Table 1.

Clinical Features of Cases and Cytogenetic Localization of Breakpoints in Cases and Controls

Group	Number	ABa	Code	Cytogenic BPb	Clinical Features
Cases	1	XATc	GILLE	t(X;11)(p22.3;p12)	Superior atypical coloboma, foveal hypoplasia, inferior vermis cerebellum
	2	Recipd	MARTA	t(8;9)(q21;q21)	Peters anomaly
	3	Recip	SG-3301	t(2;17)(q32;q24)pat	Micrognathia,glossoptosis, cleft palate
	4	Recip	ROOJA	45,X,t(5;7)(q21;q33)	Hemolytic anemia, Turner syndrome, prenatal onset short stature Developmental delay?
	5	Recip	MAGAN	t(3;4)(q23;q31)	Severe short stature, hemolytic anemia, recurrent hypoglycemia
	6	Inve	CRENA	inv(4)(q21q35)	Bilateral coloboma, hypotonia
	7	Recip	F92-2253	t(5;11)(q15;p15.5)	Global developmental delay
	8	Recip	T86-0593	t(5;12)(q11.2;q12)	Testicular atrophy
	9	Inv	GILL	inv(12)(p11.2q24.3)	Cleft palate, severe learning disabilities
	10	Recip	B97-1182	t(2;10)(q11.2;q22.3)	Mild learning disability
	11	Recip	B01-2958	t(4;14)(q31.22;q11.2)	Moderate learning difficulties, particular problems with numeracy
	12	Recip	B96-0581	t(2;3)(q21.3;q21.3)	Attention deficit hyperactivity disorder
	13	XAT	F03-0432	t(X;8)(q26.?1;p23.?1)	Abnormal ultrasound
	14	Recip	B01-2957	t(14;18)(q24.1;p11.32)	Learning difficulties: spelling dificulties, on learning support. Height and weight normal
	15	Recip	B99-1983	t(13;18)(q31.1/q22.3;q22.1)	Global developmental delay. dysmorphic features. IUGR, brachydactyly
	16	Recip	B04-0611	t(1;9)(p32.3?;q33.2)	Precocious puberty
	17	Inv	B90748	inv(1)(p36.1q25.3)	Familial MDSf, ALLg
	18	Recip	CMS5859	t(3;7)(q28;p21.3) by FISH	Anophthalmia with AEGh
	19	Recip	B04-0880	t(2;3)(/q32.2/q33;q26.3/q27)	Autistic spectrum disorder, severe learning disability, Piere Robin sequence
	20	Recip	T86-0404	t(2;6)(p23;q14)	Sirenomelia
	21	Recip	CV1012	t(5;17)(q15;q23)pat	Pierre Robin sequence
	22	Recip	NCL-B04-2316	t(3;6)(q23;p21.1)	Complex congenital heart disease, asplenia, malrotation
	23	Recip	COLJA	t(11;13)(p15.3;q22)	Cleft palate, prominent ears, small chin, tapering fingers
	24	Recip	B00213	t(2;7)(q33;p21)	Cleft palate, mild learning disability
	25	Recip	BB45	t(2;11)(q32;p14)	Cleft palate, mild learning disability
	26	XAT	BL02-1299	t(X;10)(q22.3;q24.3)	AVSDi, hypopituitary, posterior embryotoxin, myopia, dislocated hips
	27	XAT	BL02-0828	t(X;11)(q21.2;q13.5)	Premature menopause
	28	Recip	F0124/00	t(2;16)(p15;q22)	Low birth weight, hypotonia, learning difficulties, pulmonary hypertension, delayed visual maturation
	29	Recip	BL02-3104	t(9;22)(q34.2;q11.21)	Learning difficulties, mild bilateral hearing loss
	30	Recip	AC114	t(10;11)(q24;p13)	Ventricular septal defect, cleft palate, XY sex reversal, hydronephrosis
	31	Recip	BL03-1791	t(7;8)(q32.2;q22)	Marfanoid habitus, learning difficulty
	32	Recip	CV345	t(6;9)(p23;q22.3)	Cleft lip and palate, other dysmorphism
	33	Inv	BL02-2567	inv(1)(q32.1q44)	Agenesis of the corpus callosum, Dandy Walker, dysmorphisms
	34	Recip	BL03-0967	t(9;20)(p13.1;p13)	Cataracts, microcephaly
	35	Recip	BL03-1789	t(5;9)(p13.1;q22.1)	Spastic paraparesis
	36	Recip	BL03-2425	t(11;13)(p15;q32)	Infantile seizures, myopia, ptosis
	37	Recip	CV1222	t(1;7)(q21.3;q34)	Learning disability, celiac disease
	38	Recip	BL04-0107	t(5;6)(q13;q23)	Non specific dysmorphism, small hands,bilateral hernias, tremor, delayed puberty
	39	Recip	BL03-3077	t(1;20)(q32.1;q13.3)	Non-specific dysmorphism, slim hands and feet, high arched palate, clinodactyly
	40	Recip	CV1456	t(1;2)(q24.2;q31.3)	Mowat-Wilson syndrome
	41	Recip	BL04-2026	t(5;6)(q15;q25.1)	Severe mental handicap
	42	Recip	BL04-2240	t(9;15)(q21.2;q26)	Abnormal baby, mild dysmorphism, developmental delay
	43	XAT	BL04-3772	t(X;4)(p11.4;p16)	Primary ammenorhea
	44	Recip	BL04-1899	t(6;16)(q15;q13)	Renal cancer, brother also has translocation and rare cancer
	45	Recip	BL05-0692	t(1;13)(q44;q32)	Agenesis of the corpus callosum
	46	Recip	BL03-2183	t(5;14)(q15;q24)	Primary amenorrhoea
Controls	1	Recip	B98-0026	t(1;15)(q24.3;q22.3)	N/A
	2	Recip	F00-1558	t(15;16)(q22.3;q22.1)	N/A
	3	Recip	B97-0349	t(3;11)(p13;q12.2)	N/A
	4	Recip	B04-0088	t(3;9)(p26;p22)	N/A
	5	Recip	F96-1781	t(5;6)(q31.3;p21.3)	N/A
	6	Inv	SISCO	inv(1)(p31q43)	N/A
	7	Recip	PETEN	t(7;12)(q32;p13)	N/A
	8	Recip	EDINN	t(1;14)(q42;q11)	N/A
	9	Recip	JOGAR	t(X;14)(p11.21;q32.2/32.3)	N/A
	10	Recip	B01-2804	t(4;12)(p16.1;q24.31)	N/A
	11	Recip	BL03-0187	t(2;8)(p15;q13)	N/A
	12	Recip	BL03-0186	t(1;7)(p32;q34)	N/A
	13	Recip	BL03-0185	t(2;4)(q37.1;p15.32)	N/A
	14	Recip	BL03-0362	t(2;5)(q31;q33.3)	N/A
	15	Recip	BL03-0356	t(3;12)(q27;p13)	N/A
	16	Recip	BL03-0426	t(4;11)(q31;p13)	N/A
	17	Recip	BL03-1970	t(6;15)(q23.1;q21.2)	N/A
	18	Recip	BL03-1979	t(6;14)(q32;q32.1)	N/A
	19	Recip	F0440	t(8;15)(q22;q22.1)	N/A
	20	Recip	BL03-0876	t(1;11)(q42.1;p15.5)	N/A
	21	Recip	BL03-3032	t(5;18)(p15.1;p11.32)	N/A
	22	Recip	BL04-0339	t(5;6)(q11.2;q23.1)	N/A
	23	Inv	BL03-2725	inv(14)(q22.1q32.1)	N/A
	24	Recip	BL04-2024	t(5;7)(p15.1;q31.2)	N/A
	25	Recip	BL04-2025	t(3;6)(q25;q15)	N/A
	26	Recip	CV1510	t(6;14)(p23;q13)	N/A
	27	Recip	BL04-3994	t(3;9)(p25;q13)	N/A
	28	Recip	BL04-4270	t(6;8)(q25;q12)	N/A
	29	Recip	BL05-0379	t(5;9)(p14;p13.1)	N/A
	30	Recip	BL03-2435	t(6;12)(q21;q24.1)	N/A

The breakpoints shown in this table are those reported by the referring clinical cytogenics laboratories. For consistency, these breakpoints are used throughout the text. The FISH-mapped breakpoints and the flanking or breakpoint-spanning clone identifiers are available online in Tables S1 and S2, respectively.

^a“AB” denotes “aberration category.”

^b“BP” denotes “breakpoint.”

^c“XAT” denotes “X-autosome translocation.”

^d“Recip” denotes “reciprocal translocation.”

^e“Inv” denotes “inversion.”

^f“MDS” denotes “myelodysplastic syndrome.”

^g“ALL” denotes “acute lymphoblastoid leukemia.”

^h“AEG” denotes “anophthalmia.”

ⁱ“AVSD” denotes “atrioventricular septal defect.”