Using DNA testing for the precise, definite, and low-cost diagnosis of sickle cell disease and other Haemoglobinopathies: findings from Tanzania

Christopher, Heavenlight; Burns, Adam; Josephat, Emmanuel; Makani, Julie; Schuh, Anna; Nkya, Siana

doi:10.1186/s12864-021-08220-x

Table 2 Summary of all non-synonymous variants obtained through conventional screening methods, confirmatory Sanger Sequencing, and nanopore sequencing

From: Using DNA testing for the precise, definite, and low-cost diagnosis of sickle cell disease and other Haemoglobinopathies: findings from Tanzania

Sample ID	Sample Type	Cohort	Results from conventional screening		Results of nanopore sequencing				Final Diagnosis
Sample ID	Sample Type	Cohort	Method	Result	Mutation	Read Depth (x)	VAF	Het/Hom	Final Diagnosis
FH	WB	Val	Sanger	Glu7Val (Het)	Glu7Val	1645	0.46	Het	Sickle cell heterozygote
G213707J	WB	Val	Sanger	Met1Thr (Het)	Met1Thr	49,715	0.56	Het	Beta⁺ thal heterozygote
G213708H	WB	Val	Sanger	Met1Thr (Het)	Met1Thr	43,165	0.44	Het	Beta+ thal heterozygote
G213709R	WB	Val	Sanger	Met1Thr (Hom)	Met1Thr	80,434	0.77	Hom	Beta+ thal intermedia
G213711L	WB	Val	Sanger	Met1Thr (Het)	Met1Thr	127,405	0.41	Het	Beta+ thal heterozygote
Z	WB	Val	Sanger	Glu7Val (Het)	Glu7Val	4744	0.50	Het	Sickle cell heterozygote
TMK-1196	DBS	Val	IEF	FS	Glu7Val	91,193	0.81	Hom	Sickle cell disease
TMK-1258	DBS	Val	IEF	FAS	Glu7Val	118,680	0.45	Het	Sickle cell heterozygote
TMK-1259	DBS	Val	IEF	FAS	Glu7Val	46,389	0.55	Het	Sickle cell heterozygote
TMK-1260	DBS	Val	IEF	FAS	Glu7Val	32,431	0.55	Het	Sickle cell heterozygote
TMK-1267	DBS	Val	IEF	FAS	Glu7Val	38,726	0.55	Het	Sickle cell heterozygote
TMK-1276	DBS	Val	IEF	FAS	Glu7Val	41,793	0.53	Het	Sickle cell heterozygote
TMK-1287	DBS	Val	IEF	FS	Glu7Val	86,884	0.95	Hom	Sickle cell disease
TMK-1345	DBS	Val	IEF	FS	Glu7Val	17,534	0.85	Hom	Sickle cell disease
TMK-1536	DBS	Val	IEF	FS	Glu7Val	33,070	0.93	Hom	Sickle cell disease
Sample 144	WB	Disc	Sanger	Beta+ Thal	c.92 + 1G > A	5849	0.44	Het	Beta+ Thal, Sickle cell heterozygote
Sample 144	WB	Disc	Sanger	Beta+ Thal	Glu7Val	5845	0.48	Het	Beta+ Thal, Sickle cell heterozygote
Sample 245	WB	Disc	Sanger	Beta+ Thal	Trp38X	5817	0.40	Het	Beta+ Thal, Sickle cell heterozygote
Sample 245	WB	Disc	Sanger	Beta+ Thal	Glu7Val	6023	0.48	Het	Beta+ Thal, Sickle cell heterozygote
Sample 462	WB	Disc	Sanger	Beta+ Thal	Gln40X	5934	0.47	Het	Beta+ Thal, Sickle cell heterozygote
Sample 462	WB	Disc	Sanger	Beta+ Thal	Glu7Val	5969	0.46	Het	Beta+ Thal, Sickle cell heterozygote
Sample 647	WB	Disc	Sanger	Glu7Val (Het)	Glu7Val	11,078	0.49	Het	Sickle cell heterozygote
Sample 693	WB	Disc	Sanger	Glu7Val (Het)	Glu7Val	5967	0.51	Het	Sickle cell heterozygote
Sample 926	WB	Disc	Sanger	Glu7Val (Hom)	Glu7Val	6700	0.99	Hom	Sickle cell disease
Sample 040	WB	Disc	Sanger	Beta⁺ Thal	Glu7Val	4847	0.45	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 040	WB	Disc	Sanger	Beta⁺ Thal	Glu23X	4787	0.44	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 1077	WB	Disc	Sanger	Beta⁺ Thal	Glu 7Val	3741	0.46	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 1077	WB	Disc	Sanger	Beta⁺ Thal	Glu23X	3688	0.44	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 1221	WB	Disc	Sanger	Beta⁺ Thal	Glu7Val	3287	0.45	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 1221	WB	Disc	Sanger	Beta⁺ Thal	Glu23X	3258	0.45	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 832	WB	Disc	Sanger	Beta⁺ Thal	Glu7Val	3806	0.48	Het	Sickle cell heterozygote
Sample 750	WB	Disc	Sanger	Beta⁺ Thal	Glu7Val	3619	0.47	Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 750	WB	Disc	Sanger	Beta⁺ Thal	C.92 + 1G > T	2169		Het	Sickle cell, Beta⁺ Thal heterozygote.
Sample 1181	WB	Disc	Sanger	Beta⁺ Thal	Glu7val	3111	0.46	Het	Sickle cell heterozygote

WB Whole blood, DBS Dried blood spot, Val Validation, Disc Discovery, IEF Isoelectric focussing, Het Heterozygous mutation, Hom Homozygous mutation, VAF Variant allele frequency

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ISSN: 1471-2164

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