Systematic identification of phenotypically enriched loci using a patient network of genomic disorders

Reyes-Palomares, Armando; Bueno, Aníbal; Rodríguez-López, Rocío; Medina, Miguel Ángel; Sánchez-Jiménez, Francisca; Corpas, Manuel; Ranea, Juan A. G.

doi:10.1186/s12864-016-2569-6

BMC Genomics

Table 4 The novel pathogenic phenotypically enriched locus

From: Systematic identification of phenotypically enriched loci using a patient network of genomic disorders

PEL ID	Type*	Chr	Start	Length (Kb)	Phenotype	Cases/Carrier (DGV)	P value^a	P ^b
PEL 3	d	3	181296306	175.931	Anophthalmia	6/9 (0)	1.80E-15	100
PEL 5	d	7	95693340	89.973	Ectrodactyly	7/10 (0)	1.70E-14	100
PEL 4	d	3	181296306	175.931	Abnormality of globe size	8/9 (0)	1.90E-14	100
PEL 4	d	3	181296306	175.931	Aplasia/Hypoplasia affecting the eye	8/9 (0)	1.90E-13	100
PEL 71	d	2	200208169	38.268	Abnormality of the palate	11/19 (0)	2.10E-11	100
PEL 31	d	3	181166306	576	Abnormality of globe size	6/9 (0)	4.10E-11	100
PEL 105	d	2	200208169	38.268	Abnormality of the oral cavity	12/19 (0)	2.50E-10	100
PEL 84	d	15	100019051	189.992	Growth delay	13/18 (0)	2.70E-10	100
PEL 31	d	3	181166306	576	Aplasia/Hypoplasia affecting the eye	6/9 (0)	2.70E-10	100
PEL 128	d	2	200208169	38.268	Abnormality of the mouth	14/19 (0)	1.90E-09	100
PEL 131	d	15	100019051	189.992	Growth abnormality	14/18 (0)	6.40E-09	100
PEL 129	d	15	99057570	65.959	Growth delay	11/16 (0)	8.10E-09	100
PEL 69	d	11	31735689	39.768	Aplasia/Hypoplasia affecting the eye	5/8 (0)	1.00E-08	100
PEL 126	d	2	166091754	49.616	Seizures	10/15 (0)	1.00E-08	100
PEL 175	d	7	112349829	160.71	Delayed speech and language development	12/18 (0)	1.00E-08	100
PEL 78	d	14	29904720	411.94	Aplasia/Hypoplasia of the cerebrum	10/12 (0)	1.50E-08	100
PEL 82	d	14	29904720	411.94	Aplasia/Hypoplasia of the cerebrum	10/12 (0)	1.50E-08	100
PEL 141	d	7	114297499	533.997	Delayed speech and language development	11/15 (0)	4.50E-08	100
PEL 166	d	2	166244769	311.476	Seizures	9/14 (0)	6.00E-08	100
PEL 202	d	15	99057570	65.959	Growth abnormality	12/16 (0)	8.80E-08	100
PEL 152	d	14	29904720	411.94	Microcephaly	8/12 (0)	1.60E-07	100
PEL 159	d	14	29904720	411.94	Microcephaly	8/12 (0)	1.60E-07	100
PEL 216	d	2	200208169	38.268	Abnormality of the palate	7/13 (0)	1.60E-07	100
PEL 385	d	2	200246437	0	Abnormality of the face	16/19 (0)	1.60E-07	100
PEL 137	d	6	76509712	359.49	Joint laxity	5/9 (0)	1.60E-07	100
PEL 390	d	7	112349829	160.71	Neurodevelopmental delay	13/18 (0)	1.60E-07	100
PEL 412	d	13	92065689	29.285	Growth delay	9/17 (0)	2.00E-07	100
PEL 419	d	13	92065689	29.285	Growth delay	9/17 (0)	2.00E-07	100
PEL 436	D	16	3831263	32.469	Abnormality of the face	15/18 (0)	4.20E-07	100
PEL 222	d	2	201936560	57.623	Abnormality of the mouth	10/13 (0)	4.80E-07	100
PEL 222	d	2	200208169	38.268	Abnormality of the mouth	10/13 (0)	4.80E-07	100
PEL 242	d	7	114297499	533.997	Neurodevelopmental delay	12/15 (0)	5.20E-07	100
PEL 114	d	13	48557360	146.432	Abnormality of the globe	8/9 (0)	5.90E-07	100
PEL 250	d	7	119973023	238.728	Delayed speech and language development	9/13 (0)	8.80E-07	100
PEL 123	d	12	66224830	22.517	Short stature	7/8 (0)	1.10E-06	100
PEL 184	d	1	28743173	21.263	Deeply set eye	4/7 (0)	1.90E-06	100
PEL 462	d	1	11270844	47.828	Abnormality of the skull	10/14 (0)	1.90E-06	100
PEL 417	d	2	201936560	57.623	Abnormality of the mouth	9/13 (0)	2.00E-06	100
PEL 330	d	14	29781404	230.359	Seizures	7/12 (0)	2.10E-06	100
PEL 227	d	9	77206264	34.573	Seizures	7/10 (0)	2.10E-06	100
PEL 133	D	2	219965169	9.153	Cutaneous finger syndactyly	3/5 (0)	2.30E-06	100
PEL 116	d	3	181296306	6.681	Abnormality of the ocular region	9/9 (0)	2.50E-06	100
PEL 173	D	2	59105866	181.965	Midface retrusion	3/5 (0)	4.00E-06	100
PEL 120	D	2	59105866	181.965	Strabismus	5/5 (0)	4.40E-06	100
PEL 276	d	7	94174003	41.631	Decreased body weight	4/7 (0)	7.20E-06	100
PEL 329	d	7	95693340	89.973	Abnormality of limb bone morphology	8/10 (0)	1.30E-05	100
PEL 304	d	X	133530468	102.522	Global developmental delay	6/8 (0)	1.50E-05	100
PEL 388	d	10	28842276	86.821	Abnormality of the eyelid	6/8 (0)	1.70E-05	100
PEL 210	D	2	59105866	181.965	Feeding difficulties in infancy	4/5 (0)	1.70E-05	100
PEL 455	d	10	28842276	86.821	Abnormality of the palpebral fissures	5/8 (0)	2.00E-05	100
PEL 251	d	13	41726952	39.763	Abnormal eye morphology	6/7 (0)	2.00E-05	100
PEL 470	d	10	28842276	86.821	Abnormality of the hair	5/8 (0)	2.20E-05	100
PEL 358	d	1	28743173	21.263	Abnormality of globe location	5/7 (0)	2.90E-05	100
PEL 460	d	3	181648378	93.928	Abnormality of the ocular region	7/9 (0)	3.60E-05	100
PEL 338	d	5	170676605	370.857	Abnormality of the cardiac septa	4/6 (0)	3.90E-05	100
PEL 133	D	2	219965169	9.153	Toe syndactyly	3/5 (0)	4.00E-05	100
PEL 454	d	1	177800358	362.172	Short stature	5/7 (0)	4.40E-05	100
PEL 369	d	14	57423809	185.438	Abnormality of the eye	7/8 (0)	4.50E-05	100
PEL 449	d	7	94174003	41.631	Abnormality of the foot	5/7 (0)	4.90E-05	100
PEL 294	d	1	157149743	12.346	Abnormal hair quantity	3/4 (0)	5.70E-05	100
PEL 213	d	1	157149743	12.346	Abnormality of the lip	4/4 (0)	5.70E-05	100
PEL 327	d	19	10640379	140.937	Abnormal genital system morphology	4/5 (0)	7.00E-05	100
PEL 448	d	14	58205713	144.654	Abnormality of the skull	7/8 (0)	8.00E-05	100
PEL 203	d	13	33963658	138.576	Abnormality of the neck	3/3 (0)	8.20E-05	100
PEL 423	d	3	181692255	50.051	Abnormality of the face	9/9 (0)	1.10E-04	100
PEL 324	d	7	94953990	5.573	Growth abnormality	6/6 (0)	2.20E-04	100
PEL 456	D	2	219965169	9.153	Abnormality of the lower limb	4/5 (0)	5.20E-04	100
PEL 361	D	7	106664270	182.398	Strabismus	3/3 (0)	5.40E-04	100
PEL 404	D	7	107527586	136.426	Abnormality of eye movement	3/3 (0)	8.20E-04	100
PEL 407	D	1	113036203	122.933	Abnormality of the palate	3/3 (0)	1.00E-03	100

^*Duplication (D) and deletion (d). ^a Adjusted P-values from the Fisher’s Exact test of the case–control analysis. ^b This table show only those PELs with a penetrance higher than 100 %. The penetrance was calculated as described by Cooper et al. [8, 28]

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