypic consequence.

Using region-specific BACs as FISH probes, we have refined the location of the chromosome 3 and 12 breakpoints. The chromosome 3 breakpoint has been mapped to within a ~2 Mb region of 3p25.3, defined by RP11-115G3 (proximally) (Fig. 2C) and RP11-128A5 (distally) (Fig. 2D). Patients 1 and 2 are monosomic for BAC RP11-128A5 (Fig. 2D); in the mother of these children, this BAC is translocated to 12p (Fig. 2E). The chromosome 12 breakpoint has been mapped to within a ~2.4 Mb region of 12p13.3, defined by RP11-88D16 (proximally) (Fig. 2F) and RP11-79K20 (distally) (Fig. 2G). Patients 1 and 2 are trisomic for BAC RP11-79K20 (Fig. 2G); in the mother of these children, this BAC is translocated to 3p (Fig. 2H). These data localize the chromosome 3 breakpoint distal to RP11-115G3 and the chromosome 12 breakpoint distal to RP11-88D16. These children (Patients 1 and 2) are, therefore, deleted for ~10 Mb of terminal chromosome 3p and duplicated for ~ 3 Mb of terminal chromosome 12p.

Clinical Features

The clinical features of these two children with der(3)(3;12)(p25.5;p13.3) are compared with other cases of monosomy 3p25 (Table II) and trisomy 12p13 (Table III). The two children presented here have clinical features consistent with CdLS but also have significant clinical overlap with del(3)(p25) syndrome.

TABLE III.

Clinical Findings in Individuals With Terminal Duplications of 12p13

	dup(12) (p13.1pter)	dup(12) (p13.3p13.1)mosa	dup(12) (p13.33p13.1)mosb	dup(12) (p13.2pter)	dup(12) (p13.33pter)
	Zelante et al. [1994]	Leana-Cox et al. [1993]	Rauch et al. [1996]		This report	This report
Sex	Female	Male	Female	Female	Male	Female
Birth weight (kg)	3.85 (75–90th)	NR	4.51 (50th, 6 w)	3.1 (50–75th)	2.63 (50–75th)	2.27 (<10th)
Age at report	7 y	NR	4 y	9 m	8 y 8 m	7 y
Weight (kg)	97th	NR	50th	97th	<5th	<5th
Length/height (cm)	75th	NR	50th	97th	<5th	<5th
OPC (cm)	>90th	NR	<50th	<3rd	<5th	<5th
Phychomotor retardation	Yes	NR	Yes (language)	Yes	Yes	Yes
Short neck	NR	NR	Yes	Yes	No	No
Hypotonia	NR	Yes	No	hyper	No	No
Clinodactyly	5th	NR	No	No	Yes	Yes
Craniofacial
Round face/promenent cheeks	Yes	NR	Yes	Yes	No	No
Epicanthal fold	NR	NR	Yes	Yes	No	No
Large philtrum	Yes	NR	Yes	Yes	Yes	Yes
Thin upper vermilion	NR	NR	Yes	No	Yes	Yes
Broad everted lower lip	Yes	NR	Yes	Yes	No	No
Broad nasal bridge	Prominent	NR	Yes	Yes	Yes	Yes
Short nose	Yes	NR	Yes	Yes	Yes	Yes
Anteverted nostrils	Yes	NR	Yes	Yes	Yes	Yes
Ear anomalies	Yes	Yes	No	Yes	Yes	Yes

mos, mosaic; NR, not reported; w, week; m, month; y, year.

^a60%, lymphocyte.

^b10%, lymphocyte.

Array Comparative Genomic Hybridization

Array comparative genomic hybridization (CGH) has been performed on eight (seven sporadic cases and one familial) individuals with typical CdLS in whom NIPBL mutations (by CSGE and/or direct sequencing) were not identified. Five of these eight children were screened (by FISH with a NIPBL-containing BAC probe, RP11-14I21) for a NIPBL deletion; no deletions were detected. Three of these five children had standard G-banded chromosome analysis performed; all three were normal. No pathologic rearrangements were identified by array CGH. In one individual (with normal G-banded chromosomes), a duplication of two overlapping BAC clones (RP11-287P18 and RP11-122N11) on 8p23.1 was identified; since these clones contain segmental duplications and have been shown to be polymorphic, this is likely not a disease-associated change.

DISCUSSION

Approximately two-dozen reports of children with CdLS and chromosomal abnormalities have been published (Table I).

Chromosomal rearrangements have proven valuable in mapping genes implicated in many genetic disorders. Recently, a chromosomal rearrangement involving 5p13 was helpful in identifying NIPBL as a CdLS disease gene [Krantz et al., 2004; Tonkin et al., 2004]. Interestingly, a report by Taylor and Josifek described a child with “multiple congenital anomalies, thymic dysplasia, severe congenital heart defects, and oligosyndactyly” and a 5p deletion; in retrospect, it is clear that this child has CdLS [Taylor and Josifek, 1981]. To date ~50% of individuals with CdLS are found to have a mutation in NIPBL [Gillis et al., 2004]. It is unclear if this is due to suboptimal detection of mutations or if other CdLS genes exist.

In order to evaluate other possible loci, we present two siblings, each with clinical features suggestive of CdLS and an unbalanced t(3;12) chromosomal rearrangement; we used this case as a catalyst to review the literature for other reports of suspected CdLS-associated chromosomal abnormalities (Table I).

The two half siblings reported here (Patients 1 and 2) have the same unbalanced chromosomal rearrangement (der(3)t(3;12)(p25.3;p13.3)mat) inherited from a balanced rearrangement (t(3;12)(p25.3;p13.3)) in their mother. FISH analysis, utilizing region-specific BACs as probes, indicates that the siblings have a deletion of the terminal ~10 Mb of chromosome 3p and a duplication of the terminal ~3 Mb of chromosome 12p (Fig. 2).

The published case with the most similar chromosomal rearrangement is that of a male with der(3)(3;12)(p26.3;p13.1)-mat [Suzumori et al., 1998]. This patient was born at 37 weeks gestation, weighed 2.5 kg (25–50th centile), and had “multiple congenital malformations, including left syndactyly, cryptorchism, and mental retardation.” Although this clinical information is limited, this phenotype is consistent with that of others with chromosome 3p deletions (Table II).

Prior to the identification of a chromosomal rearrangement in these siblings, a diagnosis of CdLS was a major consideration. Many of the features seen in these children are consistent with a diagnosis of CdLS (prenatal onset growth failure, microcephaly, developmental delays, synophrys, facial features (particularly in the female sibling), small hands, and feet). Many of these features are also seen in individuals with chromosome 3p deletions (Table II), including the growth delays, microcephaly, and many of the facial characteristics. The half siblings reported here have few features similar to individuals with duplication of distal 12p (Table III); their features are more consistent with those seen in individuals with 3p deletions. There is significant phenotypic overlap between individuals with chromosome 3p deletion and CdLS; however, given the lack of linkage to this region, this may represent a phenocopy that is etiologically unrelated to CdLS.

There have been many reports of individuals carrying a clinical diagnosis of CdLS who also have a chromosomal abnormality (Table I). While there are multiple chromosomal loci implicated in these reported cases, there are very few consistently involved regions. It is often difficult to determine if the chromosome abnormalities are causative of the CdLS phenotype or co-incidental events. In cases in which the chromosome abnormality has a well-described associated phenotype (e.g., 45,X/46,XX or 45,X/46,XY), the CdLS phenotype is likely unrelated to the chromosome abnormality. Another such example is the case of an individual with a 46,XY,t(13q;14q) karyotype that was also found in the mother and maternal grandmother, both of whom were phenotypically normal [Beck and Mikkelsen, 1981]. In other cases, the phenotype associated with the abnormality has not been well described or may simply have features that overlap with CdLS.

Associated but unrelated chromosomal abnormalities may be identified in individuals with CdLS as most individuals with this diagnosis have standard G-banded chromosome analysis performed. Balanced translocations have a prevalence of 1/500 in the general population [Van Dyke et al., 1983; Hook et al., 1984]; therefore, many balanced rearrangements in CdLS may be coincidental events. One such case is that of a child with a de novo balanced 14;21 translocation (karyotype, 46,XX,t(14;21)(q32;q11.2)) in whom a NIPBL mutation (S1459) was identified; this translocation was not related to the CdLS phenotype [Gillis et al., 2004]. Similarly, a de novo, balanced 3;17 translocation [Ireland et al., 1991] has been extensively studied [Tonkin et al., 2001] with no clear identification of a causative gene disrupted at the breakpoint. Conversely, however, in two cases with deletions in 5p13 [Taylor and Josifek, 1981; Hulinsky et al., 2003] (Table I), the chromosome abnormality is directly responsible for causing the CdLS phenotype in these individuals. One child, with a balanced de novo translocation involving 5p13, was particularly helpful in identifying NIPBL as the causative gene (Table I) [Krantz et al., 2004; Tonkin et al., 2004]. Additionally, an evaluation by array CGH (~1Mb genome-wide resolution) on a limited cohort of eight NIPBL mutation negative CdLS probands failed to identify any pathologic chromosome abnormalities. From this high-resolution chromosome evaluation (by array CGH) of a limited number of individuals with CdLS, we suggest that if a disease-associated chromosomal abnormality exists, it is not present in the majority of individuals. The importance of chromosomal rearrangements to disease gene identification is clear; however, it can at times be a confounder. It is important to carefully phenotype individuals with chromosomal rearrangements and assign diagnoses (such as CdLS) cautiously.