Applying next generation sequencing with microdroplet PCR to determine the disease-causing mutations in retinal dystrophies

Wang, Xinjing; Zein, Wadih M.; D’Souza, Leera; Roberson, Chimere; Wetherby, Keith; He, Hong; Villarta, Angela; Turriff, Amy; Johnson, Kory R.; Fann, Yang C.

doi:10.1186/s12886-017-0549-5

Table 1 Clinical correlated pathogenic variants

From: Applying next generation sequencing with microdroplet PCR to determine the disease-causing mutations in retinal dystrophies

Sample ID	Clincial Diagnosis	Family Inheritance	Candidate Gene(s)	Transcript	Nucleotide Change	Amino Acid Change	Genotypes (Sanger confirmed)	HGMD or dbSNP IDs	References (or in silico Analysis)
RD13–01	CRD	Autosomal dominant	GUCA1A	NM_000409.3	c.296A > G	p.Y99C	Heterozygous	CM980960		[26]
RD1–07	RP	Autosomal dominant	PRPF31	NM_015629.3	c.220C > T	p.Q74*	Heterozygous	CM063073		[27]
RD20–06	CRD	Autosomal dominant	PRPH2	NM_000322.4	c.514C > T	p.R172W	Heterozygous	CM930639		[28]
RD20–07	CRD	Autosomal dominant	PRPH2	NM_000322.4	c.514C > T	p.R172W	Heterozygous	CM930639		[28]
RD2–01	RD	Autosomal dominant	RGR	NM_001012720.1	c.824dupG	p.I276N*77	Heterozygous	CI993291		[16]
RD11–03	RP	Autosomal dominant	RHO	NM_000539.3	c.574dup	p.Y192Lfs*139	Heterozygous	novel	(predicted as pathogenic)
RD14–07	RP	Autosomal dominant	TOPORS	NM_005802.4	c.2474dupA	p.Y825*	Heterozygous	CSI075704		[29]
RD10–02	OCMD	Autosomal dominant	RP1L1	NM_178857.5	c.133C > T	p.R45W	Heterozygous	CM105618		[20]
RD5–08	RP	Autosomal recessive	CERKL	NM_001030311.2	c.1045_1046del	p.M349Vfs*20	Heterozygous	Novel (predicted as pathogenic)
					c.316C > T	p.R106C	Heterozygous	Novel	(predicted as likely pathogenic)
RD14–08	RP	Autosomal recessive	USH2A	NM_206933.2	c.2276G > T	p.C759F	Heterozygous	CM001372		[30]
					c.4108G > C	p.V1370 L	Heterozygous	novel	(predicted as pathogenic)
RD20–08	RP	Autosomal recessive	USH2A	NM_206933.2	c.2299delG	p.E766Sfs*21	Heterozygous	CD982997		[9]
					c.2276G > T	p.C759F	Heterozygous	CM001372		[30]
RD20–05	CSNB	X-linked	CACNA1F	NM_005183.3	c.2576 + 1G > A	IVS20 + 1G > A	Hemizygous	novel	(predicted as pathogenic)
RD6–08	CHM	X-linked	CHM	NM_000390.2	c.49 + 2dupT	IVS1 + 2dupT	Hemizygous	CI137323		[31]
RD12–02	RP	X-linked	RPGR	NM_000328.2	c.1088_1089delinsA	p.V363Dfs*18	Hemizygous	novel	(predicted as pathogenic)
RD4–04	RP	Sporadic	ABCA4	NM_000350.2	c.1804C > T	p.R602W	Homozygous	CM990025		[32]
RD6–01	RP	Sporadic	BBS1	NM_024649.4	c.1169 T > G	p.M390R	Homozygous	CM021489		[33]
RD12–06	RP	Sporadic	CERKL	NM_001030311.2	c.481 + 2 T > G	IVS2 + 2 T > G	Homozygous	CS140556		[7]
RD5–05	RP	Sporadic	CRB1	NM_201253.2	c.3983C > A	p.A1328D	Heterozygous	rs762975680	(predicted as likely pathogenic)
RD4–06	RP	Sporadic	EYS	NM_001142800.1	c.2259 + 1G > A	IVS14 + 1G > A	Heterozygous	CS150721		[34]
					c.6137G > A	p.W2046*	Heterozygous	novel	(predicted as pathogenic)
RD6–07	RP	Sporadic	EYS	NM_001142800.1	c.8473_8474insT	p.V2804 fs	Heterozygous	novel	(predicted as pathogenic)
					c.1153 T > G	p.C385G	Heterozygous	Novel	(predicted as unlikely pathogenic)
RD12–05	RP	Sporadic	EYS	NM_001142800.1	c.6416G > A	p.C2139Y	Heterozygous	CM102730		[25]
					c.7868G > A	p.G2623E	Heterozygous	novel	(predicted as likely pathogenic)
RD15–04	RP	Sporadic	EYS	NM_001142800.1	c.2975G > T	p.C992F	Homozygous	rs566917467	(predicted as pathogenic)
RD13–05	CRD	Sporadic	GUCY2D	NM_000180.3	c.2375C > T	p.P792L	Heterozygous	rs763774686	(predicted as pathogenic)
RD11–08	RP	Sporadic	IMPDH1	NM_000883.3	c.931G > A	p.D311N	Heterozygous	CM020283		[35]
RD15–03	RP	Sporadic	IMPDH1	NM_000883.3	c.931G > A	p.D311N	Heterozygous	CM020283		[35]
RD5–04	RP	Sporadic	RHO	NM_000539.3	c.68C > A	p.P23H	Heterozygous	CM900197		[36]
RD13–02	RP	Sporadic	RHO	NM_000539.3	c.68C > A	p.P23H	Heterozygous	CM900197		[36]
RD12–08	RP	Sporadic	RHO	NM_000539.3	c.561 T > G	p.C187W	Heterozygous	novel	(predicted as pathogenic)
RD12–07	RP	Sporadic	RHO	NM_000539.3	c.936 + 1G > T	IVS4 + 1G > T	Heterozygous	CS920776		[37]
RD14–06	RD	Sporadic	PRPH2	NM_000322.4	c.514C > T	p.R172W	Heterozygous	CM930639		[28]
RD12–03	RP/LCA	Sporadic	RPE65	NM_000329.2	c.886dup	p.R296Kfs*7	Homozygous	CI107001		[38]
RD12–01	RP	Sporadic	RPGR	NM_000328.2	c.197A > G	p.Q66R	Hemizygous	novel	(predicted as pathogenic)
RD6–05	MD	Sporadic	TIMP3	NM_000362.4	c.29 T > A	p.L10H	Heterozygous	Novel	(predicted as pathogenic)
RD20–03	CSNB	Sporadic	TRPM1	NM_002420.5	c.1197G > A	p.P421=	Heterozygous	CS097758		[25]
					c.215A > G	p.Y72C	Heterozygous	CM097760		[25]
RD6–04	CSNB	Sporadic	TRPM1	NM_002420.5	c.2947_2948delGCinsAT	p.A983I	Heterozygous	Novel	(predicted as pathogenic)
					c.3125 T > G	p.L1042R	Heterozygous	Novel	(predicted as likely pathogenic)
RD5–07	RP	Sporadic	USH2A	NM_206933.2	c.2276G > T	p.C759F	Homozygous	CM001372		[30]
RD14–02	RP	sporadic	USH2A	NM_206933.2	c.11411del	p.P3804Lfs*13	Heterozygous	CD149996		[39]
					c.8431C > A	p.P2811T	Heterozygous	rs111033529	(predicted as likely pathogenic)
RD11–04	RP	Sporadic	USH2A	NM_206933.2	c.13335_13347delinsCTTG	p.E4445_S4449delinsDL	Heterozygous	CX104126		[40]
Additional affected family members
RD14–04	CRD	Autosomal dominant	GUCA1A	NM_000409.3	c.296A > G	p.Y99C	Heterozygous	CM980960		[26]
RD2–02	RD	Autosomal dominant	RGR	NM_001012720.1	c.824dupG	p.I276N*77	Heterozygous	CI993291		[16]
RD10–02	OCMD	Autosomal dominant	RP1L1	NM_178857.5	c.133C > T	p.R45W	Heterozygous	CM105618		[20]
RD10–06	OCMD	Autosomal dominant	RP1L1	NM_178857.5	c.133C > T	p.R45W	Heterozygous	CM105618		[20]
RD15–02	RP	Autosomal recessive	CERKL	NM_001030311.2	c.1045_1046del	p.M349Vfs*20	Heterozygous	Novel	(predicted as pathogenic)
					c.316C > T	p.R106C	Heterozygous	Novel	(predicted as likely pathogenic)
RD20–02	RP	Autosomal recessive	USH2A	NM_206933.2	c.2299delG	p.E766Sfs*21	Heterozygous	CD982997		[9]
					c.2276G > T	p.C759F	Heterozygous	CM001372		[30]

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ISSN: 1471-2415

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