Clinical utility of genomic investigations in a Middle Eastern pediatric gastroenterology disease cohort

Table 1 Summary of positive genetic testing results and detected variants in the study cohort

ID	Primary indication	Technology used	Test done	Variants	Inheritance	Zygosity	Classification
6	Very early onset IBD	NGS	WESTRIO	NM_000377.3(WAS):c.383T>C; p.(Phe128Ser)	X-linked recessive	Hemizygous	LP
14	Very early onset IBD	CMA	CMA	Xp21.1p11.4 (CYBB gene) deletion 1.83 Mb	X-linked recessive	Hemizygous	Pathogenic
15	Recurrent peri-anal abscess	CMA	CMA	Xp21.1p11.4 (CYBB gene) deletion 1.83 Mb	X-linked recessive	Hemizygous	Pathogenic
16	Very early onset IBD	NGS	WES	TTC7A: NM_020458.4, c.133_166del (p.Gly45SerfsTer23)	AR	Heterozygous	LP
17	Liver failure and direct hyperbilirubinemia	NGS	Custom gene panel	NM_002437.5(MPV17):c.280G>C; p.(Gly94Arg)	AR	Homozygous	LP
19	Direct hyperbilirubinemia, multiple congenital anomalies	CMA	CMA	arr[GRCh37] 18p11.32q23(136,227_78,014,123)x3	Chromosomal disorder	-	Pathogenic
20	Persistent indirect hyperbilirubinemia	NGS	UGT1A1 full gene sequencing	NM_000463.3(UGT1A1):c.625C>T; p.(Arg209Trp) NM_000463.3(UGT1A1): C.-41_-40dupTA; p.?	AR AR	Homozygous homozygous	Pathogenic LP
21	Persistent indirect hyperbilirubinemia	NGS	Cholestasis panel	NM_000463.3(UGT1A1): C.-41_-40dupTA; p.?	AR	Homozygous	Pathogenic
23	Persistent indirect hyperbilirubinemia	NGS	Cholestasis panel	NM_005603.4(ATP8B1):c.3040C>T; p.(Arg1014*)	AR	Homozygous	Pathogenic
24	Persistent indirect hyperbilirubinemia	NGS	Cholestasis panel	NM_000463.2(UGT1A1): C.1021C>T; p.R341*	AR	Homozygous	Pathogenic
25	Persistent elevated liver enzymes, congenital heart anomalies	NGS	Alagile syndrome	NM_000214.2(JAG1): C.1052delG; p.(Cys351 Leufs*61)	AD	Heterozgous	Pathogenic
26	Persistent elevated liver enzymes, congenital heart anomalies	NGS	Unknown	NM_000214.2(JAG1): C.1052delG; p.(Cys351 Leufs*61)	AD	Heterozgous	Pathogenic
27	Elevated liver enzymes and hepatosplenomegaly	NGS	WES	NM_000443.4(ABCB4):c.3634-4A>G; p.? NM_000443.4(ABCB4):c.1864G>T; p.(Gly622Trp)	AD/AR	Compound heterozygous	VUS
28	Elevated liver enzymes and hepatosplenomegaly	NGS	Custom gene panel	NM_000443.4(ABCB4):c.158A>T; p.(Asp53Val) NM_004004.6(GJB2):c.-23+1G>A; p.?NM_001042351.3(G6PD):c.563C>T; p.(Ser188Phe)	AR AR X-linked recessive	Homozygous homozygous hemizygous	VUS pathogenic pathogenic
34	Direct hyperbilirubinemia	Sanger	Targeted variant analysis	NM_025193.4(HSD3B7):c.45_46del; p.(Gly17 Leufs*26)	AR	Homozygous	Pathogenic
35	Persistent indirect hyperbilirubinemia	NGS	Gilbert syndrome genetic test	NM_000463.3(UGT1A1): C.-41_-40dupTA; p.?	AR	Homozygous	Pathogenic
37	Persistent indirect hyperbilirubinemia	NGS	Crigler-Najjar syndrome genetic test	NM_000463.3(UGT1A1): C.-41_-40dupTA; p.?	AR	Homozygous	Pathogenic
38	Persistent indirect hyperbilirubinemia	NGS	UGT1A1 full gene sequencing	NM_000463.3(UGT1A1): C.-41_-40dupTA; p.?	AR	Homozygous	Pathogenic
40	Direct hyperbilirubinemia	NGS	WGS	4.70 Mb deletion JAG1 gene 20p12	AD	Heterozygous	Pathogenic
43	Chronic pancreatitis	NGS	WES	NM_002769.4(PRSS1):c.365G>A; p.(Arg122His)	AD	Heterozygous	Pathogenic
44	Recurrent pancreatitis	NGS	Pancreatitis panel	NM_007272.3 (CTRC):c.738_761del; p.(Lys247_Arg254del)	AD	Heterozygous	Pathogenic
45	Chronic congenital diarrhea	NGS	Custom gene panel	NM_021102.4(SPINT2):c.442C>T; p.(Arg148Cys) NM_000277.3(PAH):c.157C>T; p.(Arg53Cys) NM_144687.4(NLRP12):c.1854C>G;p.(Tyr618*)	AR AR AD	Homozygous homozygous heterozygous	LP LP LP
48	Chronic congenital diarrhea	NGS	Unknown	NM_001080467.3(MYO5B):c.1966C>T; p.(Arg656Cys)	AR	Homozygous	LP
49	Chronic congenital diarrhea	NGS	Unknown	17 kb deletion in EPCAM gene 2p21	-	-	-
50	Chronic congenital diarrhea	NGS	Unknown	NM_001080467.3(MYO5B):c.1966C>T; p.(Arg656Cys)	AR	Homozygous	LP
51	Chronic congenital diarrhea, albinism, dysmorphism	NGS	Unknown	NM_014639.4(SKIC3):c.4070del; p.(Pro1357 Leufs*10)	AR	Homozygous	LP
52	Chronic congenital diarrhea	NGS	Chronic Congenital Diarrhea panel	NM_001080467.3(MYO5B):c.82del; p.(Thr28Profs*47)	AR	Homozygous	LP
53	FTT, persistent diarrhea, direct hyperbilirubinemia	NGS	Cholestasis panel	NM_020198.3(CCDC47):c.1234C>T; p.(Arg412*)	AR	Homozygous	LP
56	Non-mechanical intestinal obstruction, diarrhea	NGS	WES	NM_000111.2(SLC26A3):c.559G>T; p.(Gly187*)	AR	Homozygous	Pathogenic
57	FTT	NGS	Custom gene panel	NM_006408.4(AGR2):c.104del; p.(Asp35Alafs*38)	AR	Homozygous	LP
58	Chronic congenital diarrhea	NGS	WESTRIO	NM_001080467.2(MYO5B):c.2062C>T; p.(Arg688*) NM_000463.2(UGT1A1):c.1075G>A; p.(Asp359Asn) NM_000492.3(CFTR):c.1163C>T; p.(Thr388Met)	AR	Homozygous heterozygous heterozygous	Pathogenic VUS VUS
59	FTT, and chronic congenital diarrhea	NGS	WES	NM_012079.5(DGAT1):c.1374G>A; p.(Trp458*)	AR	Homozygous	LP
61	FTT	NGS	Cystic fibrosis panel	NM_000492.4(CFTR):c.1521_1523del; p.(Phe508del)	AR	Homozygous	Pathogenic
63	FTT	Sanger	Targeted variant analysis	NM_001012331.1(NTRK1):c.1624del; p.(Glu542Argfs*110)	AR	Homozygous	LP
64	FTT	NGS	Comprehensive lung panel	NM_001013838.3(CARMIL2):c.950dup; p.(Pro318Thrfs*44)	AR	Homozygous	LP
65	FTT	NGS	WESTRIO	NM_004333.6(BRAF):c.1574T>C; p.(Leu525Pro)	AD	Heterozygous	Pathogenic
68	Ileal mass and polyps	NGS	Unknown	NM_000455.5(STK11):c.300dup; p.(Gly622Trp)	AD	Heterozygous	LP
69	Multiple Polyp on multiple occasions	NGS	Unknown	STK11 gene deletion (unknown)	AD	Heterozygous	Pathogenic

IBD: Inflammatory bowel disease; NGS: Next-generation sequencing; CMA: Chromosomal microarray analysis; WES: Whole exome sequencing; FTT: Failure to thrive; AD: Autosomal dominant; AR: Autosomal recessive, LP: Likely pathogenic; VUS: Variant of uncertain significance; WESTRIO: Whole exome sequencing trio.

Table 2 Genetic testing modalities and diagnostic yield

Test/panel	Positive	Total	%
WES	5	8	62.5
WESTRIO	3	3	100.0
WGS	1	1	100.0
VEOIBD panel	0	12	0.0
Custom gene panel	4	4	100.0
Cholestasis panel	4	10	40.0
CMA	3	7	42.9
UGT1A1 full gene sequencing	2	2	100.0
Gilbert syndrome genetic test	1	2	50.0
Crigler-Najjar syndrome genetic test	1	1	100.0
Targeted variant analysis	2	2	100.0
Pancreatitis panel	1	2	50.0
Chronic congenital diarrhea panel	1	3	33.3
Cystic fibrosis panel	1	1	100.0
Comprehensive lung panel	1	1	100.0
Alagille syndrome	1	1	100.0
Congenital mono- and disaccharide disorders panel	0	2	0.0
Unknown	7	7	100.0

WGS: Whole genome sequencing; WES: Whole exome sequencing; CMA: Chromosomal microarray analysis; VEOIBD: Very early-onset inflammatory bowel disease; WESTRIO: Whole exome sequencing trio.

Table 3 Patient-specific clinical diagnoses and impact on medical management

ID	Clinical diagnosis	Clinical implication
6	Wiskott-Aldrich syndrome or related phenotypes	Nil
14	X-linked chronic granulomatous disease	Requires BMT; no response to conventional therapy
15	X-linked chronic granulomatous disease	Requires BMT; no response to conventional therapy
16	Combined immunodeficiency with multiple intestinal atresias	Initiated leflunomide, counseled on immunodeficiency risk
17	Mitochondrial DNA depletion syndrome	Liver transplant referral; neurology referral; prenatal screening recommended
19	Trisomy 18	Liver transplant not pursued
20	Crigler-Najjar (and Gilbert syndrome)	Intensive phototherapy; phenobarbital; transplant counseling; potential gene therapy
21	Gilbert syndrome	Avoidance of further testing
23	PFIC 1	UDCA, IBAT inhibitor; hearing test; anticipate cirrhosis and possible liver transplant
24	Crigler-Najjar	Intensive phototherapy; phenobarbital; transplant counseling; potential gene therapy
25	Alagille syndrome	Screening for associated disorders: Cardiac, ocular, vascular, and renal
26	Alagille syndrome	Screening for associated disorders: Cardiac, ocular, vascular, and renal
27	PFIC 3	UDCA, IBAT inhibitor; slower disease progression
28	PFIC 3/autosomal recessive nonsyndromic hearing loss/glucose-6-phosphate dehydrogenase deficiency	UDCA, IBAT inhibitor; slower disease progression; counseling on post–liver transplant recurrence; G6PD precautions; hearing test; ENT referral
34	Congenital bile acid synthesis defect	Bile acid replacement therapy; liver transplant considered
35	Gilbert syndrome	Avoidance of further testing
37	Gilbert syndrome	Avoidance of further testing
38	Gilbert syndrome	Avoidance of further testing
40	Alagille syndrome	IBAT inhibitor, screening for associated disorders: Cardiac, ocular, vascular, and renal
43	Hereditary pancreatitis	Annual pancreatic cancer screening; regular monitoring of exocrine/endocrine function
44	Chronic pancreatitis	Regular monitoring of exocrine/endocrine function
45	TE, hyperphenylalaninemia, familial cold autoinflammatory syndrome	Family counseling for future pregnancies; MVT not favored as symptoms may improve
48	MVID	Family counseling for future pregnancies; renal screening; MVT likely as symptoms unlikely to improve; lifelong TPN anticipated
49	TE	Family counseling for future pregnancies; MVT not favored as symptoms may improve
50	MVID	Family counseling for future pregnancies; renal screening; MVT likely as symptoms unlikely to improve; lifelong TPN anticipated
51	Trichohepatoenteric syndrome	Screening for hypogammaglobulinemia, screening for liver disease
52	MVID	Family counseling for future pregnancies; renal screening; MVT likely as symptoms unlikely to improve; lifelong TPN anticipated
53	Trichohepatoneurodevelopmental syndrome	Screening for developmental delay, screening for liver disease
56	Congenital chloride diarrhea	Chloride supplementation
57	Recurrent respiratory infections and failure to thrive with or without diarrhea	Family counseling for future pregnancies
58	MVID	Family counseling for future pregnancies; renal screening; MVT likely as symptoms unlikely to improve; lifelong TPN anticipated
59	Congenital diarrheal disorder due to DGAT1 deficiency	Family counseling for future pregnancies; considering MVT
61	Cystic fibrosis	Annual screening for pancreatic insufficiency, started Trikafta
63	Autosomal recessive TRK 1 positive congenital insensitivity to pain with anhydrosis	Antipyretics and cooling measures; trauma precautions due to absent pain; screen for immunoglobulin deficiency
64	Immunodeficiency	Screening for immunodeficiency
65	BRAF gene related disorders (cardiofaciocutaneous syndrome, Noonan syndrome and LEOPARD syndrome)	Family counseling regarding high risk of developing tumors, referral to cardiology, started Growth hormone
68	Peutz-Jeghers syndrome	Regular endoscopic screening; genetic testing for first-degree relatives
69	Peutz-Jeghers syndrome	Regular endoscopic screening; genetic testing for first-degree relatives

TE: Tufting enteropathy; BMT: Bone marrow transplant; UDCA: Ursodeoxycholic acid; IBAT: Ileal bile acid transporter; MVT: Multi-visceral transplant; TPN: Total parenteral nutrition; PFIC: Progressive familial intrahepatic cholestasis; ENT: Ear, nose, throat; MVID: Microvillous inclusion disease.